48: Optic Tectum Decision Threshold

A simple model of decision making uses WTA (winner take all) where the option with the highest evidence takes control. The important part of WTA is the “take-all” part [Mysore and Kothari 2020]. Although the process of representing the highest evidence is well studied, the take-all part is less well studied. Little is known about the circuit mechanisms underlying unitary output generation [Mysore and Kothari 2020].

When choosing to turn left or right, the OT (optic tectum) in the midbrain is a central player. In mice the OT has a head-movement motor map where specific regions will turn the head left or right along the yaw, roll, or pitch axis. These output neurons are marked by the pitx2 transcription factor [Masullo et al 2019], [Choi JS et al 2021], [De Malmazet and Tripodi 2023]. Interestingly, these pitx2 head movement neurons receive essentially no visual movement, but receive multimodal input, particularly whisker input in mice [Xie Z et al 2021].

The simulated animal for this essay has only limited visual input, non-image photosensors, restricted to simple phototaxis. It does have a lateral line sense, where in fish senses surrounding water motion to detect obstacles and potential prey. Zebrafish can forage in the dark, which requires the lateral line [Carrillo and McHenry 2015], specifically the head lateral line.

Race to threshold – Mauthner cell

As a simplified example of decision making, the acoustic startle reflect and the hindbrain Mauthner cells in fish. There are two Mauthner cells in R4 (hindbrain rhombomere 4), one on each side. This startle reflex is a very fast (20ms) three-synapse circuit to escape danger. A loud sound drives acoustic sense neurons, which drives the ipsilateral Mauthner cell, which drives contralateral motor neurons to quickly turn in a “C-start” before swimming away [Bátora et al 2021]. This simple circuit is essentially a Braitenberg vehicle [Braitenberg 1984]. The Mauthner cells can also be driven by touch, vestibular, or by OT, and in zebrafish larvae, the head touch connections develop first, before the acoustic inputs [Kohashi et al 2021].

A flowchart illustrating the decision-making process in a neural circuit involving sensory inputs and motor connections, labeled with 'Sense.L', 'Sense.R', 'R4.mc.L', 'R4.mc.R', 'N.mn.L', and 'N.mn.R'.
Core of the Mauthner escape circuit. Sense input such as loud noise drive the Mauthner cell, which accumulates and fires when passing the action potential threshold. The Mauthner cell drives spinal motor neurons, which drive muscles. N.mn (spinal motoneurons), R4.m (Mauthner cell in rhombomere 4).

The above diagram shows the Braitenberg-like circuit of the Mauthner cell. Danger sensing neurons, acoustic, touch, or OT, drive the ipsilateral R4.mc (Mauthner cell in rhombomere 4), which drives contralateral N.mn (spinal motor neurons). This circuit, however, implicitly assumes that a danger sense will be dominated by one side or the other because it can’t compare the left and right signals.

Although touch from the animal bumping into an obstacle is often unilateral, sound is bilateral, which means the decision needs to handle some comparison between the two sides. A simple decision model is a race to threshold [Vickers 1970], but a simple race model is not optimal. Instead it is more efficient to compute differences between alternatives [Bogacz and Gurney 2007]. One of these models has two leaky accumulators with lateral inhibition [Usher and McClelland 2001]. DDM (drift diffusion) is another popular model with only a single accumulator with positive and negative inputs [Ratcliff 1978], but that system doesn’t fit this Mauthner cell circuit. In a race to threshold decision, the first accumulator to reach a threshold wins.

In the Mauthner cell circuit, the cell’s membrane voltage can serve as an accumulator and the neuron’s action potential as the threshold. The first R4.mc to reach the action potential threshold wins. The first graph below shows this race.

Graph showing the race to threshold in a neural decision-making model, illustrating the membrane voltage changes over time for left (v.L, blue) and right (v.R, red) accumulators. Includes sub-graphs for both firing and feedback inhibition dynamics.
Race to threshold simulations for a Mauthner-cell-like leaky accumulator circuit. The second graph shows the losing side (right) also firing its Mauthner-cell. The final graph shows the addition of feedback inhibition where the winner suppresses the loser from firing. ap.L (action potential burst of the left Mauthner cell), v.L (membrane voltage of the left Mauthner cell).

The above graphs show a simple race to threshold model for the Mauthner cells. The second graph shows the main issue: the firing of the winning side doesn’t prevent the losing side from also continuing to accumulate and fire. The models here are purely qualitative toy models for illustration. There is no attempt at accuracy to actual R4.mc values.

The current circuit can’t prevent the losing R4.mc from continue accumulating and firing shortly after, which might muddle the downstream motor neurons, possibly preventing a proper C-start and escape. In the actual Mauthner cell circuit, this conflict is solved by feedback inhibitory neurons that suppress the contralateral R4.mc [Koyama et al 2021]. Interestingly, this suppression is by direction electrical connectivity, not by inhibitory neurotransmitters. This feedback inhibition stop the accumulation of the contralateral R4.mc by hyper polarizing the membrane voltage directly, essentially resetting to zero.

Diagram depicting the Braitenberg-like circuit of the Mauthner cell with sensory inputs (Sense.L and Sense.R), ipsilateral Mauthner cells (R4.mc.L and R4.mc.R), feedback inhibition neurons (fbIN), and contralateral spinal motor neurons (N.mn.L and N.mn.R).
Adding post-firing feedback inhibition. When the winning R4.mc fires, it inhibits the losing R4.mc using a feedback interneuron. fbIN (feedback interneuron), N.mn (motoneuron), R4.mc (Mauthner cell).

The above diagram adds feedback neurons to suppress the losing R4.mc after an event. This suppression needs to be relatively short. The Mauthner cell only fires a brief burst, not an extended sustained output, which means the feedback inhibition only applies to the immediate event. This system may be a sufficient lockout for the highly specialized startle reflex, but a more general decision system may need a more complicated lockout system.

OT locking out for WTA

Let’s consider the OT crossed turning projection, which is used for orienting and seeking, while the OT uncrossed output is used for avoidance. OT decides to turn left or right for many input types, including visual, auditory, lateral line, touch, and even abstract cognitive decisions from cortical inputs. OT.co (OT crossed output) neurons project to R6.rs (mid-hindbrain reticula-spinal), which then projects to N.mn (spinal motoneurons) [Wheatcroft et al 2022]. This R.rs accumulation circuit exists in frog tadpoles, where they receive direct N5 (trigeminal) head touch input [Buhl et al 2015]. This circuit is roughly similar to the Mauthner cell circuit above, where OT.co replaces the sensory neurons, and the contralateral/ipsilateral crossing patterns are different.

Diagram comparing OT crossed turning and OT turning with action lockout in a neural circuit.
Simplified model of OT as input to mid-hindbrain turning to show parallel to Mauthner cell circuit. The second model shows how ongoing actions can disable OT output to turning neurons. H.zi (zona incerta), N.mn (spinal motoneuron), OT (optic tectum), R6.rs (reticulospinal turning neurons in hindbrain R6), Snr (substantia nigra pars reticulata).

So, let’s apply an ongoing-action lockout to the OT turning circuit by disabling OT output when an action is occurring. Unlike the specialized Mauthner cell circuit, which directly inhibited R4.mc, support the lockout suppresses the OT input to the accumulation circuit. In mammals, OT.co are inhibited by Snr (substantia nigra pars reticulata) and H.zi (zona incerta) [Doykos et al 2020]. H.zi is closely associated with movement, which suggests it could be a broad movement corollary / efference copy [Hormigo et al 2023]. H.zi appears to activate after or around movement onset, not during decision making [Hormigo et al 2023]. This timing contrasts with Snr, which drops its suppression just prior to movement. Either Snr or H.zi or a combination of the two is capable of suppressing OT.co during ongoing movement, which would eliminate input from the downstream R6.rs turning neurons.

Along with an inhibition of OT.co, H.zi also inhibits ipsilateral R6.rs chx10 turning neurons [Cregg et al 2020], but that study does not report an Snr input to R6.rs.chx10. That H.zi input could serve as a similar feedback inhibition as the Mauthner cell circuit, but the following simple model only uses the OT.co suppression.

Graph illustrating the OT action lockout mechanism over time, showing the values for left and right outputs.
In this scenario, the winner of the race to threshold cuts off the input to all accumulators. The losing accumulator slowly leaks to zero. ap.L (left action potential), v.L (left accumulator value)

The above chart shows a model of R6.rs turning neurons as leaky integrators for OT.co input, where the value abstractly represents the R6.rs membrane voltage. In this configuration, an action potential for turning left disables the OT input, but does not disable the R6.rs neurons directly. The OT input to R6.rs stops, and the R6.rs neurons leak back to their initial condition.

Increasing gain to avoid metastability

The R4.mc circuit is hyperoptimized for speed, including the feedback lockout circuit, which means it can lock out the loser within a short time, but even the hyper optimized circuit has limits. The Mauthner cell itself takes time to fire, and the feedback neurons also take time to fire. If the lower reaches its AP (action potential) threshold before the feedback inhibition takes hold, both R4.mc will fire, which will disrupt the animal’s escape. This issue of in-between decisions of greater for other decision circuits that aren’t as optimized as the Mauthner cell circuit. In frog tadpoles, disconnecting the midbrain impairs hindbrain decisions because of too many bilateral synchronous firing instead of limiting activation to a single side [Larbi et al 2022]. To improve the response, we need additional circuitry to distinguish the winner from the loser.

FFI (feedforward inhibition) can act as a high-pass filter, moving noise and weak signals from the accumulation in a gated accumulator model [Schall et al 2011]. Contralateral FFI could inhibit the weaker signal, increasing the division between the weaker and the stronger. But contralateral FFI works much better after the addition of lateral disinhibition [Koyama et al 2016].

Diagram depicting a neural circuit for decision-making involving sense inputs (left and right), feedforward inhibition (FFI), and motor neurons (N.mn) guiding actions.
Adding contralateral FFI to distinguish winner from loser in a WTA decision circuit. FFI (feedforward inhibition), N.mn (motoneuron), R4.mc (Mauthner cell).

The above circuit adds FFI neurons to the Mauthner cell escape circuit. A left sensory input will suppress the right Mauthner cell and vice versa. This contralateral inhibition should increase the difference between the two signals. Note, that the diagram has omitted the feedback inhibition because here we’re only interested in the ramp to threshold, not the lockout phase discussed earlier.

Graphs depicting a decision-making model showing plain ramp to threshold, weak contralateral feedforward inhibition (FFI), strong contralateral FFI, and large input difference related to Mauthner cell circuits.
Charts showing the effect of contralateral FFI. The first chart shows plain accumulation with two close inputs. The second and third show weak and strong contralateral FFI. The last shows the circuit when the inputs have a larger difference. ffi.L (value of FFI neurons), v.L (value of accumulator neurons).

The above charts show several scenarios with the FFI added to the circuit. The first chart shows a plain ramp to threshold without any FFI added. The second shows the addition of weak FFI. Weak FFI increases the time difference between threshold crossing at the cost of slowing the decision slightly.

However, increasing the FFI weights further causes the system to break entirely as in the third chart. Because the two signals are nearly equal, and because the FFI is strong, the FFI ends up inhibiting both choices and the decision never reaches threshold [Koyama et al 2016]. This problem is mainly when the inputs are fairly close. As the final chart shows, if the inputs are widely separated, the large FFI inhibition still allows the winner to reach threshold. However, widely separated inputs were never the original problem.

Although this dual output suppression is a problem for the escape circuit because it seeds to make an immediate decision, it could be a benefit in a more leisurely situation where the decision should be postponed until a clear winner emerges. A good deal of decision research considers delayed response time as a measure of conflict.

But for the escape circuit, this dual suppression is a problem. Contralateral inhibition can accentuate the differences, but at the cost of squashing the result entirely. A solution is to add lateral disinhibition between the FFI neurons [Koyama et al 2016]. Only the stronger input can inhibit the contralateral choice.

Diagram illustrating a neural circuit for the Mauthner cell escape reflex, featuring sensory inputs, feedforward inhibition (FFI), and motor output pathways.
Adding lateral disinhibition to the contralateral FFI circuit. FFI (feedforward inhibition), N.mn (spinal motoneuron), R4.mc (Mauthner cell).

The above decision circuit adds lateral disinhibition to the two FFI neurons. If the left sense is stronger, it with both inhibit the right R4.mc and disinhibit the left R4.mc by inhibiting the right FFI neuron. This should minimize the situation where nearly equal inputs inhibit both outputs.

Graph comparing plain ramp to threshold decision-making model on the left and FFI with disinhibition model on the right, showing action potential thresholds over time for left and right inputs.
The right chart shows how the disinhibition circuit widens the difference between the winning input and the lower. ffi.L (value of the left feedforward inhibition neuron), v.L (accumulator value of the left Mauthner cell).

The above chart shows the plain ramp to threshold and the FFI with disinhibition circuit for the same inputs. As the graph on the right shows, the disinhibition circuit greatly amplifies the difference between the inputs, making a clear decision.

This disinhibition pattern can also be modulated by top-down control, creating a two-phased decision [Shen B et al 2023]. Before the top-down disinhibition is activated, the two options accumulate evidence with only a minor suppression of their competitor. Enabling disinhibition quickly forces a WTA choice.

Lamprey optic tectum

While R4.mc supports a specialized escape circuit, OT supports a general orientation decision to turn left or right. As its name suggests, OT receives optical information from the retina, but in mammals it also receives whisker information, in fish it receives lateral-line information, and in lampreys and some fish it receives electrosensory information. The lateral-line and elestrosensory systems are closely related. The question immediately arises for the OT: which sense came first? Larval lampreys do not have image forming retinas, but only ocellus-like photoreceptors [Salas 2016], and the larval lamprey retinal area does not project to OT [Barandela et al 2023]. The larval OT does project to M.rs (midbrain reticulospinal, specifically nMLF – nucleus of the medial lateral fasciculus) [Barandela et al 2023], but I haven’t found any study reporting the inputs to the larval lamprey OT.

A later lamprey metamorphosis expands both the retina and the OT into image supporting systems and connects the two [Barandela et al 2023]. During that metamorphosis OT greatly expands and becomes a seven layered structure comprised of alternating white and grey layers.

A diagram illustrating the integration of optic and electrosensory inputs in the optic tectum (OT), showing pathways to left and right ramp outputs.
Layers and inputs to the OT. Visual inputs connect to the superficial OT.s layer. Lateral-line and electrosensory input connect to the intermediate OT layer. The output OT.co layer combines the visual and electrosensory input.

In adult lampreys the retinal connects to OT.s (superficial layer of OT) and the ELL (electrosensory) connects to OT.i (intermediate layer of OT) with minimal overlap [Kardamakis et al 2016]. The output OT.co (crossed OT output neurons) extend dendrites to both OT.s and OT.i and integrate the two senses [Kardamakis et al 2016].

This essay will focus on the electrosensory path and OT.i. First, because, like the lamprey larva, the simulation animal does not have an image forming eye, but does have a lateral-line sense. Second, because the mammalian OT pitx2 turning area is also in OT.i [Masullo et al 2019], and receives whisker input but minimal or no visual input [Zahler et al 2021], [González-Rueda et al 2024]. Mexican blind cavefish show denser somatosensory in OT with increased somatosensory input [Patton et al 2010].

For OT as a decision circuit, there are two questions: how does any lateral inhibition between the left and right choice connect, and is the inhibition system feedforward like the Mauthner cell or a feedback system? For visual and auditory input, the lateral inhibition uses R.is (nucleus isthmus). In all vertebrates, R.is provides a donut-like center enhancement and surrounding inhibition [Mahajan and Mysore 2022], which includes suppressing contralateral input [Schryver 2021], but does not project contra laterally to the midbrain [Fenk et al 2023]. However, the OT.i lateral line may not use R.is. In lamprey an electrosensory distractor does not suppress a visual stimulus, it doesn’t suppress another electrosensory stimulus [Kardamakis et al 2016]. This suggests that visual and lateral line use different systems for lateral inhibition. In mammals the R.is (R.pbg parabigeminal in mammals) provides ACh to the visual OT.s layer as part of the selection process, but OT.i and OT.d (deep OT) receive ACh from Ppt (pedunculopontine tegmentum) and P.ldt (laterodorsal tegmentum) not from R.is.

The second question is whether the decision sharpening uses feedforward inhibition or feedback inhibition. The R.is circuit seems more of a feedforward inhibition system, because it inhibits based on ongoing input, not sampling from a ramping population of neurons. But the mammalian OT is a central accumulator in a decision loop involving the basal ganglia and cortex [Brody and Hanks 2015], which is only possible as a feedback loop. This feedback loop requires a ramping population of recurrently connected neurons, because an integrate-and-fire system like the Mauthner cell only fires when the final decision is made, but a feedback loop needs intermediate values. OT has recurrent connections in mammals [Basso and May 2017], [Liu Z et al 2016], frogs [Khakhalin et al 2014], [Felch et al 2015], [Jang EV et al 2016], and zebrafish OT shows edge-of-chaos spontaneous avalanche behavior, which likely also requires recurrent connectivity [Zylbertal and Bianco 2023], but I don’t know of any lamprey recurrent connectivity, or whether it exists in OT.i or OT.co. It’s possible that the feedback-based population decision system developed jawed vertebrates after the lamprey split.

Diagram illustrating the decision-making circuit involving electrosensory information and output pathways for turning actions in a neural model.
Lamprey OT decision system, focusing the ELL input to OT.i. Here, Snr is used to inhibit the output, not for lateral inhibition. V.pt DA connectivity as a decision onset amplifier to output neurons. DA (dopamine), OT.co (crossing OT projecting), OT.i (intermediate ELL input layer), R.ovl (hindbrain octavolateral nucleus for electrosense), R.rs (reticulospinal turning neurons), Snr (substantia nigra pars reticulata), V.pt (posterior tuberculum).

The decision output should be isolated from the decision ramping process to prevent premature action. In the Mauthner cell system, the neuron itself provided that isolation because it only fires after the decision is made. But a population ramping system needs additional circuitry to isolate the decision. Like other vertebrates, the lamprey OT.co are inhibited by Snr (substantia nigra pars reticulata), which could prevent a premature decision from driving action by suppressing output while the decision is incomplete. As a parallel decision sharpening system, the lamprey midbrain dopamine system V.pt (posterior tuberculum), believed to be homologous to the mammalian Snc (substantia nigra pars compacts), receives input from OT [Suryanarayana et al 2021] nd enhances locomotor output by projections to MLR [Ryczko et al 2013], [Ryczko et al 2016], [Ryczko and Dubuc 2023] and R.rs [Ryczko et al 2020], [Ryczko and Dubuc 2023], and also projects to OT.co [Pérez-Fernández et al 2017]. In mammals Snr has a phasic increase around action onset. The V.pt DA boost amplifies and extends locomotor output. For decision sharpening, this system would invigorate the action only after the ramping process was complete or near complete while discouraging pre-decision action.

Note, the R.rs output stage can be considered its own accumulator, because the R.rs neurons themselves integrate and fire. Two-stage accumulators have advantages over a single stage [Balsdon et al 2023], [Verdonck et al 2021]. So, this system could be viewed as a two-stage accumulator system.

While the lamprey may have all the pieces to form a decision system using OT, too much is unknown about the lamprey OT to use it as the basis for the simulation. Instead, I’ll incorporate research from the mammalian OT decision system, which is much better studies, but does have the disadvantage of possibly including mammal-specific features. For example, the mammalian OT has both ramping and bursting neurons, suggesting a distinct ramping population from the OT.co output population, unlike the lamprey, which combines ramping and output in a single neuron population.

OT ramping with feedback excitation and inhibition

Consider the OT as a feedback decision system, particularly focusing in OT.i (intermediate layer of OT), because in mice a subpopulation of OT.i marked by pitx2 (a gene transcription factor) turns the head in the yaw, roll, and pitch axes [Liu X et al 2022]. Because the essay animal is fish-like with no neck, and also two dimensional, we can focus on the left-right yaw. This left-right decision is also important singe the bilateral organization of the brain means the left-right circuits are distinct from any unilateral decision, because they require commissural connections.

The mammalian OT has both ramping neurons and bursting neurons [Basso and May 2017], although the exact circuitry is not known. OT.ramp may project to burst neurons such as OT.co that send the action. For this model I’ll assume that the ramping neurons are a subpopulation distinct from the bursting and that OT.co are the bursting neurons, but this assumption is not based on any research I can find.

After a decision commits, the system needs to lockout further decisions until the new action completes. As discussed above, this lockout function is compatible with the known Snr and H.zi suppression of OT.co [Comoli et al 2012]. This lockout function is speculative because I haven’t found research about lockout for OT decisions.

A diagram illustrating the decision-making circuit involving optic tectum (OT) inputs, ramping neurons, crossed outputs, and their connections to downstream motor neurons.
OT decision circuit with ramping and bursting output. The output neurons are suppressed by H.zi and Snr as an action lockout. H.zi (zona incerta), N.sp (spinal motoneurons), OT.co (crossing OT output), OT.ramp (ramping OT neurons), OT.input (ELL input neurons), R.rs (reticulospinal turning neurons).

The above diagram shows the OT decision circuit. In general, OT.input is very flexible and can include abstract input from the cortex in mammals [Thomas et al 2023], as part of the cortex decision circuit. The OT.i.pitx2 neurons for mouse head turning have strong whisker input from N5 (trigeminal cranial nerve), but weak or no visual input [Xie Z et al 2021]. Although this whisker primary and the OT.i.pitx2 head turning could be a novel mammal system, the fish lateral line serves a similar function as mammal whiskers. Zebrafish larvae, for example, can learn to hunt in darkness using the lateral line, despite being primarily visual hunters [Whestphal and O’Malley 2013]. A proto-vertebrate with lateral-line sensors but without an image-forming retina could use this mammalian OT.i.pitx2 circuit for decisions. The OT accumulation and delay sustain are primarily OT.i [Basso et al 2021].

The LCA (leaky competing accumulator) model of decision making [Usher and McClelland 2001], uses a pair of leaky accumulators with feedback lateral inhibition. That model, like other decision models such as DDM (drift-diffusion), are intended to describe higher level decision making, such as modeling human tasks, but the structure is inspired by neural circuits like the OT decision system.

The OT.ramp are likely a population of recurrently connected neurons, unlike the paired Mauthner cell which integrated with its membrane potential and only fired a single AP once the threshold was crossed. OT.ramp are likely to use both membrane integration and recurrent connectivity for their ramping. For simplicity, I’m trading OT.ramp neurons as leaky integrators, which does obscure important details about the firing model, including issues with E/I (excitation/inhibition) balance and edge-of-chaos positive feedback behavior. Because OT.ramp fire during the integration, unlike Mauthner cells, the competition between left and right can use feedback inhibition instead of relying on contralateral, disinhibiting feedforward inhibition.

Diagrams comparing two types of feedback inhibition in a decision-making circuit: Soma feedback inhibition on the left and Dendrite feedback inhibition on the right.
Two models of lateral inhibition. The soma feedback inhibition directly inhibits the accumulator. The dendrite feedback cuts off input from the accumulator. in.L (left OT input), ramp.L (left OT ramping), OT.co.L (left OT crossing output).

The above diagram shows two styles of feedback inhibition: inhibiting the OT.ramp neuron soma directly and inhibiting the OT.ramp input by inhibiting their dendrites. The soma inhibition could also include axon output inhibition. In the cortex SST (somatostatin) interneurons inhibit dendrites, PV (parvalbumin) interneurons inhibit the soma directly, and CCK interneurons inhibit the axon output. PV neurons may not be unique in inhibiting the soma, and the PV role in the cortex is more about E/I balance than lateral inhibition. However, OT neurons and cortex neurons are not developmentally related: all OT neurons derive from OT progenitors [Cheung et al 2024]. The analogy with the cortex is only to illustrate that different inhibitory neurons can target specific areas of the target neuron, and specifically introduce the ability to inhibit input to the neuron.

Let’s take a toy model of OT.ramp, as if they were a single leaky integrator for each side. Unlike real neuron population spiking, these model OT.ramp produce continuous output, which the feedback neurons can use. The purpose is to get a qualitative idea of how FBI (feedback inhibition) might work for soma-targeted inhibition and dendrite-targeted inhibition.

Graphs illustrating decision-making models with feedback inhibition. Top left: No feedback between left (e.L) and right (e.R) choices. Top right: Inhibition at the soma impacting both choices. Bottom left: Inhibition at dendrites affecting left and right choices differently. Bottom right: Combined inhibition at both soma and dendrites, demonstrating decision dynamics across time.
Ramping values for different feedback circuits. Soma inhibition directly inhibits the accumulator. Dendrite inhibition blocks input to the accumulator. e.L (left accumulator value)

The above graphs show the leaky integrator OT.ramp with either no FBI, soma-only FBI, dendrite-only FBI, and both soma and dendrite FBI. Unlike the Mauthner cell FFI, the dendrite input FBI does not drive both OT.ramp to zero, which likely means that the FFI disinhibition circuit is less important. Also, unlike the Mauthner cell simulation, which measured the membrane voltage, the graphed value is a general excitation level.

Graphs illustrating the effects of weak and strong feedback inhibition on left and right neural responses over time.
Varying connectivity strength for the feedback inhibition.

The above graphs show the behavior with variations in FBI strength. The weak FBI shows a significant difference between soma-only and dendrite-only inhibition. Weak soma FBI allows both options to fire, while the weak dendrite FBI clearly distinguishes between the options. Both strong FBI circuits distinguish their outputs.

In the real recurrent neural system, output spikes are not a continuous functions, and the population may be too small to use population encoding to approximate continuity. The input itself isn’t continuous, and includes noise. In addition, recurrent excitation is a positive feedback system, and in combination with normalizing inhibition, can produce chaotic transitions between states. This model does not support edge-of-chaos behavior, which may be important to the actual system. It also doesn’t include detailed timing and oscillatory behavior, and OT is known to produce gamma (25-100Hz) oscillations, and oscillations can interact with feedback, such as for SST neurons in the postsubigulum head direction system [Simonnet et al 2017]. All of these limitations may mean that cases such as the strong FBI or the weak FBI graphs above are physically impossible.

OT feedback commissures

The left/right decision requires contralateral communication, which is relatively rare, and can help isolate some of the decision circuitry. The OT.ramp decision model above required contralateral inhibition, which means commissural feedback paths between the OT sides are particularly important. There are three main contralateral paths in the OT that I’ve found studies for:

  • Direct OT to OT contralateral connections [Doykos et al 2020].
  • R.is (nucleus isthmus) contralateral inhibition in some species [Gambrill et al 2016].
  • Contralateral Snr and Ppt.a (anterior pedunculopontine tegmentum) inhibition, either related to the Sprague effect [Durmer and Rosenquist 2001], or as part of the basal ganglia output [Jiang H et al 2003].

The lamprey has OT input from the contralateral OT, and bilateral M.rf (midbrain reticular formation) [de Arriba and Pombal 2007], which likely includes Snr. The Lamprey OT.co has input from Snr [Kardamakis et al 2015]. Because “midbrain reticular formation” is so broad, these two studies may not contradict each other. The majority of contralateral OT projections is from OT.i with some from OT.s and OT.pv (periventricular aka deep) and more from OT.l than OT.m [de Arriba and Pombal 2007], which could correspond to the mammalian OT.i pitx2 group.

The direct OT to OT connectivity is the simplest for this circuit. OT.i to contralateral OT.i exists in the anterior OT [Doykos et al 2020]. OT.burst have projections to the contralateral OT [Basso and May 2017]. OT to contralateral OT exists for deeper OT.s and deeper of OT.id [Broersen et al 2025]. In lamprey, the majority of OT to contralateral OT is OT.i [de Arriba and Pombal 2007]. OT contralateral projections include competitive inhibition for choice, and OT contralateral projections reflect choice earlier than other decision brain regions [Essig et al 2020]. OT to OT is generally restricted to anterior OT, and about 50% of OT to OT are excitatory and 50% are inhibitory.

Diagram illustrating the circuitry involved in decision-making in the optic tectum, showing connections between various neurons including OT.i.R, OT.i.L, Snr, Ppt.a, and R.is.
Several of the major OT commissures. The core includes direct OT to OT projections and loops including Ppt.a and Snr. The R.is inhibition is important for visual and auditory, but may not be used for lateral-line and touch. Broader contralateral loops use T.pf and the striatum and in mammals T.pf and C.m2. C.m2 (premotor cortex), OT.i.L (left intermediate optic tectum), Ppt.a (anterior pedunculopontine tegmentum), R.is (nucleus isthmi), S.d (dorsal striatum), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus)

R.is is critical for visual and auditory competitive choice between targets on a single hemisphere [Kawakami et al 2021]. Disabling R.is.mc (magnocellular R.is) in owls abolishes all competitive OT in a single hemisphere, but that study did not examine contralateral effects [Mysore and Knudsen 2013]. In pigeons, disabling R.is.mc reduces inhibition of R.is.pc (parvocellular R.is) [Marín et al 2007], but again this study was unilateral and did not examine effects on the contralateral OT. In bearded dragons, R.is.mc is required for bilateral competition during REM sleep, but in those animals it does not project to the contralateral midbrain [Fenk et al 2023], which would include OT. The primate R.pbg (parabigeminal), which is the mammal homolog of R.is, does project to the contralateral OT [Deichler et al 2020], but the mammal R.pbg is connected with OT.s (superficial OT) visual lateral particular for ACh (acetylcholine), while OT.id (intermediate and deep OT) receives ACh from Ppt and P.ldt (laterodorsal tegmentum) [Krauzlis et al 2023], [Wolf et al 2015]. I haven’t found a study specifically examining contralateral inhibition from R.is, and while some species do have contralateral connectivity, it doesn’t appear to be directly used for the orienting/head turning decisions for this essay.

OT.i receives contralateral inhibition from a portion of Snr, particularly Snr.al (anterolateral Snr) [Jiang H et al 2003], [Velero-Cabré et al 2020], although most (75%) of Snr inhibition of OT is ipsilateral [Jiang H et al 2003]. Ppt.a and Snr are important for the Sprague effect, where inhibition of unilateral C.vis (visual cortex) input to OT results in hemispheric attentional neglect, but is restored when Ppt.a and/or contralateral Snr projections are also inhibited [Krauzlis et al 2023]. Most Snr.l projections are modulatory and depend on movement direction and modulate choice, and find little evidence for strong Snr suppression of OT.id [Doykos et al 2025], but note that this study specifically examines Snr.dl, but Snr.vm also projects to OT and has a different progenitor origin and functionality. For mice licking tasks, which use OT.l, the Snr to OT.l projection is important for licking accuracy [Lee J and Sabatini 2021]. OT.i.pitx2 projections include Snr [Masullo et al 2019].

There are OT.id projections to Ppt [Coizet et al 2009], [Melleu and Canteras 2024], [Leiras et al 2022], [Tubert et al 2019], major input from OT to Ppt GABA and ACh neurons [Morgenstern and Esposito 2024], and OT.id bidirectional connectivity with Ppt [Comoli et al 2012], [Krauzlis et al 2013], [Melleu and Canteras 2024], [Wu and Zhang 2023]. Ppt correlates with orienting of eyes, body, and limbs [Wolf et al 2015]. In contrast with studies consistently reporting OT projections to Ppt, only a few studies report any direct projections to Snr, but does include a report of OT.i.pitx2 to Snr [Masullo et al 2019]. Note, however, that Snr.p and Ppt.a are contiguous, and Ppt.a GABA can be seen as a continuation of Snr [Mena-Segovia et al 2009], and Ppt is somewhat arbitrarily defined by the location of its ACh neurons [Mena-Segovia et al 2009], which may not precisely define the limits of its glutamate and GABA neurons.

The OT projection through Ppt to Snr could participate in the inhibitory feedback loop, or implement parts of it. Snr, Ppt and the basal ganglia can affect or even determine OT decisions. This modulation could be added to an existing OT decision circuit that only uses OT to OT commissural projections for feedback inhibition, or it could be part of the original feedback inhibition.

ACh sharpening the decision output

The mammalian division between OT.ramp and OT.burst demonstrates an important issue with decisions: downstream areas should see the results of the decision, not the intermediate ramping process leading up to the decision. Mammalian decisions appears to use systems outside of OT like Ppt and Snr to produce sharp, cleanly defined bursts. How might an evolutionary progression for a proto-vertebrate decision sharpening progress, specifically to isolate downstream R.rs from the ramping process?

One potential method is to amplify the output when a decision is made. R.is.pc (parvocellular R.is) is a distinct R.is nucleus with ACh feedback projections to OT. Like the rest of R.is, R.is.pc is a short feedback loop with OT, but unlike the negative feedback in the WTA system, this is positive feedback. In birds an OT projection to T.nr (thalamus nucleus rotundus) requires ACh input to burst. Without the ACh amplification, the OT signal is too weak to drive T.nr [Basso et al 2021].

The mammalian OT.i.pitx2 turning region receives ACh from Ppt and P.ldt. The mammalian R.pbg is considered homologous to the first and bird R.is, but mammalian R.pbg ACh appears to be specific to the OT.s visual layers [Krauzlis et al 2013]. R.pb and Ppt/P.ldt are sibling neural areas, produced by the same progenitor pool in R1 at different development times [Volkman et al 2010]. Unfortunately, although R.is is well-studied for fish and bits, Ppt is not, so I don’t know if the mammalian Ppt/P.ldt ACh projection to OT orientation neurons is ancestral but simplified in fish and birds, or if the R.is ACh is ancestral and the Ppt/P.ldt ACh is a mammalian adaptation. OT varies widely among species because it’s a major visual system under strong evolutionary pressure. Even considering the basic layering, the lamprey OT has 7 layers [Basso et al 2021], the mammalian OT has 6 layers, the bird OT has 15 layers [Basso et al 2021], and the first OT is divided into paraventricular soma and a large neuropil layer, where the neuropil itself can be divided into layers. Because the essays have uses the non-visual-first model of OT evolution, I’ll use the mammalian model as ancestral and R.is/R.pbg as later refinements after image-forming vision developed.

A diagram illustrating the relationship between the Ppt area and OT.ramp neurons, showing connections to the OT.co neurons and R.rs.m turn actions, with ACh signaling highlighted.
Ppt as providing an ACh boost to output nodes after a decision is made. ACh (acetylcholine), OT.co (crossing output of the optic tectum), OT.ramp (OT ramping neurons), Ppt (pedunculopontine tegmentum), R.rs.m (mid-hindbrain reticulospinal turning neurons)

In the above model, Ppt acts as a high-pass filter. A distinct OT ramping population produces a non-choice-selective measure of the decision progress [Horwitz and Newsome 1999], which projects weakly to Ppt. This model uses individually weak projections from OT.ramp are insufficient to drive Ppt ACh until they are collectively and possibly synchronously active. Only higher level input will drive ACh, when then boosts OT.co output and enabling boosting. The OT.id threat-avoidance system uses a similar architecture of individually weak and unreliable projections that require simultaneous activation to drive threat escape to M.pag.d (dorsal periaqueductal grey) [Evans et al 2018]. The OT.co turning system might use a similar circuit with Ppt. Note also that Ppt intrinsically produces gamma oscillations [Garcia-Rill et al 2018], which could synchronize output neurons, providing a stronger burst. Ppt could enhance OT.co bursting not only from ACh release, but also by entraining gamma oscillations in OT.

H.stn sharpening decisions by inhibiting OT.co

Another method for sharpening the R.rs decision signal is disabling the OT.co output while a decision is in progress. In larval zebrafish, swimming occurs in bouts of about 500ms, primate saccades are carefully timed around 200ms, and in rodents, stimulating OT produces step-like saccade-like head movements at around 350ms, instead of a continuous turning motion [Masullo et al 2019]. This saccade-like process around 200ms to 350ms suggests a gating system, either internally or externally driven.

As mentioned in the lockout discussion, Snr and H.zi are responsible for OT.co inhibition [Doykos et al 2020]. At the onset of primary saccades, tonic Snr suppression pauses to allow OT bursting. Snr itself is driven by H.stn (subthalamic nucleus), which itself is driven by OT [Al Tanner et al 2023], [Ricci et al 2024]. H.stn is also driven by Ppt [Al Tanner et al 2023], which is strongly interconnected by OT. When OT is activated, it can increase H.stn tonic firing from 27Hz to 45Hz [Coizet et al 2009]. Interestingly, bursting input to H.stn can produce long-lasting H.stn output over several hundred milliseconds [Ammari et al 2010]. Putting this together, OT.ramp could use H.stn to inhibit its OT.co output while the decision is in progression, possibly using H.stn as a 200ms to 300ms timing mechanism as an initial internal-only ramping period.

Diagram illustrating the feedback circuit involving H.stn, Snr, Ppt, OT.ramp, and OT.co, showing how these components connect in a decision-making process for motor control.
Output gating system using H.stn and Snr to suppress OT.co output until the ramping completes. H.stn (subthalamic nucleus), OT.co (optic tectum crossing output), OT.ramp (OT ramping neurons), Ppt (pedunculopontine tegmentum), R.rs (mid-hindbrain reticulospinal turning), Snr (substantia nigra pars reticulata)

The above diagram shows the basic flow. When a decision starts, OT.ramp signals H.sth, which inhibits OT.co using Snr. Note that this diagram is primarily for a proto-vertebrate, although these connections exist in mammals. In mammals, the full circuit would include the rest of the basal ganglia and the cortex.

Wei W et al propose a sharpening function for H.stn using the full basal ganglia to sharpen cortical decisions [Wei W et al 2015]. In their model, ramping input to S.d (dorsal striatum) suppresses spontaneous P.d (external globus pallidus) activity, which increases H.stn, which then cancels out the primary S.d1 (striatum projection neuron with D1 dopamine receptor) to Snr disinhibition. Because P.d can only be suppressed to zero, the H.stn suppression of the decision is also limited, and eventually the decision ramp overcomes the suppression [Wei W et al 2015].

A diagram illustrating the decision-making circuit in the optic tectum, showing connections between various components including OT.ramp, OT.co, H.stn, and Snr.
H.stn and the basal ganglia as suppressing incomplete decisions. The S.d1 and S.d2 paths compete, but the S.d2 is limited by P.d and eventually loses. H.stn (subthalamic nucleus), OT.co (OT crossing output), OT.ramp (OT accumulator neurons), P.d (dorsal pallidum), R.rs (mid-hindbrain reticulospinal turning), S.d1 (striatum projection neuron with D1.s dopamine receptor), S.d2 (striatum projection neuron with D2.i dopamine receptor), T.pf (parafascicular thalamus)

The above diagram shows a reinterpretation of the Wei W et al sharpening model, with their cortex focus replace by this essay’s OT focus. The oppositional paths of S.d1 (striatum projection neuron with D1.s dopamine receptor) and S.d2 (striatum projection neuron with D1.i dopamine receptor) prevent the OT.co output from firing while the decision is in progress. Because the S.d2 indirect path is limited by P.d, which can only be inhibited to zero, it eventually saturates, and limits H.stn activity, allowing the S.d1 path to continue increasing and eventually overcome the H.stn inhibition. This model is compatible with the view of H.stn as a decision slowing circuit during conflict [Frank 2006].

H.stn neuron activity is diverse with some studies showing at least three clusters of decision-related responses [Branam et al 2024], one of which is compatible with the Wei W et al model. This cluster of H.stn responses shows an early, sharp rise during the initial stimulus with a gradual decline until action onset.

Dopamine for sharpening and sustaining decisions

Midbrain dopamin in Snc (substantia nigra pars compacta) may play a role in further sharpening and sustaining the decision. Vertebrates have a descending Snc DA projection to MLR (midbrain locomotor region) for lamprey [Ryczko et al 2013], [Grätsch 2018], [Beauséjour et al 2025], salamander and rat [Ryczko et al 2016] and R.rs for lamprey [Ryczko and Dubuc 2017], [Beauséjour et al 2024], which enhances locomotor vigor [Ryczko et al 2016], [Ryczko and Dubuc 2017], [Grätsch 2018]. In lamprey, this descending DA projection outnumbers ascending projections to the basal ganglia by eleven to one [Ryczko et al 2013]. In zebrafish larvae, the basal ganglia primarily receives DA from local forebrain dopamine regions with either minimal or no V.da (midbrain dopamine) input [Rimmer 2020]. For a proto-vertebrate, it seems reasonable to focus on the descending DA projection instead of the smaller ascending one to the basal ganglia.

A diagram illustrating the neural circuitry involved in the decision-making process, showing OT.ramp and OT.co as components influencing the R.rs.m turn, with DA input from the Snc.v area.
Descending dopamine for decision sharpening and sustaining. DA (dopamine), OT.co (OT crossed output), OT.ramp (OT accumulation), R.rs (mid-hindbrain reticulospinal turning), Snc.v (substantia nigra pars compacta, ventral area).

In lamprey, salient input from OT projects to V.pt (posterior tuberculum) DA neurons, considered an Snc homolog [Suryanarayana et al 2022]. V.pt DA projects to R.rs [Beauséjour et al 2024], and OT also receives V.pt input [de Arriba and Pombal 2007]. These projections enhance the activity of the downstream neurons.

In the context of decision sharpening, DA activity around movement onset would activate downstream action activity, distinguishing that action from the pre-decision ramping time.

In mammals, OT projects both to Snc [Huang M et al 2021], [Masullo et al 2019] and to the contralateral V.rmtg (rostromedial tegmentum) [Pradel et al 2021], [Guillamón-Vivancos et al 2024], which inhibits Snc. These projections collectively support turning, but not increase locomotion, place preference, or learning [Poisson et al 2024].

Diagram illustrating the structure of the OT ramp decision circuit, showing connections between OT left and right ramping neurons, dopamine inputs from Snc.v, and projections to R.rs.
OT projections to midbrain dopamine, considered as enhancing turning decisions. DA (dopamine), OT (optic tectum), R.rs (mid-hindbrain reticulospinal turning), Snc.v (substantia nigra pars compacta, ventral part), V.rmtg (rostromedial tegemenum).

The above diagram has been organized to emphasize its similarity to the Mauthner cell FFI decision circuit. In the Mauthner cell circuit with contralateral FFI, a simultaneous left and right input would suppress both outputs. For that escape circuit, this dual suppression was bad because it suppressed escape, but for DA decision sharpening, the dual suppression is perfect because it inhibits partial decisions. As long as the left and right accumulators are active, the contralateral FFI circuit suppresses DA output. When one choice decisively wins, the output is disinhibited and quickly reports the decision.

Graph depicting the ramping activities of left (ramp.L) and right (ramp.R) optic tectum (OT) signals, along with dopamine (DA) levels for left (DA.L) and right (DA.R) choices over time.
Time course of a decision. The red and blue graphs show the left and right accumulators. As long as the accumulators are sufficiently close, they suppress the DA output with the contralateral FFI. When the left choice decisively wins, the DA output is disinhibited and quickly rises. DA (dopamine), DA.L (left DA), FFI (feedforward inhibition), ramp.L (left accumulator)

The above graph shows the time course of the decision. The amber DA choice is suppressed while the left and right accumulators are in conflict. Once the conflict resolves, the DA quickly rises. In this simulation, the FFI contralateral suppression is 2:1, so the DA is release once the winner is twice the loser. The unshackled DA will now enhanced the downstream turning R.rs, committing the decision.

The V.da neurons here are the non-food-related motor DA in Snc.v, marked by aldh1a1 in mammals, and likely the specific subgroup marked by anx1a. Broadly speaking, V.da can be split into three groups: and eating and food seeking group, an action-only group, and a threat and avoidance group. An Snc.v group (aldh1a1 /anxa1) which produces movement, but does not respond to food or produce food conditioning [Seiler et al 2024], [Azcorra et al 2023], [Hadjas et al 2025]. It seems likely that the OT projection to Snc.v would be to this aldh1a1/anxa1 group, but I don’t have a paper that shows that specific connection.

Simulation

The simulations added a simple electrosense for food, which produces left and right signals depending on the heading with some noise. When the simulated animal heads directly toward the food, the left and right inputs have equal values. When the food is to one side, the closer side has a stronger signal.

Although the simulation itself didn’t produce anything particularly interesting, it did raise two larger questions about the decision making. First, whether the 2AFC (two alternative forced choice) model makes any sense at all for this evolutionary stage. Second, more questions about timing, particularly with rapid movements, and aborted choices.

2AFC (two alternative forced choice)

2AFC is a popular experiment for studying decision making. Typically, the experiment has a central cue: sound, visual, tactile (whisker), or odor for mice, and the mice must move to a left or right door port to get food, or lick to a left or right spout to water. In primate experiments, a monkey might see drifting dot patterns and must saccade to a left or right target to signal if the drift is more to the left or to the right. In these experiments, two nearly equal cues still produce a strong left or right action.

But in the electrosense simulation, two nearly equal left and right inputs would generally mean the food is straight ahead. If the food is straight ahead, the animal should make smaller turns to center the turn, not side decision-like turns. The OT is organized to make this kind of adjustment decision. Turning in the anterior OT are smaller than the wide turns in the posterior OT, and the anterior OT shows more activity as the animal moves toward the target [Essig and Felsen 2021].

If two food sources were equally distance from the animal, or their signal/distance matched, a left or right choice would be better than moving straight, but that situation would be metastable and likely resolve itself without additional decision circuitry. If the animal drifted to one side by chance, one food source would be nearer, and the animal would approach it.

Obviously, mammals have the ability to make two 2AFC decisions, but it’s not clear when that ability would be an evolutionary advantage for simpler animals. The 2AFC experiments are artificial cued situations that don’t resemble natural foraging. Although mammals can solve these situations, it seems more likely this is a byproduct of advantages aimed at a more direction situation, but generalized enough to cover the odd experiment.

Some decision researchers argue that real world options are generally sequential [Ballesta and Pado-Shioppa 2019]. Some argue that sequential decisions contrast the current option with the background, as opposed to drift-diffusion with two opposing actions, and contrast tug of war models vs sequential models [Kacelnik et al 2012]. Pure 2AFC is rare in nature [Ellerby 2028]. Reality includes competition with rivals and the potential for resources to accumulate and deplete.

Dynamic environment and slow accumulation

The second issue the simulation raised was when the animal’s situation changed more quickly than the accumulator. The dynamic environment produces obsolete partial data [Piet et al 2018]. In the simulation, the underlying non-decision behavior is a random walk. The new decision system overrides the random walk when it has a result, but the random walk does not stop for the decision. So, the random walk can turn sharply and reverse the left and right accumulators. If the accumulators are sufficiently slow, or insufficiently leaky, the partial results are now a mixture of invalid data from the past and new valid data.

There are a few immediate improvements. Shortening the accumulation or increasing the leak would shorten the timescale to minimize corruption. In mice, the midbrain accumulation timescale appears to have a τ=250ms delay time with longer integration requiring the cortex [Khilkevich et al 2024]. Rats can dynamically change the integration timescale when the environment becomes more unreliable [Piet et al 2018].

In theory, the animal could avoid making movements while it’s deciding to avoid corrupting the data, such as pausing random-walk turns by disabling the ARTR (anterior hindbrain turning region) in zebrafish. But this doesn’t seem to be a general solution because the animal would be continually pausing as it’s making a decision.

Another solution could reset the accumulators at any action, including non-decision actions like the random walk. The OT.s visual system does have a reset using V.lc (locus coeruleus) Ne (norepinephrine) to OT astrocytes [Uribe-Arias et al 2023], as a response to an escape action. In the cortex, movement preparation collapses at movement onset for that decision as a reset [Khilkevich et al 2024].

Animals rarely miss choices [Lu W and Wan X 2025], possibly suggesting an urgency signal [Cisek et al 2009], [Thura et al 2012]. An efference copy from the random walk ARTR, or a shared efference copy from the swimming CPG might force the turn decision circuit to curtail its evidence accumulation to make a decision before the random walk.

But again, I don’t know if these are general solutions. Research experiments generally work to reduce dynamic activity, such as head-fixed mice, or reporting neural activity after the animal has overtrained to produce stereotyped behavior, and introducing delays to separate neural signals to better distinguish which brain areas are active in each time period of a decision. But those necessary simplifications also erase any measurement of how the decision systems deal with dynamism [Gordon et al 2021]. Some research in auditory streaming does support dynamic decision making [Cao R et al 2021], although that study is for the cortex, and it’s unclear if those results apply to OT.

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42: Optic Tectum Decision

The key element of decision making is the commitment to an action: all-or-none, both sustaining a decision and locking out competing action. In contrast, the choice part of decision-making is less important. Even a simple random choice or first choice is an effective decision mechanism, but losing out the all-or-none means the decision isn’t a decision. The key is ensuring that once a choice is made, the animal sticks to that choice. The losing action should not interfere with the winner. Specifically a decision suppresses dithering: switching between competition actions [Redgrave et al 1999].

This essay uses wall-following from essay 41 as the decision. If the animal detects a wall to the right, it will follow that wall for a time, improving search over random walk by reducing the search to a single dimension. In this case, the choice is left or right, which particularly matters because the choice requires communication between the two sides, which requires specific circuits because commissures are relatively rare.

Decision: two-phase commit

Decision-making has two main components: the choice (preparation) and commitment. A decision that doesn’t sustain or that doesn’t lock out competing stimuli isn’t a decision. Decision-making can split into a preparation / selection phase, which compare options — taking time if necessary, followed by a commit winner-take-all phase where the winning action goes forward and any losing action is locked out.

Decision as a two-phase process

Most decision research is focused on the preparation phase because people are interested in choosing A vs B, and much less research on the commitment implementation, the timeout and lock-out. For the essay simulation, the commitment is more important and needs to be implemented first. Without the commitment, a losing option can continually interrupt the animal, distracting it from its goals. The requirements for commitment are something like:

  • Sustain
  • Timeout: prevent the sustain from becoming perseveration
  • Lockout: prevent competing actions

Orientation and wall-following

For a decision, this essay uses wall-following (thigmotaxis), continuing from essay 41. Wall-following needs to be treated as a decision beyond a single swimming cycle. Consider the alternative where a lateral-line sense is a simple sensory-action reflex for each swimming cycle. Without a longer conception of the decision, the animal can’t avoid perseveration: it would circle a pillar or a convex arena endlessly. Any timeout needs to curtail wall-following, not right turns. Similarly, without persistence the animal might alternate left and right wall-following in a crowded environment, where both the left and right lateral-line indicates obstacles. Of the two, the timeout issue is more critical, but the ability to continue an action, is necessary to enable a “win-stay” strategy.

Because the research hasn’t located the circuit for wall following, these essays need to choose a brain location for it. The previous essay proposed R1.a (anterior hindbrain) as the driver of thingmotaxis, but an alternative uses OT (optic tectum) as an orientation center for thigmotaxis. Because OT receives lateral-line input via M.ts (torus semicircularis / inferior colliculus) [Zeymer et al 2018], it has the sensory information needed to turn toward a wall. OT is known as an orientation center. When a surprising or salient sensation appears, the animal turns toward it. If we imagine the proto-vertebrate as non-cortical, then that orient is likely OT. Even in mammals with a strongly developed cortex that can provide orientation functionality, OT is perhaps the strongest [Schall 2019].

Two architectures for orientation decisions. On the left, the orientation sustains its own decisions and is directly modulated by timeout. On the right, a separate module is responsible for sustaining the decision, possibly incorporating motor efference copies as part of the sustain system.

One immediate question is if the orientation also implements sustain. Compare the left and right model. In the left model, the orientation system implements sustain itself, driving and sustaining a turn action. The right model has a distinct sustain system, which may be driven by motor efference copies. The known connectivity of OT could support either model.

OT has independent sustaining capabilities, in part due to sodium channel modulation [Ghitani et al 2016], [Thompson AC and Aizenman 2023]. OT also has a loop with T.pf (parafascicular thalamus) and S.d (dorsal striatum), which can implement the timeout using A2a.s (adenosine G-s coupled stimulatory receptor) and adenosine accumulation. Although the left model is possible, several studies report OT burst neurons activate at the decision point [Lintz et al 2019], [Stine et al 2023], with ramping neurons before the decision and action [Munoz and Wurtz 1995], [Lintz et al 2019], not after the decision, suggesting the model on the right. Ppt (pedunculopontine tegmental nucleus) is well-suited as a central node of the sustain role. Ppt maintains activity from one decision to another in tasks that repeat decisions [Thompson JA et al 2016]. It also receives widespread input from hindbrain motor areas, including R1.a and R5.my.gi (medulla giganocellular chx10 turning neurons) [Huerta-Ocampo et al 2021].

If wall-following uses the midbrain orientation circuitry, then a combination of OT and Ppt is plausible following the model on the right. Note, though, that the sustain may not be only Ppt, but could also include other anterior hindbrain systems like R1.a, V.rn (serotonin Raphé nuclei), and possibly R.ip (interpeduncular nucleus), because all of these are associated with brainstem sustained attention network [Alves et al 2022].

S.nr tri-value logic

S.nr (substantia nigra pars reticulata) is a key player in commitment. S.nr provides tonic suppression over essentially every voluntary action. For this essay, consider S.nr as a tri-value logic. The tonic, middle level of S.nr allows ongoing actions to continue, but inhibits starting a new action. A low S.nr value, the classic disinhibition model, allows new actions to start. A high S.nr value stops ongoing actions. The tonic level itself might be adjustable. For decision-making, this tri-value S.nr can support the commitment requirements of sustain, timeout (Stop), and lockout (passive inhibition with overriding Go).

S.nr as a tri-value system. The tonic activation allows sustain of an ongoing action. A Go signal disinhibits an action, allowing it to start. A Stop signal inhibits an ongoing action.

In the diagram above, the tonic S.nr inhibits new actions, but ongoing actions would continue, or a sufficiently strong sense input could start an action. An explicit Go signal would allow a weak sensory input to start an action. An explicit Stop signal would stop all action, regardless of the sense strength. The adjustable tonic level can be influenced by sleep and wake pressure, since S.nr.m is associated with sleep [Liu D et al 2020]. As the animal grows tired, a higher tonic S.nr would discourage new actions and encourage stopping of sustained actions, but the sleep pressure would not outright prevent action.

In the context of decision commitment, disabling S.nr eliminates orientation selectivity: mice are unable to resist orienting to any object in the whisker field [Redgrave et al 1999]. In PD (Parkinson’s disease) an overly-active S.nr produces bradykinesia (slow movements) and akinesia (lack of voluntary movement), and inhibiting S.nr can reduce akinesia and bradykinesia [Hu Y et al 2023], [Lin C et al 2024]. However, an underactive S.nr can produce dyskinesia (twisted postures) where opposing actions activate at the same time, and stimulating S.nr can reduce dyskinesia [Hu Y et al 2023].

Action sustain and timeout

An immediate consequence of commitment is timeout. Without a timeout, an unending commitment can lock an animal into a decision forever. A previous essay already covered a possible timeout circuit using adenosine as a timing neurotransmitter. The S.d2 (striatum with D2 dopamine-receptor) projection neuron have A2a.s (adenosine G-s coupled stimulatory) receptors, and some studies use A2a.s receptors to identify the S.d2 neurons as S.a2a as opposed to the S.d2 convention in the essays. Adenosine builds up around active neurons, partially produced by astrocytes that monitor glutamate activity [Ma et al 2022]. This adenosine progressively activates S.d2 neurons, which stops action using the indirect path.

Basal ganglia timeout circuit. Ongoing left wall-following provides an efference copy to S.d2. As time continues, adenosine enables S.d2, and eventually activates the indirect path to stop the left action. H.stn (subthalamic nucleus), P.ge (globus pallidus, external), S.d2 (striatum D2-receptor projection neuron), S.nr (substantia nigra pars reticulata), T.pf (parafascicular thalamus).

The above diagram shows a possible timeout circuit for thigmotaxis following a left wall. During the left wall-following, an efference copy via T.pf (parafascicular thalamus) drives glutamate to S.d2 in the striatum. Sustained glutamate in S.d2 produces adenosine, which progressively activates S.d2, which then inhibits the current action using the indirect path of P.ge (external globus pallidus) to H.stn (subthalamic nucleus) to S.nr to stop the left action.

Note that the P.ge / H.stn circuit is complex and oscillatory. This path isn’t necessarily a straight chain as the above diagram would suggest. For example, S.d2 to H.stn / P.ge can switch the mode from irregular, unsynchronized firing to a regular oscillation [Terman et al 2002], or switch from a gamma (~80Hz) to a beta (~20Hz) frequency [Wang Y et al 2024].

Interrupting sustained action

Sometimes sustained actions need to be interrupted, either for dramatic reasons like a predator attack or more mundane situations like stubbing a toe. These interrupts need to be fully general, halting the current action, no matter which action path happens to be active. Note the similarity to sleep, where sleep needs to halt any action.

Two ways of halting action are either a direct halt signal or a deadman’s switch. In a deadman’s switch, a tonic signal maintains normal behavior, and the absence of the signal stops the action. The brain uses this pattern with several instances of high-affinity Gi (G-protein coupled inhibitory) receptors that saturate in normal, tonic activity, but disengage when the neurotransmitter drops. In particular the D2.i (dopamine G-i inhibitory) receptor is high affinity, quickly saturating, that is fully active at normal tonic levels of dopamine and only shuts off when dopamine levels drop.

Adding a dopamine deadman’s switch to the timeout circuit. An interruption drops DA, which immediately activates the timeout circuit from S.d2. H.stn (subthalamic nucleus), P.ge (external globus pallidus), S.d2 (striatum D2 projection neuron), S.nr (substantia nigra pars reticulata), T.pf (parafasciculus thalamus), V.da (midbrain dopamine), V.rmtg (rostral medial tegmentum).

The diagram above adds a dopamine deadman’s switch to the timeout circuit. Tonic dopamine from V.da (midbrain dopamine) normally inhibits S.d2, allowing for a normal timeout. Because D2.i is a high affinity receptor, a low tonic level of dopamine activates it and quickly saturates the receptor. When dopamine drops below a threshold, the D2.i receptor will deactivate and disinhibit the S.d2 neuron, which rapidly fires the timeout using the indirect path, stopping the action. Dopamine will drop if V.rmtg (rostromedial tegmental) activates. V.rmtg is activated by pain or itch sensations and by many more general failure or disappointment systems.

Lockout and the Sprague effect

The commitment phase needs to lockout alternative distractors. I haven’t found any research on this specific scenario. Decision research generally studies artificial forced-choice scenarios, where each choice is separated by several seconds from another choice, and is forced by a single decision point, like a T-maze or Y-maze, or turning left or right from a central cue port. The design of the typical experiment removes the scenario of sequential, continuous choices. Because of the lack of direct studies, the following discussion is more speculative. Attention is a related, but distinct research area to decision-making. Sustained attention is similar to this commitment issue.

The Sprague effect is related to OT attention. In mammals OT receives excitatory input from C.vis (visual cortex). If the left C.vis is lesioned, the animal will ignore items in contralateral, right visual field. Paradoxically, a following lesion to contralateral, right OT will restore attention to the left visual field [Gambrill et al 2018], [Gebhardt et al 2019], [Jiang et al 2003], [Krauzlis et al 2013]. Further studies have shown this effect with the second lesion to the tectal commissure [Gambrill et al 2018] or to the specific area of contralateral S.nr [Krauzlis et al 2013] or to the entire contralateral Ppt [Valero-Cabré et al 2020].

In frogs there is a direct OT to contralateral OT connection. Unilateral OT legion impairs bilateral visual behavior regardless of looming direction [Gambrill et al 2018]. In contrast unilateral OT lesion deficit in behavior only in lesioned hemifield [Gambrill et al 2018].

Possible Sprague effect circuit, showing lockout of contralateral wall-following. OT.d (deep layers of optic tectum), Ppt.a (anterior pedunculopontine tegmental nucleus), Ppt.p (posterior Ppt), S.nr (substantia nigra pars reticulata).

This above diagram shows a potential circuit for the Sprague effect. (For simplicity, straightening out crossed output to the motor.) Once a decision to follow a right wall has been made, the ongoing motor action sends an efferent copy to Ppt [Caggiano et al 2018], which projects to S.nr [Durmer and Rosenquist 2001], which inhibits the contralateral OT.d [Durmer and Rosenquist 2001]. Similarly, a motor efferent copy to Ppt also projects to the ipsilateral OT.d [Valero-Cabré et al 2020], which enhances attention to continue following the right wall.

This Ppt sustained attention circuit is similar to the R.is (nucleus isthmus / parabigeminal) circuit in fish [Henriques et al 2019] and birds [Marín et al 2007], covered in essay 19. Like Ppt, R.is has both ACh and GABA components, although in Ppt the components are mixed salt-and-pepper, while R.is has distinct nuclei. Ppt and R.is are sibling areas, both generated from the same progenitors in R1 (hindbrain rhombomere 1), but one is generated before the other [Morello et al 2020]. R.is is better understood because it has simpler connectivity than Ppt. When zebrafish hunt paramecia, R.is sustains attention to a target prey and inhibits attention to other visual areas [Henriques et al 2019]. R.is provides a similar effect in birds [Knudsen 2011], [Marín et al 2007], [Mysore and Knudsen 2011], [Reynaert et al 2023].

Although Ppt has much more complicated connectivity and function, like R.is, it has reciprocal connectivity with OT. Ppt is also active during actions, and it highly heterogenous, and connected with much of the hindbrain motor, both R.pn (pons, anterior hindbrain) and R.my (medulla, central and posterior hindbrain). Like R.is, Ppt proves ACh attention to OT [Isa et al 2021], [Mena-Segovia et al 2008], [Mena-Segovia et al 2017], [Krauzlis et al 2013], [Wolf et al 2015] and as the Sprague studies show, it inhibits the contralateral OT via S.nr.

At the time of choice, many Ppt reflect previous action and outcome. Ppt lesions reduce influence of recent experience on action selection. The Ppt ACh input to OT is possible as a Bayesian prior [Thompson et al 2016].

Passive lockout

An alternative to an active of alternative actions is a passive lockout, which inhibits actions without needing input from a sustain system. Once an action commits, the passive lockout prevents new action. A possible passive lockout involves the H.stn / P.ge pair, which is hyperactive in PD. Akinesia like PD is exactly what’s needed for passive lockout.

H.stn / P.ge as a passive lockout system. H.stn (subthalamic nucleus), P.ge (external globus pallidus), S.nr (substantia nigra pars reticulata).

In the above circuit, H.stn and P.ge form a spontaneously oscillating circuit at beta frequencies. In PD, this circuit is hyperactive, oscillating at beta frequencies, providing broad movement inhibition [Fischer et al 2017]. This circuit drives S.nr, which inhibits the action.

This description vastly oversimplifies the P.ge / H.stn circuit. The P.ge / H.stn circuit can operate in at least two modes: inhibitory at beta frequencies (H.stn exciting S.nr), and excitatory at gamma (P.ge inhibiting S.nr) [Fisher et al 2017], [Terman et al 2002]. H.stn also has distinct subregions, with H.stn.vm (venture-medial) as almost an extension of H.l [Haynes and Haber 2013], while H.stn.l as distinct functionality [Baunez and Lardeux 2011], [Pasquereau and Turner 2017].

Studies seem to divide on whether H.stn is suitable for a commitment function. H.stn activity terminates at onset of movement [Espinosa-Parrilla et al 2013], which would argue against passive lockout. H.stn gamma increases during movement for humans [Fischer et al 2017], but others point out that H.stn beta are brief bursts, not sustained [Feingold et al 2015], and H.stn beta in humans is active for acute stopping [Wessel et al 2016].

A second passive lockout is in the striatum itself, discouraging new actions by default. S.pn (striatum projection neurons), both S.d1 (D1 receptor S.pn) and S.d2, are hyper polarized, making them harder to drive than most neurons. Secondarily, new actions are inhibited by the feedforward, fast-spiking S.pv (parvalbumin) neurons, which inhibit S.d1 and S.d2 before they can be activated. S.pv activates before S.d1 and S.d2 [Gage et al 2010], [Lee C et al 2019], [O’Hare et al 2017], [Yim et al 2011].

Striatum passive lockout using the inhibitory S.pv neurons. Once an action starts, an endocannibinoid sub circuit disinhibits the action, allowing sustained activity. eCB (endocannibinoid neurotransmitter), S.d1 (striatum D1-receptor neurons), S.d2 (striatum D2-receptor neurons), S.pv (striatum parvalbumin inhibitory neuron), T.pf (parafascicular thalamus).

This S.pv inhibition is suppressed by sustained action using a retrograde eCB (endocannabinoid) system that disinhibits both S.d1 and S.d2 by inhibiting GABA release from S.pv [Narushima et al 2006], [Adermark et al 2009], [Mathur and Lovinger 2012].

Active initialization

A passive lockout system needs to be paired with an active initialization. If new actions are passively inhibited by default, a new action needs extra effort to cross the barrier. Possible active initialization nodes include OT, Ppt, as well as the S.d1 direct path.

The following diagram shows a possible active initialization. The passive lockout subcircuit is the same as before. The active initialization would logically use the S.d1 path. Phasic dopamine activates the Go path, both by enabling the S.d1 input and their output, because D1.s receptors are on inputs to S.d1 and on the axons in S.nr, which enables the direct path to disinhibit the S.nr.

Explicit active Go circuit to override the passive lockout circuit. H.stn (subthalamic nucleus), LL (lateral-line), OT (optic tectum), P.ge (external globus pallidus), Ppt (pedunculopontine tegmentum), S.d1 (D1-receptor striatum), S.nr (substantia nigra pars reticulata), T.pf (parafascicular thalamus), V.da (midbrain dopamine).

This Go circuit is for wall-following, which uses the lateral-line as a wall distance sensor. The lateral line sense is input to the OT orientation circuit, which excites both the S.d1 path via T.pf and the V.da path, which will add a phasic DA burst to enhance the S.d1 circuit, giving it an extra boost to overcome the barriers.

Note that OT / Ppt also inhibits contralateral OT as described in the Sprague effect system, and the OT to V.da excitation is ipsilateral, but OT also inhibits the contralateral V.da via V.rmtg [Pradel et al 2021]. So this circuit is also part of the active lockout system.

Consider the striatum passive lockout circuit again, which discouraged new actions but enabled sustained actions. That passive lockout implies the necessity of an extra push for new actions. Phasic dopamine bursts could provide that extra push. A burst of dopamine activates the low-affinity D1.s receptors in S.d1, allowing S.d1 to override its intrinsic hyperpolarization and the feedforward S.pv inhibition and initiate a new action.

Striatum passive lockout circuit with sustain from eCB disinhibition and new actions enabled by DA burst. DA (dopamine), eCB (endocannabinoid), S.d1 (D1-receptor striatum projection neuron), S.d2 (D1-receptor striatum projection neuron), S.pv (striatum parvalbumin inhibiting interneuron), T.pf (parafascicular thalamus).

Pretectum suppression of OT

This essay uses the aquatic-only lateral-line for thigmotaxis. Thigmotaxis is an interesting system because the animal must be weakly attracted to the wall but simultaneously repelled by the wall to avoid collision. M.pt (pretectum) is an obstacle avoidance system in the midbrain and OT is an orienting system. In non-mammalian vertebrates (reptiles, birds, frogs), the striatum projects directly to M.pt, which inhibits OT [Krauzlis et al 2018]. If the animal gets too close to the wall, M.pt should inhibit the OT orientation and avoid the wall, but if the animal is far enough from the wall, it should approach the wall with thigmotaxis, suppressing the avoidance circuit.

Thigmotaxis balancing attraction from OT orientation and avoidance from M.pt obstacle avoidance. LL (lateral line), M.pt (pretectum), OT (optic tectum), S (striatum), T.pf (parafascicular thalamus).

The above circuit shows this potential thigmotaxis circuit. Normally, M.pt avoids the wall and suppresses OT to keep any OT orientation from running into the wall. But during thigmotaxis, the S circuit will suppress M.pt to allow the animal to get closer to the wall.

Simulation

The simulation divides thigmotaxis into several systems. An obstacle system roughly corresponds to M.pt and keeps the animal from running into a wall. An orientation system provides an attractive drive toward the wall. These two systems are now designed as independent and general, where sensory input is external. For example, the lateral line drives both the obstacle and orient systems, but the code for obstacle and orient systems are ignorant of the lateral line itself.

Outline of simulation modules for lateral-line thigmotaxis.

The decision commitment uses a loop with a sustain module and a striatum module. The sustain roughly corresponds to Ppt with possible associated areas like V.dr and R1.a, because the simulation is more abstract than directly implementing each neural ganglia. The striatum module provides with timeout function with an adenosine-lie timeout. The sustain also provides an active inhibitory lockout function, following the Sprague effect studies.

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Essay 34: Looming and Dimming

In an earlier essay that covered tunicates, the tunicate larva has two distinction visual action paths, one for phototaxis and one for looming. The two paths use different photoreceptors. Phototaxis photoreceptors are directional with pigment cells blocking light from one direction, while dimming photoreceptors are unidirectional with no shadow from pigment cells.

Looming and dimming are signals of both predators above the animal that block light from the sky, and of obstacles, which also blocks out light from the sky as the animal nears the barrier. In this essay I’ll be focusing on obstacle avoidance using a similar simulation approach as [Zhao et al 2023]. In general, the sky is the brightest, the ground is also light, such as sand, and obstacles are darker. So, if the eye is next to a barrier the average light is dim, while if it’s far from the wall the light is bright because the sky above and the lighter ground below are unobstructed.

Views from the left and right eye for a barrier to the left of an animal. The left is darker because it’s close to the wall, and the right is brighter because it has a clear horizon.

The above screenshot shows a fish-like create with a wall to its left. The left eye is next to a wall, and the right eye views the open field. If the image is reduced to a single average value, the left eye is dimmer, while the right is almost as bright as a full open field. As the first approaches the wall, the image dims rapidly.

Tunicate ascidian dimming

The tunicates (ascidian sea squirts) are the closest non-vertebrate chordates, although evolution has optimized them by removing features, making it difficult to draw direct comparisons to vertebrates [Holland 2016]. The ascidians have a simple larva form that swims for less than 24 hours before settling and becoming a sessile filter feeder.

The ascidian larva has a single ocellus (simple, non-image-forming photoreceptor area) has two distinct photoreceptor types and corresponding action paths, one that produces phototaxis and another that responds to rapid dimming [Ryan et al 2016].

Ascidian tunicate visual action paths.
Ascidian nervous system for both phototaxis action path and dimming escape. PR-1 is the directional photoreceptor for phototaxis. PR-2 is the unidirectional photoreceptor for looming escape. mgIN-L and MN-L are motor neurons. AMG is ascending motor feedback.

The above diagram of part of the ascidian larva nervous system, the PR-1 photoreceptors are directional for the top phototaxis path, while PR-2 non-directional photoreceptors produce dimming. The boxes above represent individual neurons, not larger functional groups. MgIN and MN are motor control and motor neurons [Ryan et al 2016].

Larval lamprey primitive eye

Lampreys and hagfish are the only remaining agnathans (non-jawed vertebrates), representing a much larger agnathan vertebrate group that preceded the jawed vertebrates, most of which were filter feeders or sediment feeders [Mallat 2023]. Lamprey larvae are unique among vertebrates in having a primitive non image-forming eye, more like the ascidian ocellus [Bayramov et al 2022]. The adult image-forming retina expands in rings around the more primitive center [Barandela et al 2023].

This central primitive eye is responsive to dimming, and it projects to an equivalent M.pot (pretectum), which handles several optical action paths in zebrafish, including dimming responses, phototaxis, OMR (optomotor reflexes), OKR (optokinetic reflex), and hunting.

Zebrafish retina arborization fields

The zebrafish N.rgc (retina ganglion cell) projects to ten distinct AFs (arborization fields), each with a distinct purpose, from AF1 to H.scn (suprachiasmatic nucleus) for circadian timing to AF10 to OT (optic tectum) [Baier and Wullimann 2021]. In most cases distinct N.rgc neuron types project to distinct arborization fields. Even with the largest field AF10 for OT, individual N.rgc neurons project to distinct OT layers. The temporal phototaxis of a previous essay used the projection to AF4 to thalamus to Hb.m (medial habenula, dorsal Hb in zebrafish) [Cheng et al 2017], [Chen and Engert 2014].

Zebrafish arborization fields. H.lg.v (ventral lateral geniculate), H.scn (suprachiasmatic nucleus), M.pot (pretectum), N.rgc (retina ganglion cells), OT (optic tectum), Poa (preoptic area)

The diagram above shows the zebrafish arborization fields and their targets, although the function of many of the targets is not fully known. Dimming fields include AF6, AF8 and OT [Baier and Wullimann 2021], [Temizier et al 2015]. It seems likely that AF6 and AF8 have distinct functionality, although the distinction is not yet known. In lamprey the central ocellus-like photoreceptors project to M.pot, while the outer, lateral image areas project to OT [Cornide-Petronio et al 2011]. The OT dimming response is directional, dimming in one side produces turning [do Carmo et al 2018].

Optic tectum

OT (optic tectum) has the largest arborization and it is the largest nucleus in the midbrain, larger than the entire zebrafish forebrain (cortex / basal ganglia). The optic tectum responds to looming objects and in zebrafish is used for visual hunting [Liu et al 2022]. Since the early vertebrates were filter feeders, the hunting functionality would be unnecessary, leaving obstacle and predator avoidance.

Optic tectum comparison between zebrafish and mammals. C (cortex/pallium), M.pag (periaqueductal grey), M.tl (torus longitudinal), N.rgc (retina ganglion cells), OT (optic tectum)

The optic tectum is layered with retina information arriving in the superficial layers, integrative information from other senses in intermediate layers, and motor actions from the intermediate and deep layers.

The above diagram shows a rough correspondence between zebrafish and mammal optic tectum layers. For simplicity, I’ll use the mammalian names. It’s not clear to me if the PV layer (periventricular layer) of zebrafish is equivalent to M.pag.d (dorsal periaqueductal grey), but I haven’t read any study addressing the physical similarity either as homologous or non-homologous, so it’s probably best to assume the location similarity is merely coincidental.

In zebrafish, the OT.s (superficial grey layer, SFGS in zebrafish) itself is layered with each layer receiving distinct N.rgc input [Liu et al 2022]. Dimming input goes to the deepest layer of OT.s [Temizier et al 2015], which is used by OT.d for looming responses [Heap et al 2018]. In mammals, OT.s receives retina input, OT.i produces turn actions, OT.d produces seek and avoid actions, and M.pag.dm produces fast escape from predators.

In vertebrates, OT uses visual expansion (looming) in combination with dimming [Nakagawa and Hongjian 2010], and dimming by itself does not trigger escape [Dunn et al 2016]. However, in the context of the essay’s simulation of a more primitive animal, expansion requires more sophisticated processing from an image-forming eye, which is only available for later vertebrates and not available to even the larval lamprey.

Torus longitudinus

In teleosts (most bony fish), M.tl (torus longitudinal) is a unique nucleus between the left and right OT. M.tl averages the dimming value between the right and left [Folgueira et al 2020]. It also has a sustain role, maintaining behavior after an initial signal.

Torus longitudinus between both OT. M.tl (torus longitudinal), OT (optic tectum).

Interestingly, M.tl is a CB-like (cerebellum-like) structure [Folgueira et al 2020]. Other CB-like ares such as MON (CB-like for LL) and DON (CB-like for electro sensation) act like adaptive filters for the lateral line to cancel out self-motion effects from sensors [Bell et al 2008], [Montgomery et al 2012].

Note that M.pot also communicates with its opposite side through the posterior commissure [Suzuki et al 2015], which could resemble an ancestral visual system. So, although M.tl is directly relevant to the looming response in zebrafish, it may be a specific teleost system, not an indication of an ancestral architecture.

nMLF optical motor output

The zebrafish reticulospinal motor control neurons are divided into several groups with distinct action paths. Optical motor output uses M.nmlf (nucleus of the medial longitudinal fasciculus), a midbrain reticulospinal group composed of 20 neurons on each side [Severi et al 2014]. M.nmlf avoidance is distinct from the Mauthner cell startle circuit in r4 in R.mrs. Although the OT looming / dimming can trigger the startle response [Temizer et al 2015], it generally uses the lower-priority M.nmlf [Bhattacharyya et al 2017].

nMLF as the output of the dimming/looming response. AF (retina arborization field), M.pot (pretectum), N.rgc (retina ganglion cell), N.sp (spinal cord), OT (optic tectum).

This direct OT to M.nmlf projection applies to early zebrafish larva. As the fish ages, OT adds projections to R.mrs (middle reticulospinal) in r4-r6 of the hindbrain [Barandela et al 2023], including turning neurons marked by chx10 [Cregg et al 2020]. For this essay, I’m using the simpler early projection to M.nmlf.

Dimming information goes to AF6 and AF8, which are dendrites of M.pot [Heap et al 2018], which projects to M.nmlf [Portugues and Engert 2009].

Looming can produce zebrafish O-bends (u-turns) as well as directional turns [Portugues and Engert 2009], [Marques et al 2018]. For this essay, I’m assuming that M.pot produces a base O-bend command that the OT can modify by choosing a turn direction. This split between motivation and turning also occurs in R.mrs, where MLR (midbrain locomotive region) produces a non-directional forward movement, while chx10 neurons in R.mrs receive OT turning commands for looming [do Carmo et al 2018], [Cregg et al 2020].

Simulation

This essay’s simulation uses dimming as an obstacle avoidance system, similar to the simulation in [Zhao et al 2023], but with a minimal dimming input. The essay’s simulation condenses the input to the simplest dimming structure, where each eye has only a single averaged luminance value. The retina also calculates a dimming value as the difference between the current luminance and the previous value. Although the vertebrate retina uses distinct unsigned ON and OFF channels, the simulation uses a single signed value.

The looming module triggers a looming response when the dimming value passes a threshold as a proportion of the current luminance. This part of the model represents M.pot (pretectum). If no further information is available, the looming triggers a u-turn (O-bend in zebrafish) using M.nmlf.

If the left and right eyes have a difference in brightness, the model converts the u-turn into a left turn or right turn. This part of the model represents the OT’s dimming response. Like the M.pot output, this OT turn signal uses M.nmlf, as in the early zebrafish larva.

Screenshot showing the animal avoiding a wall to its left. The left and right retina displays are for human viewing.

The above screenshot shows the animal avoiding an obstacle to its left. The two low-resolution images at the lower right are for human viewing and are higher resolution than the animal uses. The animal itself only uses a single averaged value for each eye. This view from the left eye is dominated by the wall, which blocks the light. The right eye mostly sees a clear view to the horizon.

Discussion

Qualitatively, the system works surprisingly well despite its simplicity. In some of the narrow corridors the u-turn behavior will reverse out of the corridor, and the entrance to the corridors is something of a barrier because only the center of the corridor will avoid triggering avoidance.

The model doesn’t adjust speed, which is an interesting potential improvement. If the animal slowed near obstacles, raised the threshold for obstacle avoidance, and reduced the turn angles, it might more easily navigate corridors. Since searching already has a roam vs dwell mode for ARS (area restricted search), triggered by serotonin, a slow-moving obstacle avoidance mode could use the same mechanism. V.dr (dorsal raphe serotonin) does reduce looming defense [Huang et al 2017]. Alternatively, since OT.d looming does habituate [Lee et al 2020], that habituation could reduce the excessive u-turning of the model. H.lgn.v (ventral lateral geniculate nucleus), which responds to overall light levels, can also inhibit the looming response [Fratzl et al 2021].

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Essay 30: Real Time Place Avoidance

I’m looking to improve the foraging algorithm with an idea from essay 17, which suggested that when the foraging fails, the animal should avoid the failed area. The foraging task uses an odor cue to seek food. Currently when the model gives up (times out), it disables seeking, but doesn’t actively avoid the current place, but returns to the wide-ranging roaming search.

For now, I’m still avoiding memory, but consider the alternating T-maze used in rodent behavior [Deacon and Rawlins 2006]. Mice are released at the base of the T and choose one of the directions to search for food. If the experiment repeats (by picking up the mice and restarting) mice will tend to explore the unexplored end first.

But for our foraging task, let’s use the same device for a different purpose. Instead of repeating the experiment by unnatural teleportation, consider the simpler problem of foraging with this device as an environment.

T-maze exploration. Food might be at either the red dot or the blue dot.

When rodents are foraging and reach one end, they will reverse and search the other end. Because rodents are far more advanced than the toy model, they can remember which arm of the maze they’ve already explored. But consider a simpler sub-strategy that uses RTPA (real-time place avoidance) where the animal temporarily avoids the current area or areas associated with food. By actively avoiding the already-explored area, the animal will save time by avoiding repeated searching.

A difficulty in finding the neural correlates of RTPA is the great diversity of reasons for RTPA, and circuits even in the brainstem. There are many reasons for place avoidance:

  • Startle: reflex escape
  • Escape from an imminent predator
  • Escape from an environment hazard (CO2, temperature)
  • Avoiding innate cues (predator odors)
  • Avoiding learned cues (CPA conditioned place avoidance)
  • Search optimization: avoiding already searched areas

Because this topic is large and the number of circuits is also large, I’ll start with a more abstract view to provide some context for a later dive into details. The two architectures will be a set of labeled path seek and avoidance circuits, and a secondary consensus circuit to coordinate the labeled paths.

Labeled path

A labeled path architecture uses individual circuit paths for each behavior and sense, as opposed to bringing all stimuli into a central node with a general decision algorithm [Helmbrecht 2018]. (Helmbrecht uses “labeled line,” which conflicts with the fish “lateral line” sense.) As least to some extend, the brainstem is designed around labeled paths, which is particularly evident if using the chimera model of the bilateral brain [Tosches and Arendt 2017].

The chimera model posits that brains of bilateral animals combine features from apical (unilateral) and bilateral (“blastoporal” in their terminology because they focus on zooplankton larvae). The apical mode is associated with the front of the brain, such as the hypothalamus, and its locomotion is temporally gradient based, like the tumble-and-run of bacteria. The bilateral mode is more reflexive, turning left if touched on the right, like Braitenberg vehicles [Braitenberg 1984]. Apical systems include olfactory search and phototaxis, while bilateral touch, lateral line, auditory and bilateral vision in a second system. For zebrafish one study describes multiple paths as a “high road” through Hb (habenula, apical) and a “low road” through OT (optic tectum, bilateral) [do Camo Silva et al 2018].

Some labeled paths for locomotion in vertebrates. H.l (lateral hypothalamus), Hb (habenula), MLR (midbrain locomotive region), N8 (acoustic-vestibular cranial nerve 8), OT (optic tectum), R.ip (interpeduncular nucleus), R.mcell (Mauthner-cell), R.rs (reticulospinal motor command)

The above diagram shows some vertebrate labeled paths, which is clearer in simpler vertebrates like the lamprey and zebrafish. In the zebrafish startle reflex, a sudden noise triggers a fast C-bend turn followed by rapid swimming. The trigger can be a noise, vestibular, or lateral line motion [Berg et al 2018]. The startle circuit is only three synapses from the original sensor to the muscle, from the N8 auditory/vestibular nerve to the giant M-cell (Mauthner cell in r4) to the motor neuron that drives locomotion. In young zebrafish larva, head touch neurons (N5 trigeminal) connect to M-cells and are later replaced by N8 [Kohashi et al 2012]. M-cells fire only once per escape to drive the initial turn. Interestingly the escape turn choice uses an axo-axonic repeater and amplifier [Guan et al 2021].

In a different path looming and dimming visual signals that represent predators or obstacles drive OT (optic tectum), which can drive escape that either uses or bypasses the M-cell depending on the threat level [Bhattacharya et al 2017]. OT also pre-programs the M-cell circuit by suppressing the left or right to avoid an obstacle [Zwaka et al 2022].

Phototaxis (seeking or avoiding light) uses a temporal gradient system composed of left Hb.m (medial habenula) and R.ip.d (dorsal interpeduncular nucleus), which projects to the R.rs (reticulospinal motor command) neurons via relays in V.mr (median raphe) and P.ldt (laterodorsal nuclei) [Chen and Engert 2014]. Food odor seeking uses the right Hb.m and R.ip.v (ventral interpeduncular nucleus) [Chen et al 2019].

In lamprey a distinct food-seeking path through V.pt (posterior tuberculum – possibly homologous to vertebrate Vta/Snc) to MLR (midbrain locomotor region) and finally to R.rs [Derjean et al 2010]. Zebrafish has a similar dual path through Hb.l (lateral habenula) through a midbrain TSN circuit [Koide et al 2018].

Slower escape uses a distinct prepontine (rhombomere r0-r1) circuit, which is suppressed by the M-cell escape circuits [Marquart et al 2019].

Some of these paths have shared elements, particularly at the motor control like MLR, but the general pattern is multiple labeled paths for each behavior. The paths already mentioned don’t include more complex food-seeking paths through the basal ganglia and hypothalamus.

Multiple labeled paths immediately raises the difficulty of coordination. How does the system juggle priorities? Even the simple startle reflex needs to be modulated because the animal shouldn’t startle if the loud sound is expected, such as near a waterfall. In contrast in a dangerous area with possible predators the animal should increase the reflex to a hair-trigger. Similarly if the threat is weak and the animal is hunting or eating and hungry, it might ignore the threat to continue eating. A second architecture, distinct from the label path, emphasizes the coordination of multiple paths, possibly using a consensus system to decide on an appropriate action.

Consensus loops

While the labeled paths have strong evidence, the consensus loop is only a thought experiment to tie the paths together. Multiple paths for food seeking and for avoiding is a distributed system, and distributed systems makes decision circuitry more complicated because they’re not central decision node. Every node needs to agree with the decision. Whether to avoid or approach needs to be agreed on by all the systems. It wouldn’t make sense for one system to believe the animal is approaching an object but another system believes the action is avoiding. Voting distributes the consensus.

Illustration of a consensus loop. Multiple drives or labeled paths vote for approval to drive motor output.

The above diagram shows the model. The different labeled paths of seeking or avoiding join a voting consensus system in a motivational look, which allows one path to drive motor output.

Consensus system showing one path. The driving sense or motivation tries to disinhibit itself by voting in the consensus loop.

A single labeled path has a sense or motivation drive that tries to act on motor output, but is inhibited by the consensus system. For example, if a predator odor arrives, the odor avoidance path votes to enable its own locomotion. If the consensus system agrees, it will disinhibit the odor avoidance path, letting the animal escape. Note that a high priority threat could bypass the consensus system.

Seek and avoid consensus system

This system can manage conflicts between seek and avoidance, such as animals continuing to eat if a predator threat exists but is low. Consider a simplified consensus system with only one seek node and one avoid node, using the consensus to select one when there’s a conflict.

Managing conflicts between seeking and avoiding.

If there’s a food cue and no conflicting threats, the food vote passes easily and the animal seeks the food. Similarly a predator odor with no conflict will enable avoidance. If there’s a conflict, the system can weigh the costs and benefits of the threat and the food, possibly depending on hunger state or a more sophisticated threat assessment.

Keeping these general ideas of the labeled path and consensus systems in mind, let’s start working through several specific paths. The end goal is to organize the main brainstem locomotive areas into a simplified, unified model. The two major paths will be apical paths through Hb (habenula) using temporal gradients (klinotaxis) [Chen and Engert 2014] and bilateral paths through OT (optic tectum) using spatial gradients (tropotaxis).

Apical and bilateral avoidance

Because there are many labeled paths, dividing them up might help organize the model. An early division between labeled paths goes back to the bilaterian (worm-like, slug-like) ancestors, which added bilateral, dual-sensory navigation (tropotaxis, spatial gradient) to an older single-sensor navigation that used the animal’s movement to choose a direction (klinotaxis, temporal gradient), such as the simple tumble-and-run that even bacteria and simple radial zooplankton use for seeking odors (chemotaxis) and seeking or avoiding light (phototaxis). This chimera hypothesis [Tosches and Arendt 2013] considers bilateral animals as a fusion between the locomotive systems. The apical zooplankton larvae of bilaterian worms may have been a secondary development to escape predation [Mallatt 2021]. In vertebrates, apical klinotaxis is implemented by Hb (habenula) temporal gradient seeking and H.l (lateral hypothalamus) motivation. Bilateral tropotaxis navigation is implemented by several labeled path systems, typified by OT (optic tectum) and the M-cell start reflex.

A primitive apical example is the helical phototaxis of many annelid (marine worm) zooplankton larvae, and a primitive bilateral example is the mollusk sea slug navigation.

Zooplankton apical phototaxis

One type of zooplankton is essentially a globe with a fringe of cilia and an apical tuft for chemical processing, such as the Platynereis larva.

Apical zooplankton with cilia navigation.
Platyneris annelid (marine worm) zooplankton larva

Phototaxis for this larva depends on its helical movement (helical klinotaxis). As it moves forward, the larva also rotates and wobbles, which means that parts of the equatorial band are nearer the light or further from the light depending on the rotation. If the upper cilia halt, the larva will steer toward the light. If the lower cilia halt, the larva will steer away from the light [Randel and Jékely 2016].

Phototaxis for an zooplankton larva.

The system depends on a directional eye, which uses a photoreceptor and a pigment cell that imposes directionality by shading the photoreceptor, because other cells of the larva are transparent. The photoreceptor compares the current brightness to its average brightness as the larva rotates. If it’s brighter than average, then it must be facing the light, and will signal the cilia to briefly halt, using ACh (acetylcholine) as a neurotransmitter. This trivial one-neuron circuit is sufficient for simple phototaxis [Randel and Jékely 2016].

Although this example larva uses two photoreceptors, it’s not truly bilateral and the two photoreceptors don’t communicate. Ablating one photoreceptor doesn’t abolish phototaxis, although it does reduce efficiency. Using three or four photoreceptor/pigment pairs would work, as well as removing all but one. This system is apical klinotaxis, not bilateral tropotaxis, which makes sense because the above zooplankton is not bilateral. While this zooplankton uses helical klinotaxis, another common form of klinotaxis is a side to side “casting” motion used by other simple animals like c. Elegans [Izquierdo and Lockery 2010].

If zooplankton phototaxis is an example of apical navigation, then the mollusk sea slug is an example of bilateral navigation.

Mollusk sea slug seek and avoid

The mollusk sea slug circuit is a pure bilateral circuit, almost directly a Braitenberg circuit [Braitenberg 1984], discussed in essay 14. The following shows a rough schematic of the sea slug seek and avoid. This circuit is interesting because with only a few neurons, the slug can switch from turning toward a food odor when hungry to turning away from the odor when not hungry [Gillette and Brown 2015].

Odor seek and avoid circuit for a sea slug. Hunger switches a food odor from seek to avoid.

In the diagram above, the central grey area is a switchboard circuit. Hunger reconfigures the switches connecting the odor to the turn motor neurons. When the slug is hungry, the right odor sensor connects with the left turn muscle, seeking the odor. But when the slug is sated, the right odor sensor connects with the right turn muscle, avoiding the odor. When the slug is hungry, it approaches food but when it’s not hungry, it avoids food odor cues.

A similar animal with a different circuit configuration uses serotonin to switch from avoidance to approach [Hirayama et al 2014].

For the goal of this essay, avoiding a failed food cue, this circuit is perfect because when the animal finds a false cue, it reversed movement from seek to avoid, which exactly fits the essay needs. Unfortunately, the vertebrate circuits aren’t nearly as straightforward. As a start for the vertebrate navigation paths, the startle reflex managed in vertebrates by the giant Mauthner cells is a simple starting point.

Amphioxus fast twitch reflex

The fast twitch startle reflex is a clear example of a bilateral labeled path avoidance circuit. A noxious sense on one side causes a fast turn away from the sense. The sense can be a touch on the head, such as running into an object, or a loud sound or a vestibular imbalance signal. This circuit predates vertebrates and a similar circuit exists in amphioxus, a filter-feeding chordate that looks something like a fish without a distinct head and without eyes, but with several photoreceptors including a frontal “eye.”

In amphioxus the startle reflex drives fast twitch muscle fibers, where normal swimming uses slow twitch fibers [Lacalli and Candiani 2017]. This circuit path is entirely distinct even to using the different muscles. The following diagram shows part of the amphioxus motor control circuit. (Because the neuron names are specific to amphioxus, they’re not hugely important for this essay.)

Amphioxus fast twitch escape uses LPN3, glutamate large paired neuron.

The diagram shows the LPN3 (large paired neuron) fast twitch escape path, and the PPN2 normal swimming match, including intermediary motor control neurons [Lacalli and Candiani 2017]. This amphioxus escape circuit resembles the zebrafish Mauthner cell escape.

Zebrafish Mauthner cell escape

Zebrafish have a pair of large M-cell (Mauthner cell) neurons that are specialized for auditory and vestibular startle escape. These are very fast reflexes on the order of 10ms, which can be modulated by higher context [Zwaka et al 2014] including OT. Although the M-cells perform a similar role to the amphioxus LPN3, it’s not clear that they’re homologous, which requires common descent, because the large escape neuron is a common pattern in non-chordate systems.

Zebrafish startle response at right in context with other labeled paths. M-cell (Mauthner R.rs cells in r4), N8 (acoustic/vestibular cranial nerve 8), OT (optic tectum), R.pp (prepontine avoidance in r0-r1), R.rs (reticulospinal motor control)

The primary input to M-cell escape is an auditory and vestibular signal from N8 (8th cranial nerve is auditory and vestibular). In water, sound and primitive vestibular sense have some similarities, because water motion produces not just sound but animal motion, depending on the frequency. The M-cell directly connects to motor neurons to muscles. The startle escape is only a three neurons and a clear, distinct labeled path.

A second zebrafish threat avoidance path uses neurons in R.pp (pre-pontine r0-r1) [Marquart et al 2019] for more distance threats. Unlike the M-cell circuit, this R.pp path is more than a reflex, but it’s still a hardwired path. A third threat circuit uses OT (optic tectum), for example the looming response. Most vertebrates will flee or freeze from a rapid and overhead expanding dark object, representing a potential predator or an obstacle. The mammalian startle circuit shares similarity with an acoustic projection to R.pn.c (caudal pontine reticular) neurons, in an analogous area to the M-cell [Kim et al 2017].

Some of these circuits do share sub circuits. For example, hindbrain locomotion and turning are distinct circuits that are used by both bilateral and apical avoidance circuits.

Hindbrain locomotion and turning

Senses are not the only source of distinct paths because actions can be split into parts like a car’s divided steering and acceleration. In vertebrates, accelerating and turning use distinct hindbrain circuits. Although both MLR (midbrain locomotive region) and OT.d (deep layer of the optic tectum) encode seeking and avoiding, they don’t encode left or right turns. Activating the left or the right MLR produces straight movement [Brocard et al 2010]. Turning is managed from OT.i (intermediate layer of the optic tectum) to distinct R.rs motor command neurons, marked by the chx10 transcription factory [Cregg et al 2020].

Hindbrain acceleration and turning circuits. R.rs (reticulospinal motor control)

The above diagram shows the basic idea. The upstream MLR can command forward movement without specifying details, because swimming is an oscillatory process with CPG (central pattern generators) in the spinal cord and the hindbrain. To turn, the chx10 neurons inhibit the swimming stroke in one direction [Cregg et al 2020], similar functionally to the apical zooplankton inhibition of cilia for phototaxis.

Splitting out turning can simplify the system by dividing labor, where OT.i is always responsible for obstacle avoidance, but a diverse set of labeled paths decode whether to seek or to avoid.

Optic tectum and dimming

The OT is named after its retinotopic visual map that is used for avoiding looming/dimming obstacles and predators, and also for seeking prey [Basso et al 2021]. For most vertebrates, OT is the primary visual area, and the visual cortex only provides abstract context, and amphibians and fish lack a proper visual cortex [Heap et al 2018]. For this essay, OT is less important for its sophisticated visual organization, but more because it also contains motor maps for seeking or prey and avoidance of looming objects, and dimming fields. Its motor map also contains drinking and licking [Liu et al 2022].

Looming/dimming path through optic tectum. OT.m (medial, deep optic tectum), R.rs (reticulospinal motor command)

OT processes looming and dimming objects and avoids them. Since the essay’s model lacks proper vision, the dimming is currently most important. Because OT also has obstacle avoidance, it’s a more sophisticated system than simply reflex. It’s likely that other avoidance systems will use OT for obstacle handling. Even in the case of the M-cell reflex, the OT.i pre-programs the M-cell, to avoid obstacles in case of a future startle [Zwaka et al 2014].

Optic tectum and turning

This division between turning and acceleration applies to OT itself. OT is a layered structure where the top layer is a visual map, the intermediate layer integrates other senses and produces turns, and the deepest layer includes actions such as avoiding and seeking [Liu et al 2022]. OT.d (deep OT) is a motor area for seek and avoid, connected with MLR and M.pag (periaqueductal grey) motor output, and integrates general dimming from the retina with distinct expansion calculation in OT itself [Heap et al 2018], to avoid looming objects. OT.i (intermediate OT) includes multi sensory integration and turning motor area, connected with LL (lateral line) electro sensation and water motion, somatosensory (whiskers in mice), auditory input from M.ic (inferior colliculus) and optic input from OT.s (superficial OT).

Optic tectum layered structure, emphasizing turning and motion. LL (lateral line water motion), MLR (midbrain locomotor region), OT.s (superficial optic tectum), OT.i (intermediate OT), OT.d (deep OT), R.rs (reticulospinal motor command)

Because only the top layer is specifically optic, some neuroscientists use “tectum” (roof in latin) instead of OT to emphasize its multi sensory and motor function, not just the optic features. On argument suggests that the optic layer OT.s is a secondary layer, added to a more primitive OT.i and OT.d that are more connected with reticular areas like MLR and M.pag [Edwards 1980], [Basso et al 2021]. With that argument, OT is primarily a moving and turning structure, receiving turning and moving input from touch, lateral line, primitive dimming, and other directional senses and combining with seek and avoid decisions. When the visual system developed enough detail to support crude images like looming disks or moving prey-like dots, the OT integrated vision into its top layer.

On the other hand, since OT.d receives dimming information from H.lg (central lateral geniculate nucleus) for looming escape [Heap et al 2018], it’s also conceivable that the base OT function is visual escape from dimming, where the later expanding, looming visual processing is an optimization.

Optic tectum obstacle avoidance combined with MLR seek or avoid movement. MLR (midbrain locomotor region), OT.i (intermediate optic tectum), R.rs (reticulospinal motor neurons).

This separation of obstacle avoidance turning from seeking and avoiding greatly simplifies some other circuitry that doesn’t need to duplicate the obstacle avoidance. Since other circuitry from the apical path, like the Hb-R.ip (habenula – interpeduncular nucleus) has its own turning system, OT.i doesn’t have a monopoly on turning. But even in that case, OT.i obstacle avoidance can inform apical navigation.

Some of these avoidance circuits are from the bilateral part of the chimera, such as the M-cell and the looming OT circuits, and others are from the apical part, such as Hb.m phototaxis, chemotaxis, and thermotaxis. So, let’s now more from the bilateral avoidance circuits, explore the vertebrate apical navigation.

Tunicate helical swimming and phototaxis

Tunicates (including sea squirts) are the closest chordates to the vertebrates, but because they have evolved at a greater rate and in specialized directions, comparison with vertebrates is difficult [Stolfi and Brown 2016]. Ascidian tunicates (sea squirts) have a mobile tadpole stage that plants itself in under 24 hours and transforms into a sessile filter feeder, reforming the entire brain. In general, neuroscientists believe amphioxus more resembles the ancestral vertebrate, and that ascidians have lost too many ancestral structures for a reasonable comparison [Holland 2016]. But for the sake of exploration let’s run through a thought experiment as if the ascidian larva is a compressed and simplified version of the vertebrate ancestor, although possibly only the vertebrate larva.

Specifically, consider phototaxis in the apical helical klinotaxis mode that follows a temporal gradient, since both amphioxus and ascidian larva swim in a helical pattern. Even bacteria can follow odor gradients [Hengenius et al 2012] and as discussed above zooplankton phototaxis can move toward light with only a single photosensor [Randel and Jekely 2016]. Both amphioxus and ascidian larva have single unpaired eyes, amphioxus as a single frontal eye [Lacalli 2022] and ascidians with an asymmetrical eye paired with a second pigment cell used for geotaxis as a primitive vestibular sense [Hoyer et al 2024]. In both cases, the “eye” is directional with a pigment cell, but a non-image-forming collection of photoreceptors. The ascidian asymmetrical eye works because the ascidian tadpole swims in a helical pattern so the timing of the light on the eye matters more than its position [Ryan et al 2016].

Ascidian larvae swim in a helical pattern comprised of unilateral tail flicks and symmetrical swimming [Ryan et al 2017] and use the asymmetry of the photoreceptor and photopigment to swim toward light [Mast 1921], [Zega et al 2006]. Since helical swimming doesn’t need stabilizing fins or vestibular systems to manage roll, yaw, and pitch with 3d swimming, it’s available to evolutionarily simpler systems. Another advantage of helical phototaxis is that the photoreceptors are auto-calibrating by simply averaging the light in a rotation and requires less circuitry than a bilateral comparison of light [Randel and Jekely 2016].

However, unlike the trivial zooplankton circuit that directly connected the photoreceptor to arrest the cilia, ascidian larvae need to modulate the bilateral swimming in the primitive hindbrain, timing the muscle inhibition to achieve the same effect.

The ascidian ocellus (“eye”) has two types of photoreceptors with distinct responses. Type 1 has a pigment and lens and is directional (37 cells), while type 2 is non-directional (no pigment partner) [Salas et al 2018]. If the pigment is genetically deleted, the animal can’t use phototaxis but does respond to dimming with an escape response. In other words, the dimming response and phototaxis use distinct labeled paths with distinct input neurons [Kourakis et al 2019]. The following shows the circuit for the type 1 photoreceptors for phototaxis, where the boxes represent single neurons or small collections (5-8) of neurons, not large functions (from [Ryan et al 2016]).

Ascidian larva phototaxis (ocellus) and geotaxis (otolith) circuit. Ant2 (antenna geotaxis sensors), antRN (antenna relay neuron), mgIN (motor ganglion interneurons, left and right), MN (motor neurons, left and right), PR-1 (type-1 phototaxis photoreceptors), prRN (photoreceptor relay neuron)

The above diagram shows both geotaxis and phototaxis circuits, which are specific to right or left motor neurons respectively, because the ascidian larva neuron circuits are highly asymmetrical. Ascidian larva geotaxis swims upward and phototaxis swims away from light, generally downward. The combination encourages swimming to the underside of ledges, such as the underside of boats and harbor piers [Ryan et al 2016]. Because of the helical swimming, the left and right motor neurons aren’t left or right turns, but turns toward or away from the target. Although this circuit is more complicated than the purely apical zooplankton because of the interface to bilateral swimming, the helical swimming keeps the circuit relatively simple.

The above partial circuits are complicated by the coronet cells, another sensory cell that are paired with the photoreceptors, but with unknown function. The circuit connectivity is interesting, because coronet cells modulate both the phototaxis and geotaxis paths, but aren’t a path of their own. The phototaxis and geotaxis relay neurons above are partially bilateral. Only 70% of their connectivity is to the main side, but 30% of the connectivity is to the opposite side. In contract, the coronet-enabled neurons are 100% to the main connection [Ryan et al 2016].

Coronet cell modulation of phototaxis and geotaxis in the ascidian larva. ant2 (antenna geotaxis cell), ant-core (antenna-coronet relay neuron), antRN (antenna relay neuron), DA (dopamine), mgIN (motor ganglia interneuron, left and right), MN (motor neuron, left and right), PR-1 (photoreceptors type-1), pr-cor (photoreceptor-coronet relay neuron), prRN (photoreceptor relay neuron)

As a thought experiment (unsupported by scientific evidence) the main phototaxis path might be uncertain and stochastic, while the coronet-enabled path would be a certain, deterministic connection. If the coronet cells measured the certainty of the animal’s current direction, it could encourage sticking to the current path. For example, if the coronet cells were food-odor gradient sensors, they could fire when the animal was heading toward food, enabling a chemotaxis based on modulation of geotaxis and phototaxis.

Tunicate dimming response

The ascidian dimming response triggers locomotion with a strong turn as an escape response to predators [Kourakis et al 2019]. Unlike the phototaxis photoreceptor, the dimming photoreceptors are non-directional because’er not shaded by the pigment cell. There are 23 type-1 directional photoreceptors and 7 type-2 non-directional photoreceptors for dimming.

Ascidian larva dimming circuit in context with phototaxis circuit. AMG (ascending motor ganglion neurons), mgIN (motor ganglion interneuron), MN (motor neuron), PR-1 (type-1 photoreceptor), PR-2 (type-2 photoreceptor), pr-AMG (photoreceptor-AMG relay neuron), pr-RN (photoreceptor relay neuron).

The above diagram shows the dimming path in context with the previous phototaxis path. Like the phototaxis path, the dimming path starts from the type-2 photoreceptors to a relay neuron and to the control neurons in the motor ganglion. Unlike the phototaxis path, the dimming path is modulated by ascending motor signals from AMG (ascending motor ganglion) and from the phototaxis path [Ryan et al 2016], presumably so the normal helical phototaxis doesn’t trigger a dimming response.

Cement gland and attachment

The ascidian larva hatches before dawn, swims upward for a few hours because geotaxis is enabled before phototaxis neurons attach, and then swims away from the light, settling on a lively rock, preferring a ledge to settle under if possible. Larva do not feed [Ryan et al 2016]. The larva will attach with a cement gland on the front of its head, a trio of palms, and then transforms into the adult sessile filter feeder. The palp sensors trigger the attachment circuit, which stops all swimming and begins the metamorphosis [Anselmi et al 2024].

Ascidian larva attachment circuit. AMG (ascending motor ganglion), ATEN (anterior trunk touch / chemosensor), mgIN (motor ganglion interneuron), MN (motor neuron), RTEN (rostral trunk touch / chemosensory), PN (palp neuron), pnIN (palp interneuron), pnRN (palp relay neuron)

Although the full details of the above circuit [Ryan et al 2016] aren’t critical, the PN (palp neuron) senses the animal bumping into a rock modulated by chemical senses that avoid toxic area, and triggers a swimming shutdown by inhibiting the motor neurons and interneurons [Hoyer et al 2024]. Like the previous diagrams, the boxes represent individual neurons or small group, not large functional regions.

While the ascidian cement gland is permanent, several fish [Pottin et al 2010] and amphibians [Rétaux and Pottin 2011] have a homologous cement gland used for larvae, not adults. For example, frog tadpoles can attach to the bottom of leaves or to the water surface to avoid predators until they are large enough to hunt [Jamieson et al 2000], [Yoshizawa et al 2008]. Because of the widespread cement gland among many fish species and amphibians as well as the tunicates, it’s likely the original vertebrates had a similar cement gland [Rétaux and Pottin 2011]. Whether the gland was larva-only like in vertebrates or also used for adults as in tunicates is unknown. In either case, the cement gland circuit that inhibits locomotion must have been part of the original vertebrate.

Vertebrate analogies to the ascidian circuits

Because the ascidians are so specialized and reduced from the common ancestor with vertebrates, including major losses in genes, cells and structures, comparing the two is essentially impossible to be homologous (shared descent) [Holland 2016]. However, for the sake of exploration, I’m ignoring that advice, and looking for analogous vertebrate circuits to the ascidian larva.

The ascidian behavior each have distinct circuit paths that mostly only come together at the motor control neurons. The exception is the feedback from the AMG (ascending motor ganglion) neurons, which do feedback to the midbrain neurons, but the main paths are separate forward paths. Each of the geotaxis, phototaxis, dimming, cement gland attachment, and bilateral escape are circuit paths that are distinct until the motor command neurons.

Analogy between ascidian larva neurons and vertebrate neural nuclei. AMG (ascending motor ganglion), cor-pr (coronet-photoreceptor relay neuron), DA (dopamine), Hb (habenula), H.stn (subthalamic nucleus), mgIN (motor ganglion interneuron), MN (motor neuron), OT.d (deep optic tectum), P.ldt (laterodorsal tegmental nucleus), pnIN (palp interneuron), PNS (peripheral nervous system), Ppt (pedunculopontine nucleus), PR (photoreceptor), pr-AMG (photoreceptor-AMG relay neuron), R.ip (interpeduncular nucleus), R.rs (reticulospinal motor command), S/P (striatum/pallidum basal ganglia), V.mr (median raphe), Vta (ventral tegmental area).

A vertebrate analogy to the ascidian phototaxis gradient path might be the path from the retina to Hb.m (medial habenula) to R.ip (interpeduncular nucleus) and V.mr (median raphe), which then project to R.rs (reticulospinal motor command). Like the ascidian path, the Hb-R.ip phototaxis path is relatively isolated from the other paths, although Hb.m does receive large modulation from the hypothalamus. Although R.ip is mostly descending, like ascidian mgIN, V.mr is both ascending and descending like mgIN and AMG.

The dimming path from the type-2 photoreceptors resembles the dimming input to the vertebrate OT (optic tectum). Although existing vertebrates have more sophisticated eyes that can distinguish expanding objects, the dimming input to OT is still important and used for escape directionality [Fotowat and Engert 2023], [Heap et al 2018]. Retina dimming cells reach AF6 and AF8 [Temizer et al 2015], which are thalamic arborization fields before reaching OT.d. Although more complicated expanding looming response in vertebrates is better studied, expansion detection requires an image-supporting eye, and OT.d receives the simpler dimming input. Like the ascidian dimming pr-AMG (photoreceptor – ascending motor ganglion) neuron, OT.d receives multiple ascending and descending inputs that modulate the dimming response. In particular Ppt (pedunculopontine nucleus) and P.ldt (laterodorsal nucleus) both receive OT.d output and forward to R.rs, functionally similar to mgIN (motor ganglion interneuron), and send ascending feedback from R.rs to OT.d, resembling the AMG (ascending motor ganglion) functionality.

Because the cement gland exists in vertebrates, the circuit should be available, and studies do show that N5 (head touch trigeminal nerve) innervates it automatically [Pottin et al 2010], but I haven’t read any study that says this this specific group of trigeminal neurons connects to. As a through experiment, consider H.stn (subthalamic nucleus) as a choice for the cement gland, because H.stn halts ongoing action, and because H.stn receives direct input from C.i (insular cortex) and C.ss (somatosensory cortex), which are more sophisticated versions of the chemo / mechanosensory palp neurons.

The coronet path enhances taxis confidence, reducing stochastic choice, and is a set of dopamine neurons. The striatum circuit and dopamine’s role has a similar function. Without dopamine, the basal ganglia suppress weak input, and allow stochastic action. With dopamine, the basal ganglia suppresses the randomness and keep action on track. This path resembles rheotaxis food seeking, where a fish approaches a food odor by swimming upstream [Coombs et al 2020]. The “what” signal (odor) differs from the “how” signal (water current cues). Like rheotaxis, the coronet cells enhance the existing phototaxis and geotaxis, reducing the default stochastic noise.

Hb.m Medial habenula

Of the ascidian labeled paths above, the Hb (habenula) phototaxis path will be a useful anchor for the upcoming consensus circuit. Like the ascidian asymmetrical phototaxis neurons, the vertebrates Hb.m (medial habenula) is also governed by Nodal asymmetry [Roussigne et al 2009], where Nodal is a developmental genetic transcription factor. In zebrafish the left Hb.m support phototaxis, and the right Hb.m supports chemotaxis [Chen et al 2019]. Hb.m phototaxis receives both “on” and “off” neurons from the retina with a relay either in H.em (pre thalamic eminence) [Zhang et al 2017] or T.a (an area in the anterior thalamus) [Cheng et al 2017], where the connections are debated. Although Hb.m does receive dimming input from the adjacent photoreceptive pineal gland, the retina photoreceptors are more important for phototaxis [Dreosti et al 2014].

Vertebrate phototaxis circuit. Hb.m (median habenula), H.em (pre thalamic eminence), P.ldt (laterodorsal tegmental nucleus), R.gc (pontine central grey), R.ip (interpeduncular nucleus), R.rs (reticulospinal), T.a (anterior thalamus), V.dr (dorsal raphe), V.mr (medial raphe)

As an anatomical note, the zebrafish Hb.m is actually dorsal and therefore named Hb.d. Similarly the zebrafish Hb.m is ventral and named Hb.v, but as a simplification I’ve used the mammalian name.

The output path from Hb.m is through R.ip (interpeduncular nucleus), which projects to several areas including R.gc (pontine central era), V.mr (median raphe – serotonin), V.dr (dorsal raphe – serotonin), and P.ldt (laterodorsal nucleus – ACh) [Quina et al 2017]. The V.mr glutamate and GABA neurons may be more important for this circuit than the serotonin neurons, which they outnumber. Also, note that V.mr is located in the same hindbrain rhombomeres (r2-r5) as some of R.rs, but are more ventral, and are reciprocally connected. In other words, V.mr is highly action and motor associated.

As described above, the Hb.m-R.ip path is a klinotaxis path for phototaxis [Chen and Engert 2014], chemotaxis and thermotaxis, where the klinotaxis is temporal from the animals movement, but not the helical movement of the ascidian larvae. The Hb.m-R.ip klinotaxis has multiple inputs for lamprey, including light, odor, and lateral line (water movement) [Stephenson-Jones et al 2011].

Habenula klinotaxis for lamprey for light, odor, and lateral line. Hb.m (medial habenula), LL (lateral line), R.ip (interpeduncular nucleus)

Although I’ve focused on Hb.m as an avoidance gradient circuit, it’s also a food odor seeking circuit [Chen et al 2019]. The Hb.m klinotaxis for light and odor also applies to temperature, using input from Po.m (medial preoptic nucleus) [Palieri et al 2024] and social seek and avoidance [Okamoto et al 2021], [Chou et al 2016].

Habenula thermotaxis with input from Po.m Hb.m (medial habenula), P.ldt (laterodorsal tegmental nucleus), Po.m (medial preoptic area), R.gc (pontine central grey), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.dr (dorsal raphe), V.mr (median raphe)

Because Hb.m has several sub-nuclei and genetic clusters, it likely represents different labeled paths, supporting multiple distinct seek and avoidance paths. A binary seek vs avoid circuit is likely an oversimplification, because studies have found at least 5-6 olfactory Hb.m clusters in the larval zebrafish [Jetti et al 2014], [Beretta et al 2014]. Hb.m is asymmetrical, like the ascidian larva. Odors from either olfactory bulb activate the right Hb.m [Chen et al 2019]. Hb.m neurons have at least 262 neuropeptide receptors [Ables et al 2023] as well as morphine receptors [Gardon et al 2014], [Boulos et al 2020] including neuropeptides modulating hunger or social motivation from hypothalamic areas like H.l and H.pv.

R.ip interpeduncular nucleus

Since I’ve already covered some of the R.ip klinotaxis function in essay 24 and essay 25, I’m going to focus on the R.ip connectivity, particularly the ascending connectivity. R.ip descending efferents don’t target R.rs directly, but instead use intermediaries like R.gc (pontine central gray), V.mr (median raphe) and P.ldt (laterodorsal tegmental area) [Lima et al 2017], [Quina et al 2017].

Descending R.ip connectivity. Hb.m (medial habenula), P.ldt (laterodorsal tegmental), R.gc (pontine central grey), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.dr (dorsal raphe), V.mr (median raphe)

The ascending afferents of R.ip also work through intermediaries, particularly P.ldt and V.mr [Quina et al 2017], although other connectivity studies report R.ip as directly producing ascending connectivity [Lima et al 2017]. Because V.mr is directly caudal to R.ip, the disagreement is essentially about the boundaries between R.ip and V.mr.

Ascending R.ip connectivity. E.ca1.v (hippocampus ventral CA1), H.sum (supermammillary nucleus), P.ldt (laterodorsal tegmentum), R.ip (interpeduncular nucleus), S.ls.v (ventral lateral septum), V.dr (dorsal raphe), V.mr (median raphe), Vta (ventral tegmental area)

The ascending R.ip connectivity will become important in the next section on the consensus circuit because it completes the consensus loop, where other labeled path connectivity is descending. The ascending role is analogous to the ascidian AMG (ascending motor ganglion) neurons. For a consensus circuit to work, all nodes need to be informed of the consensus decision.

Consensus circuit narrative

Let’s now consider the consensus circuit and how it might develop from a strict labeled path system. This is just a thought experiment as a narrative explanation for the Hb.l (lateral habenula) system.

For simplicity, let’s restrict the narrative to apical systems only, ignoring bilateral systems like OT, and let’s start from a labeled path system. In the lamprey, odor information from Ob (olfactory bulb) splits into multiple paths. One path reaches Hb.m directly and another contacts V.pt (posterior tuberculum), considered a homologue of Vta / Snc (substantia nigra pars compacts), which then contacts MLR in lamprey [Derjean et al 2010] and zebrafish [Kermen et al 2013].

Pre-consensus labeled paths for odor seek and avoid. Hb.m (medial habenula), MLR (midbrain locomotor region), P.ldt (laterodorsal tegmentum), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.mr (median raphe), V.pt (posterior tuberculum)

In this example, these two paths are distinct with threat odors going through the Hb.m – R.ip circuit and using P.ldt as an apical version of the MLR (which in lamprey may not be distinct from Ppt MLR, since the lamprey doesn’t have distinct Ppt, P.ldt and M.cnf (cuneiform nucleus)). The animal seeks food using the V.pt to MLR path.

These two system can come into conflict. For the above simple system, suppose conflicts are resolved in R.rs itself, as a hard-coded priority where threats always win. But now consider a system where the conflict is resolved earlier in the stream by adding Hb.l as a lateral inhibition relay.

Lateral inhibition circuit giving threat avoidance a priority over food seeking. Hb.l (lateral habenula), Hb.m (medial habenula), MLR (midbrain locomotor region), P.ldt (laterodorsal tegmentum), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.mr (median raphe), V.pt (posterior tuberculum).

As a first step consider lateral inhibition of threat odor suppressing food seeking. Here the lateral inhibition path uses a relay from Hb.m to Hb.l [Gouveia and Ibrahim 2022] in a primitive Hb.l that then suppresses the V.pt path. This lateral inhibition duplicates the earlier lateral inhibition in R.rs, but is more specific because it inhibits earlier in the two paths.

In the above diagram, the blue lines represent new connections. Notice the gating pattern for V.pt resembles the gating for the consensus circuit where the action nodes are V.pt and V.mr. Hb.l then becomes the vote accumulator for the consensus circuit. Also notice the similarity with the sleep model from essay 29, where Hb inhibits food seeking for sleep. An alternative narrative might repurpose the sleep inhibition into a path inhibition [Hikosaka 2010].

Both Hb.l and Hb.m are tonically acting, meaning that without any input their resting output is a middle value, not a binary output. This means Hb.l can gate V.pt seek and also gate its opposing avoidance circuit in V.mr and P.ldt.

For the next step, let’s add both a bidirectional selection and also add some internal state management, because the animal shouldn’t seek food if it’s sated.

H.l hunger modulation

H.l (lateral hypothalamus) has access to hunger and satiety information by sensing blood levels directly and from connections from R.pb (parabrachial), which has signals from the digestive system via N10 vagus nerve through R.nts (solitary tract nucleus). When Ob (olfactory bulb) senses a food odor , H.l can modulate it with the current hunger sense. This means H.l as gating input to Hb.l is more effective than the simple lateral inhibition from Hb.m If the animal is sufficiently hungry, it might ignore weak threats. Note the similarity to the mollusk sea hare circuit, where hunger changed food odor from seeking to avoidance depending on the internal state.

Adding H.l hunger modulation to the decision between the threat odor avoidance path and the food odor seek path. H.l (lateral hypothalamus), Hb.l (lateral habenula), Hb.m (medial habenula), MLR (midbrain locomotor region), P.ldt (laterodorsal tegmentum), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.mr (median raphe), V.pt (posterior tuberculum).

In addition to hunger, other internal states can modulate Hb such as hypothalamic threat signaling ([Wagle et al 2022]. This step also adds control of the threat path, taking advantage of the Hb.l tonic activity to either inhibit food seeking or threat avoidance.

Place avoidance without a threat

Suppose we take the above circuit, but ignore or disable the threat avoidance path via Hb.m. Even without the threat path, there is an avoidance path from Hb.l to V.mr and P.ldt, where Hb.l not only disinhibits threat avoidance, but can produce place avoidance without a threat.

H.l seek / place avoid circuit without a matching threat path. H.l (lateral hypothalamus), Hb.l (lateral habenula), MLR (midbrain locomotor region), P.ldt (laterodorsal tegmentum), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.mr (median raphe), V.pt (posterior tuberculum)

The above diagram shows deletion of the threat path, while retaining the abstract place avoidance path. If place avoidance is triggered, the animal will avoid the current location without needing a specific threat to avoid. This means that H.l stimulation by itself can trigger real-time avoidance [Stamatakis et al 2016]. In mammals the H.l to Hb.l connection has at least 6 clusters [Calvigioni et al 2023], which suggests multiple paths even in the abstract place avoidance.

S.v ventral striatum digression

This model of the seek vs avoid circuit can be extended to S.v (ventral striatum aka nucleus accumbens) and P.v (ventral pallidum). Consider S.v / P.v as a generalization of H.l, providing more general context beyond hunger. This basal ganglia extension allows for a positive feedback loop. which enables multiple rounds of voting, integrating values, such as with drift diffusion.

Ventral striatum as a sophisticated extension of H.l state modulation. H.l (lateral hypothalamus), Hb.l (lateral habenula), MLR (midbrain locomotor region), P.ldt (laterodorsal tegmentum), P.v (ventral pallidum), R.ip (interpeduncular nucleus), R.rs (reticulospinal), S.v (ventral striatum aka nucleus accumbens), V.mr (median raphe), V.pt (posterior tuberculum), Vta (ventral tegmental area)

In the above, I’ve split the V.pt of the lamper into an ascending Vta (ventral tegmental area) dopamine area from mammals, but left the V.pt to represent the descending glutamate / GABA portion of Vta, despite mammals lacking a distinct V.pt. If there’s a food cue when hungry, H.l to Vta stimulation will generate high DA in S.v, enabling it, which will disinhibit V.pt to enable food seeing. Here, S.v / P.v is acting as the consensus circuit and the V.pt path is the action for food seeking.

As with the smaller Hb.l circuit, S.v / P.v is also part of a sleep / wake circuit using dopamine as a wake signal, as used in essay 29. If the animal is currently seeking food, it shouldn’t fall asleep, and the high dopamine signals to stay away. Again, from a narrative sense, this circuit could have been repurposed from a wake circuit, as opposed to a path conflict system.

In zebrafish Hb.l only projects to V.mr and does not project to any DA [Amo et al 2014], while in the more primitive lamprey Hb.l projects to both V.mr and DA [Stephensen-Jones et al 2011], which suggests that the V.mr projection is more functionally critical to this circuit than the Vta projection, or that the Vta circuit is a later development. The zebrafish V.pt has descending dopamine but the existence of significant projections to the striatum is questioned [Yamamoto and Vernier 2011].

Note that H.l retains its central role, where the S.v circuit generalizes the base H.l function without replacing it. Stimulating H.l.g (H.l GABA neurons) can trigger seeking through its projection to Vta [Nieh et al 2016], and stimulating H.l.glu (glutamate H.l neurons) can trigger place avoidance through the H.l.glu projection to Hb.l [Stamatakis et al 2016].

Hippocampus digression

For place preference and place avoidance E.hc (hippocampus) plays a natural because E.hc represents context and place such as place cells, and H.hc projection strongly to both the hypothalamus and S.v. If we add the H.hc projections to H.l via S.ls, the seek / avoidance circuit looks something like the following.

Hippocampus modulation of H.l place seek and avoid. DA (dopamine), E.hc (hippocampus), H.l (lateral hypothalamus), Hb.l (lateral habenula), P.v (ventral pallidum), S.ls (lateral septum), S.v (ventral striatum), Vta (ventral tegmental area).

H.l has neurons that represent food zones and non-food zones [Jennings et al 2015], presumably using E.hc place information, although possibly using P.bst (bed nucleus of the stria terminals) as an intermediary.

H.sum completing consensus loop

The consensus circuits needs to return the final action and motor choice back into the early layers, otherwise the motivation circuit wouldn’t know if a lower-level startle or OT looming escape took priority of the seek path. With analogy to the ascidian larva, this role resembles the AMG (ascending motor ganglia) neurons, which I associated with P.ldt and V.mr. For this consensus narrative, I’m taking H.sum (supramammillary) as the primary feedback node with an assist from Poa (preoptic area) to complete the loop to Hb.m and M.pag (periaqueductal gray).

H.sum as completing the consensus loop, linking the habenula output back to habenula input. H.l (lateral habenula), H.sum (supramammillary nucleus), Hb.m (medial habenula), MLR (midbrain locomotor region), M.pag (periaqueductal gray), P.ldt (laterodorsal tegmentum), Poa (preoptic area), R.ip (interpeduncular nucleus), R.rs (reticulospinal), V.mr (median raphe), V.pt (posterior tuberculum).

H.sum has several sub circuits with different functions, which studies are only starting to untangle. H.sum tac1 (neurotransmitter aka substance P) is strongly associated with upcoming locomotion [Farrell et al 2021]. H.sum’s Poa projection is specifically associated with threat avoidant locomotion [Escobedo et al 2023].

V.mr and P.ldt are connected with R.rs and the bilateral OT circuit, and therefore have information about the selected action at the level of the hindbrain and motor afferent copies. Both are strongly connected to H.sum. H.sum also connects with M.pag (periaqueductal gray) and H.sum activates when M.pag.d is stimulated [Pan et al 2004]. H.sum also activates when the H.vm (ventromedial hypothalamus) threat nuclei are stimulated.

H.sum is immediately rostral to Vta and highly connected with it (not shown in the diagram.) H.sum contains some DA neurons itself, which are sometimes considered as an extension of A10, the Vta dopamine neuron area, although the neuron types differ [Yetnikoff et al 2014], [Menegas et al 2015].

H.sum is strongly connected with E.hc (hippocampus) and is one of the few external input to both E.dg (dentate gyrus) and E.ca2 (cornu ammonia), and is a major theta source to P.ms (medial septum), which drives E.hc theta. Its link to E.hc are important for both novel object exploration [Chen et al 2020], [Takahashi et al 2023] and social memory [Qin et al 2022]. Although I’m not yet adding E.hc to the essays, the novel object detection will be important soon to avoid repeated exploration of the same object.

Note that Poa has already participated in the Hb.m to R.ip circuit because Poa drives thermotaxis [Palieri et al 2024] as part of the original Hb aversive apical path.

M.pag tetrapod complications

In a sense, the vertebrate brain is designed around fish navigation, exemplified by the simple M-cell startle circuit that requires only three neurons between the acoustic sense and the swimming muscles. Although the direct Braitenberg-like connections to R.rs work for fish locomotion, tetrapod locomotion is more complex. M.pag (periaqueductal grey) is a central grey area surrounding the midbrain ventricle (“periaqueductal”), and it an inner ring to OT, which is immediately dorsal to it. Naming it “OT.dd” (deep, deep layer of OT) would not be unreasonable. Among other tasks like vocalization [Jürgens 1994] and hunting [Marín-Blasco et al 2020], M.pag provides a similar to R.rs but at a higher level, like syllables to phonemes. So in the following examples, M.pag can be viewed as similar functionality to R.rs.

Unlike R.rs, M.pag can access more sophisticated navigation. Where the M-cell can only turn left or right, M.pag can use OT for obstacle avoidance and even higher navigation of the hippocampus using H.pm.d (dorsal premammillary nucleus) [Wang et al 2021].

M.pag flight

M.pag implements innate behaviors, including flight, freezing, hunting, grooming, and vocalizations. The following diagram shows some of the looming flight circuitry [Zhou et al 2019]. As before, OT.m primarily processes the looming signal and OT.m sends input to M.pag.d as an integrated threat signal, where M.pag.d computes a threshold for responding to the threat [Evans et al 2018].

M.pag flight for the looming circuit. M.pag.d (dorsal periaqueductal gray), OT.m (medial, deep optic tectum), R.rs (reticulospinal), S.a (central amygdala), Vta.g (gaba neurons of the ventral tegmental area).

In the diagram, the second interesting path is through Vta.g (Vta GABA neurons) and S.a (central amygdala). Because OT.m and M.pag.d directly output to R.rs neurons, the projects to Vta.g and S.a aren’t required for motor control, but because of the distributed consensus system, other systems need to be informed of the looming response. S.a modulates defense, hunting, and eating systems, and Vta.g also inhibits the current action by suppressing dopamine, back to the consensus loop, suppressing any current seek action.

M.pag.vl avoidance

While M.pag.d is strongly associated with fast escape, M.pag.vl is more complicated with diverse functions including hunting [Franklin 2019], [Marín-Blasco et al 2020], vocalization [González-García et al 2024], and laughter [Klingbeil et al 2021]. Since this essay focuses on avoidance, where avoidance here isn’t the high speed predator escape of M.pag.d.

M.pag.vl avoidance afferents. H.l.glu (lateral hypothalamus glutamate), H.sum (supramammillary nucleus), Po.m (medial preoptic area), P.v (ventral pallidum), V.mr.glu (median raphe glutamate), Vta (ventral tegmental area glutamate and GABA)

H.l lateral hypothalamus

As discussed above, H.l is a central motivational node, filling a similar role to the central hunger node in the mollusk sea hare navigation. However, H.l is much more complicated than a simple hunger node. One developmental paper divided H.l into nine distinct regions [Diaz et al 2013], but that anatomical division understates the complexity. A genetic transcription analysis finds 15 glutamate and 15 GABA clusters [Mickelson et al 2019]. Interestingly, the Diaz study identifies their H.l.1 area with H.sum.l, treating H.sum.l as part of H.l.

In general, H.l.glu produces place avoidance and H.l.g enables seeking, but as mentioned above with at least 15 genetic types and 9 regions, this division is almost certainly an oversimplification.

H.l seek and avoid efferents. E.ca1.v (ventral hippocampus), H.l (lateral hypothalamus glutamate and GABA), Hb.l (lateral habenula), M.pag (periaqueductal gray), S.ls (lateral septum), Vta.g (ventral tegmental area GABA).

The H.l.glu to M.pag connection is certainly capable of driving motor avoidance. Interestingly, a different H.l population is part of the M.pag hunting circuit. Both Vta.g and Hb.l enter the motivation loop. I’ve added the E.ca1.v (ventral hippocampus CA1) input to H.l because E.hc.v (ventral hippocampus) is strongly associated with place, and E.hc.v specifically with aversive context.

R.pb peribrachial nucleus

R.pb (peribrachial nucleus) is a pain, alarm, feeding, and respiration hub in the prepontine isthmus area (r0-r1). As an alarm center [Campos et al 2018], R.pb is connected with escaping and avoiding circuits. As covered in essay 29 speed, it includes a high Co2 trigger that drives place avoidance. It also includes pain triggers for escape. R.pb has multiple functions defined more by chemical markers than topology. One study explored R.pb’s role in escape and avoidance behavior [Chiang et al 2020].

R.pb avoidance circuits. dyn (dynorphin neurotransmitter), H.vm (ventromedial hypothalamus), M.pag.l (periaqueductal gray), P.bst (bed nucleus of the stria terminalis), R.pb (peribrachial nucleus), RTPA (real-time place avoidance), S.a (central amygdala), tac1 (tachykinin 1 / substance P neurotransmitter)

R.pb.dl (dorsolateral R.pb) and R.pb.el are adjacent R.pb areas that are associated with alarm and pain responses. R.pb.dl receives direct N5 (trigeminal – head, jaw) and N.sp (spinal) pain input, including pain input marked by tac1 (tachykinin 1 peptide aka substance P). Relevant to this essay, the outputs divide between direct escape behavior with not learning and indirect avoidance behavior with learning. The M.pag.l projection produces flight and jumping. The S.a (central amygdala) and P.bst (bed nucleus of the stria terminalis – extended amygdala) projections produce real-time place avoidance and are capable of CPA (conditioned place avoidance) [Chiang et al 2020]. The R.pb example is useful because it combines a direct locomotion to M.pag with output to the slower consensus circuit.

Preoptic area

Poa (preoptic area) is a multifunctional area directly anterior to the hypothalamus and often considered part of the hypothalamus, although genetic markers suggest it’s more closely related to the forebrain. Like other brainstem areas, its functionality is more organized by genetic markers than topology.

Preoptic area avoidance and seek areas. H.l (lateral hypothalamus), H.pv (periventricular hypothalamus), H.sum (supramammillary), Hb.m (medial habenula), Pom (medial preoptic area), S.ls (lateral septum)

The above diagram shows some of the Pom (medial preoptic area)functions. Temperature management has been discussed with a connection through Hb.m gradient following. Threat avoidance from signals from H.sum, H.pv (periventricular hypothalamus), or S.ls (lateral septum) can lead to RTPA through a M.pag projection [Escobedo et al 2023]. Local exploration, a RTPP function, also uses a M.pag projection [Shin et al 2023], and Pom can also enable hunting [Park et al 2018], although through a M.pag projection. The recent genetic research tools will likely unravel more of its functionality.

Poa has a strong projection to both Hb.m and Hb.l, suggesting that it’s an important node in the locomotion consensus circuit. In the thought experiment I’ve outlined above, Poa is part of the feedback system through H.sum, but Poa also receives E.hc.v (ventral hippocampus) input through S.ls (lateral septum), so it may be an important node in its own right.

Ppt / P.ldt

The ACh (acetylcholine) neurons near the midbrain-hindbrain boundary Ppt (pedunculopontine tegmentum) and P.ldt (laterodorsal tegmentum) are the core of the MLR. In simpler vertebrates like the lamprey, the MLR is only a single area, generally named P.ldt. In mammals, not only are P.ldt and Ppt split, but a chunk of locomotive action is in a different nucleus M.cnf (cuneiform). Although M.cnf is more of a direct locomotive area, the locomotive neurons don’t respect the anatomical boundary, but are a group of glutamate neurons spanning from Ppt to M.ncf, where Ppt and M.cnf are neighbors [Caggiano et al 2018]. Tetrapod locomotion is more complex than fish swimming, which may be a partial reason for the expansion and division.

Ppt connections. H.stn (subthalamic nucleus), M.pag (periaqueductal gray), OT.d (deep layer of optic tectum), P.g (globus pallidus), Ppt (pedunculopontine nucleus), R.rs (reticulospinal), S.d (dorsal striatum)

Ppt is strongly reciprocally connected with the deeper layers of OT: OT.i for turning and sensory integration, and OT.d for seek and avoid. Its connections resemble the R.pgb (parabigeminal aka nucleus isthmi) which sustains attention for the OT.s (superficial OT) [Knudsen 2011] and covered in essay 19. R.pgb, Ppt, and P.ldt are sibling nuclei that develop from the same area in r1 that also produces R.pb and cerebellum granule cells [Pose-Méndez et al 2023].

Some P.ldt connections, emphasizing that Vta connections are collaterals of R.rs. H.sum (supramammillary), P.ldt (laterodorsal tegmentum), R.rs (reticulospinal), Vta (ventral tegmental area)

P.ldt is complicated by the relative lack of recent studies of its descending projections since [Cornwall 1990] and an over-focus on its Vta connection. Because neuron tracing in [Zhao et al 2023] suggests that P.ldt has more descending connections to R.rs than Ppt and that all Vta connections are collaterals of R.rs connections, studies like [Coimbra et al 2021] and [Liu et al 2022] that find locomotion through Vta projections could be produced by its R.rs projection. P.ldt has reciprocal connections with H.sum.

Vta

Although Vta (ventral tegmental area) is most studied for its ascending dopamine projections to S.v (ventral stratum) and F.pfc (prefrontal cortex), it also contains glutamate and GABA projections, including descending connections. Non-tetrapods like fish and lamprey have a homologous V.pt (posterior tuberculum) with prominent descending locomotor connections to MLR [Ryczko et al 2017], [Derjean et al 2010]. The earlier thought experiment for the development of a locomotor consensus split out an ancient V.pt from the mammalian Vta as a way of describing the old descending functionality.

Vta glutamate and GABA connections. H.l.glu (lateral hypothalamus glutamate), Hb.l (lateral habenula), M.pag (periaqueductal gray), OT (optic tectum), P.bst (bed nucleus of the stria terminalis), S.a (central amygdala), S.am (medial central amygdala), S.msh.pv (medial shell of the ventral striatum, parvalbumin neurons), Vta.da (ventral tegmental area, dopamine), Vta.g (Vta GABA), Vta.glu (Vta glutamate)

The above diagram shows some of the connections of the glutamate and GABA Vta [Taylor et al 2014], including projections to M.pag and to Hb.l that are direct locomotor for seek and avoid. The Vta is a main dopamine source for S.v and F.pfc with multiple distinct areas. Vta.m, which projects to S.msh (medial shell of S.v) is aversive, while Vta.l, which projects to S.lsh (lateral shell of S.v) and S.core (core of S.v) promotes seek [Szőnyi et al 2019]. Vta.m is non-reinforcing, as opposed to Vta.l, which is well-studied for reinforcement.

P.v ventral pallidum

P.v is a main output of S.v and the only output of S.ot (olfactory tubercle). As essay 29 covered, it’s an important sleep/wake node. For this essay, the important bit is a split between RTPP and RTPA depending on its output.

P.v RTPA and RTPP circuits. H.l (lateral hypothalamus), Hb.l (lateral habenula), M.pag.vl (periaqueductal grey), Ppt (pedunculopontine tegmentum), P.v (ventral pallidum), V.mr (median raphe), Vta (ventral tegmental area)

Links

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Essay 19: Nucleus Isthmi

Essay 18 was trying to solve the problem of maintaining behavioral state. When a fast neuron synapse takes only 5ms, behavior that lasts seconds or minutes needs some circuit to sustain attention on the task. Essay 18 explored the striatum as a possible model to maintain behavior. In zebrafish, this problem is partial solved with a paired system consisting of the optic tectum (OT) and the nucleus isthmi (NI) [Gruberg et al. 2006].

Optic tectum

The optic tectum (OT – superior colliculus in mammals) is a midbrain action and sensor system that organizes vision, touch, sound, and action into retinotopic map like an air controller radar screen that activates only for important triggers. So, it’s not like the movie screen of primate vision, but is an action-oriented, sparse map that focuses on a few important items. In the larva zebrafish, the OT activates for hunting prey (paramecia) and avoiding obstacles and predators.

The OT itself has no persistence, When it detects potential prey and moves toward the prey, the OT doesn’t remember that it’s hunting or recall the previous location of the prey. Without enhancement, it forgets the pretend fails the hunt. The nucleus isthmi (NI – parabigeminal in mammals) provides that attention and persistence function [Henriques et al. 2019].

Nucleus isthmi circuit

The NI has a simple organization that is topologically, bidirectionally mapped to OT. The return signal from NI to OT is acetylcholine (ACh), which amplifies the sense input, biasing the next action to follow the previous action. Essentially this is a simple attention circuit that maintains consistent behavior.

Optic tectum and nucleus isthmi circuit as used in the essay 19 simulation.

In the diagram above, a left action sends an efference copy to the matching nucleus isthmi area, which can remember the activation for longer than the 5ms fast activation in the OT. In turn it sends an ACh modulator to amplify the left touch sensor, biasing the direction toward the same action.

For the essay simulation, the original problem was hitting an obstacle head-on, which triggered both left and right touch sensors, which then caused jitter as the animal randomly chose left and right without maintaining consistency. By adding an NI system, an initial left action would bias the left input sense to choose a next left action.

Acetylcholine attention system

As a speculation, or perhaps a mnemonic, this NI system where ACh enhances senses based on action might be a model for some attention mechanisms else were in the brain. NI is a sister nucleus to other ACh nuclei, specifically the parabrachial nucleus (B.pb) and the pedunculopontine nucleus (V.ppn), all developing from the same stem region near the isthmus. V.ppn is one of the major ACh attention nuclei and is part of the midbrain locomotive region (MLR). It seems plausible that V.ppn might share some organization with NI where its upstream ACh might support sense attention like the NI does for OT.

Engineering note

After implementing the nucleus isthmi support, both the proto-striatum and NI solve the jittering problem equally. The algorithms are slightly different — NI is a straight enhancement, while proto-striatum is a disinhibition with selection — but for the current complexity of the animal and environment, there’s no behavioral difference. Both proto-striatum and NI can be enabled simultaneously without interference problems.

References

Cui H, Malpeli JG. Activity in the parabigeminal nucleus during eye movements directed at moving and stationary targets. J Neurophysiol. 2003 Jun;89(6):3128-42. doi: 10.1152/jn.01067.2002. Epub 2003 Feb 26

Gruberg E., Dudkin E., Wang Y., Marín G., Salas C., Sentis E., Letelier J., Mpodozis J., Malpeli J., Cui H. Influencing and interpreting visual input: the role of a visual feedback system. J. Neurosci. 2006

Henriques PM, Rahman N, Jackson SE, Bianco IH. Nucleus Isthmi Is Required to Sustain Target Pursuit during Visually Guided Prey-Catching. Curr Biol. 2019 Jun 3

Marín G, Salas C, Sentis E, Rojas X, Letelier JC, Mpodozis J. A cholinergic gating mechanism controlled by competitive interactions in the optic tectum of the pigeon. J Neurosci. 2007 Jul 25

Motts SD, Slusarczyk AS, Sowick CS, Schofield BR. Distribution of cholinergic cells in guinea pig brainstem. Neuroscience. 2008 Jun 12;154(1):186-95. doi: 10.1016/j.neuroscience.2007.12.017. Epub 2008 Jan 28

18: Engineering issues with proto-striatum

The planned striatum model of essay 17 quickly runs into simulation problems because it’s missing priority selection between avoiding obstacles and seeking food. Obstacle avoidance needs a higher priority than seeking an odor plume, but a naive striatum doesn’t support that priority.

Broken striatum model where toward and away have no priority. Ob olfactory bulb, B.ss somatosensory touch, B.rs reticulospinal motor command.

This model fails because this striatum has no priority of away (avoid) actions from toward (approach) actions. An animal can’t simply follow an odor blindly, ignoring obstacles, but this model doesn’t support that priority.

Tectum

Adding the tectum seems like the right solution, although I was planning on putting it off until dealing with vision.

The tectum (optic tectum / superior colliculus) is better known for its vision support, but the deeper tectum layers are a general action-decision system. At its lower levels near periaqueductal gray (M.pag) it has a topographic direction-based map on its intermediate level and an action-based map in the deep level.

The tectum and M.pag are neighbors, almost layers of each other, and in animals like the frog, the M.pag is as a deeper layer of the tectum.

Relation between M.pag and OT in mammals (left) and frog (right), where the ventricle shape determines the anatomical label for homologous areas.

The tectum is an action organizer, not just a vision organizer. For the simulation, the action matters since the simulated animal doesn’t have vision.

Amphioxus, a non-vertebrate chordate that’s a model into pre-vertebrate evolution, has a few motor-related cells with the same genetic markers as the tectum [Pergner et al. 2020]. It’s conceivable that the amphioxus tectum is more action focused, since the amphioxus frontal eye is only a dozen photoreceptors with no lens.

Action categories

The tectum has split circuits for turning and for approach and avoid [Wheatcroft et al. 2022]. The simulation can use something like the following circuit.

Split tectum and striatum circuit. B.rs reticulospinal motor command, B.ss somatosensory input, M.lr midbrain locomotor region, M.pag periaqueductal gray, Ob olfactory bulb, S.d dorsal striatum, S.ot olfactory tubercle.

Approach (toward) senses like food odors excited toward actions, and avoidant (away) sense like touch excite away actions. Because the priority areas are split, each striatum can choose between non-priority options (left vs right). The priority resolves only later in the midbrain locomotor region, using context input to decide which major direction to use. In this split model, the simplified striatum circuit can work because all of striatum options are equal priority.

As a note on accuracy, the diagram misrepresents the actual olfactory path, specifically the real olfactory tubercle. In reality, olfaction has a distant, complicated path to the tectum.

Short-cut escape signal

The previous diagram is also misleading because it’s too organized, as if each function has a dedicated, planned circuit. Although the tectum itself is highly-organized, the downstream and modulating circuits are more ad hoc. For example, the zebrafish has an escape mechanism that short-cuts the tectum and drives the B.rs command motor directly [Zwaka et al. 2022].

fast escape shortcut of tectal locomotion circuit.
Fast escape shortcut of tectum-mediated locomotion.

In the above diagram, the escape circuit short-circuits any decisions of the tectum and striatum. Relatedly, the “switch” area in M.lr isn’t as tidy as the diagram suggests. It’s more like that M.lr contains multiple actions which laterally inhibit each other in a priority scheme, modulated by M.pag.

As an additional correct, many of the modulators like M.pag affect the tectum directly, instead of the diagram’s dedicated priority-resolution function.

References

Pergner J, Vavrova A, Kozmikova I, Kozmik Z. Molecular Fingerprint of Amphioxus Frontal Eye Illuminates the Evolution of Homologous Cell Types in the Chordate Retina. Front Cell Dev Biol. 2020 Aug 4

Wheatcroft T, Saleem AB, Solomon SG. Functional Organisation of the Mouse Superior Colliculus. Front Neural Circuits. 2022 Apr 29

Zwaka H, McGinnis OJ, Pflitsch P, Prabha S, Mansinghka V, Engert F, Bolton AD. Visual object detection biases escape trajectories following acoustic startle in larval zebrafish. Curr Biol. 2022 Dec 5