Hydrodynamic model of fish orientation in a channel flow

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Version of Record published: July 18, 2022 (This version)
Accepted Manuscript published: June 6, 2022 (Go to version)
Accepted: May 31, 2022
Preprint posted: November 12, 2021 (Go to version)
Received: November 3, 2021

1. Of interest
The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid

Celine Bellegarda, Guillaume Zavard ... Claire Wyart

Research Article Sep 29, 2023
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Abstract
Editor's evaluation
eLife digest
Introduction
Results
Discussion
Materials and methods
Appendix 1
Appendix 2
Appendix 3
Appendix 4
Data availability
References
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Abstract

For over a century, scientists have sought to understand how fish orient against an incoming flow, even without visual and flow cues. Here, we elucidate a potential hydrodynamic mechanism of rheotaxis through the study of the bidirectional coupling between fish and the surrounding fluid. By modeling a fish as a vortex dipole in an infinite channel with an imposed background flow, we establish a planar dynamical system for the cross-stream coordinate and orientation. The system dynamics captures the existence of a critical flow speed for fish to successfully orient while performing cross-stream, periodic sweeping movements. Model predictions are examined in the context of experimental observations in the literature on the rheotactic behavior of fish deprived of visual and lateral line cues. The crucial role of bidirectional hydrodynamic interactions unveiled by this model points at an overlooked limitation of existing experimental paradigms to study rheotaxis in the laboratory.

Editor's evaluation

The authors present a simple model of fish swimming in a channel and reacting to the surrounding flow with their lateral line and no other sensory system. They demonstrate that the fish stably orients upstream in certain conditions. Particularly, rheotaxis can emerge even in the absence of sensory feedback, purely as a consequence of passive hydrodynamic interactions in the presence of the walls.

https://doi.org/10.7554/eLife.75225.sa0

eLife digest

One fascinating and perplexing fact about fish is that they tend to orient themselves and swim against the flow, rather than with it. This phenomenon is called rheotaxis, and it has countless examples, from salmon migrating upstream to lay their eggs to trout drift-foraging in a current. Yet, despite over a century of experimental studies, the mechanisms underlying rheotaxis remain poorly understood. There is general consensus that fish rely on water- and body-motion cues to vision, vestibular, tactile, and other senses. However, several questions remain unanswered, including how blind fish can perform rheotaxis or whether a passive hydrodynamic mechanism can support the phenomenon. One aspect that has been overlooked in studies of rheotaxis is the bidirectional hydrodynamic interaction between the fish and the surrounding flow, that is, how the presence of the fish alters the flow, which, in turn, affects the fish.

To address these open questions about rheotaxis, Porfiri, Zhang and Peterson wanted to develop a mathematical model of fish swimming, one that could help understand the passive hydrodynamic pathway that leads to swimming against a flow. Unlike experiments on live animals, a mathematical model offers the ability to remove cues to certain senses without interfering with animal behavior.

Porfiri, Zhang and Peterson modeled a fish as a pair of vortices located infinitely close to each other, rotating in opposite directions with the same strength. The vortex pair could freely move through an infinitely long channel with an imposed background flow, devoid of all sensory information expect of that accessed through the lateral line. Analyzing the resulting system revealed that there is a critical speed for the background flow above which the fish successfully orients itself against the flow, resulting in rheotaxis. This critical speed depends on the width of the channel the fish is swimming in. Depriving the fish of sensory information received through the lateral line does not preclude rheotaxis, indicating that rheotaxis could emerge in a completely passive manner.

The finding that the critical speed for rheotaxis depends on channel width could improve the design of experiments studying the phenomenon, since this effect could confound experiments where fish are confined in narrow channels. In this vein, Porfiri, Zhang and Peterson’s model could assist biologists in designing experiments detailing the multisensory nature of rheotaxis. Evidence of the importance of bidirectional hydrodynamic interactions on fish orientation may also inform modeling research on fish behavior.

Introduction

Swimming animals display a complex behavioral repertoire in response to flows (Chapman et al., 2011). Particularly fascinating is the ability of several fish species to orient and swim against an incoming flow, a behavior known as rheotaxis. While intuition may suggest that vision is necessary for fish to determine the direction of the flow, several experimental studies of midwater species swimming in a channel have documented rheotaxis in the dark above a critical flow speed (Coombs et al., 2020). When deprived of vision, fish lose the ability to hold station and they may perform sweeping, cross-stream movements from one side of the channel to other (Bak-Coleman et al., 2013; Bak-Coleman and Coombs, 2014; Elder and Coombs, 2015; Figure 1).

Figure 1

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Fish rheotaxis.

(a) Illustration of the problem with notation, showing a fish swimming in a background flow described by Equation 4. (b) Schematic of the cross-stream sweeping movement of some fish species swimming without visual cues; snapshots of fish at earlier time instants are illustrated by lighter shading.

In addition to vision, fish may rely on an array of compensatory sensory modalities to navigate the flow, which utilizes tactile, proprioceptive, olfactory, electric, kinematic, and hydrodynamic signals (Montgomery et al., 2000; von der Emde, 1999). For example, fish could sense and actively respond to linear accelerations caused by the surrounding flow using their vestibular system (Pavlov and Tjurjukov, 1995). Similarly, with the help of tactile sensors on their body surface, fish could maintain their orientation against a current through momentary contacts with their surroundings (Arnold, 1969; Lyon, 1904). Several modern studies have unveiled the critical role of the lateral line system, an array of mechanosensory receptors located on the surface of fish body (Montgomery and Baker, 2020), in their ability to orient against a current (Baker and Montgomery, 1999; Montgomery et al., 1997), hinting at a hydrodynamics-based rheotactic mechanism that has not been fully elucidated. When deprived of vision, can fish rely only on lateral line feedback to perform rheotaxis? Is there a possibility for rheotaxis to be achieved through a purely passive hydrodynamic mechanism that does not need any sensing?

Through experiments on zebrafish larvae swimming in a laminar flow in a straight tube, Oteiza et al., 2017 have recently unveiled an elegant hydrodynamic mechanism for fish to actively perform rheotaxis. Utilizing their mechanosensory lateral line, fish can sense the flow along different parts of their body, which is sufficient for them to deduce local velocity gradients in the flow and adjust their movements accordingly. As further elaborated upon by Dabiri, 2017, the insight offered by Oteiza et al., 2017 is grounded in the fundamental relationship between vorticity and circulation given by the Kelvin-Stokes’ theorem, so that fish movements will be informed by local sampling of the vorticity field. While offering an elegant pathway to explain rheotaxis, the framework of Oteiza et al., 2017 does not include a way for rheotaxis to be performed in the absence of information about the local vorticity field. Several experimental studies have shown that fish can perform rheotaxis even when their lateral line is partially or completed ablated, provided that the flow speed is sufficiently large (Bak-Coleman et al., 2013; Bak-Coleman and Coombs, 2014; Baker and Montgomery, 1999; Elder and Coombs, 2015; Montgomery et al., 1997; Oteiza et al., 2017; Van Trump and McHenry, 2013).

Mathematical modeling efforts seeking to clarify the mechanisms underlying rheotaxis are scant (Burbano-L and Porfiri, 2021; Chicoli et al., 2015; Colvert and Kanso, 2016; Oteiza et al., 2017), despite experiments on rheotaxis dating back more than a century (Lyon, 1904). A common hypothesis of existing mathematical models is that the presence of the fish does not alter the flow physics with respect to the background flow, thereby neglecting interactions between the fish and the walls of the channel. For example, the model by Oteiza et al., 2017 implements a random walk in a virtual flow, matching experimental measurements of the background flow in the absence of the animal through particle image velocimetry. A similar line of approach was pursued by Burbano-L and Porfiri, 2021 for the study of multisensory feedback control of adult zebrafish.

Thus, according to these models, the fish acts as a perfectly non-invasive sensor that probes and reacts to the local flow environment without perturbing it. There are countless examples in fluid mechanics that could question the validity of such an approximation, from coupled interactions between a fluid and a solid in vortex-induced vibrations (Williamson and Govardhan, 2004) to laminar boundary layer response to environmental disturbances that range from simple decay of the perturbation to bypass transition (Saric et al., 2002). We expect that accounting for bidirectional coupling between the fluid flow and the fish will help clarify many of the puzzling aspects of rheotaxis.

To shed light on the physics of rheotaxis, we formulate a mathematical model based on the paradigm of the finite-dipole, originally proposed by Tchieu et al., 2012. Within this paradigm, a fish is viewed as a pair of point vortices of equal and opposite strength separated by a constant distance in a two-dimensional plane. The application of the finite-dipole has bestowed important theoretical advancements in the study of hydrodynamic interactions between swimming animals (Gazzola et al., 2016; Filella et al., 2018; Kanso and Cheng Hou Tsang, 2014; Kanso and Michelin, 2019; Porfiri et al., 2021), although numerical validation of the framework against full solution of Navier-Stokes equations is lacking – conducting such a validation is also part of this study. Upon validating the dipole model, we investigate the bidirectional coupling between a fish and the surrounding fluid flow in a channel. Our work contributes to the recent literature on minimal models of fish swimming (Gazzola et al., 2014; Gazzola et al., 2015; Sánchez-Rodríguez et al., 2020) that builds on seminal work by Lighthill, 1975, Taylor, 1997 and Wu, 2006 to elucidate the fundamental physical underpinnings of locomotion and inform the design of engineering systems.

We focus on an ideal condition, where fish are deprived of all sensing systems, other than the lateral line that gives them access to information about the flow. Such flow information is coupled, however, to the motion of the fish itself, which acts as an invasive sensor and perturbs the background flow. Just as fish motion influences the local flow field, so too does the local flow field alter fish motion through advection. Predictions from the proposed model are compared against existing empirical observations on fish rheotaxis, compiled through a comprehensive literature review of published work since 1900. Data presented in the literature are used to offer context to the predicted dependence of rheotaxis performance on local flow characteristics, individual fish traits, and lateral line feedback.

Results

Model of the fluid flow

Consider a single fish swimming in an infinitely long two-dimensional channel of width $h$ (Figure 1(a)). Let one wall of the channel be at $y = 0$ and the other at $y = h$ , with $x$ pointing along the channel. The fish position at time $t$ is given by ${\vec{r}}_{f} (t) = x_{f} (t) \hat{i} + y_{f} (t) \hat{j}$ , where $\hat{i}$ and $\hat{j}$ are the unit vectors in the $x$ and $y$ directions, respectively. The orientation of the fish with respect to the $x$ axis is given by $θ_{f} (t)$ (positive counter-clockwise) and its self-propulsion velocity is ${\vec{v}}_{f} = v_{0} (\cos θ_{f} \hat{i} + \sin θ_{f} \hat{j}) = v_{0} {\hat{v}}_{f}$ , where v₀ is the constant speed of the fish and ${\hat{v}}_{f}$ is a unit vector in the swimming direction.

The flow is modeled as a potential flow, which is a close approximation of the realistic flow field around a fish. This simple linear fluid model is intended to capture the mean flow physics, thereby averaging any turbulence contribution. The fish is modeled as a dipole, the potential field of which at some location $\vec{r} = x \hat{i} + y \hat{j}$ is given by

ϕ_{f} (\vec{r}, {\vec{r}}_{f}, θ_{f}) = - r_{0}^{2} (\frac{(\vec{r} - {\vec{r}}_{f}) \cdot {\vec{v}}_{f}}{{|| \vec{r} - {\vec{r}}_{f} ||}^{2}}),

where r₀ is the characteristic dipole length-scale (on the order of the amplitude of the fish tail beating), so that the circulation of each vortex is $2 π r_{0} v_{0}$ . This potential field is constructed assuming a far-field view of the dipole (Filella et al., 2018), wherein r₀ is small in comparison with the characteristic flow length scale, which is satisfied for $ρ = r_{0} / h ≪ 1$ . The velocity field at $\vec{r}$ due to the dipole (fish) is ${\vec{u}}_{f} = \nabla ϕ_{f}$ .

A major contribution of the proposed model is the treatment of the fish as an invasive sensor that both reacts to and influences the background flow, thereby establishing a coupled interaction between the fish and the surrounding environment. A fish swimming in the vicinity of a wall will induce rotational flow near the boundary. In the inviscid limit, this boundary layer is infinitesimally thin and can be considered as wall-bounded vorticity (Batchelor, 2000). Employing the classical method of images (Newton, 2011), the influence of the wall-bounded vorticity on the flow field is equivalent to that of a fictitious fish (dipole) mirrored about the wall plane. For the case of a fish in a channel, this results in an infinite number of image fish (dipoles) (Figure 2), the position vectors for which are

{\vec{r}}_{<, n}^{+} = x_{f} \hat{i} + (y_{f} - 2 (n + 1) h) \hat{j},

{\vec{r}}_{<, n}^{-} = x_{f} \hat{i} + (- y_{f} - 2 n h) \hat{j},

{\vec{r}}_{>, n}^{+} = x_{f} \hat{i} + (y_{f} + 2 (n + 1) h) \hat{j},

{\vec{r}}_{>, n}^{-} = x_{f} \hat{i} + (- y_{f} + 2 (n + 1) h) \hat{j},

Figure 2

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Method of images.

Schematic of the fish (black) in the channel (thick lines) and the set of images (gray) needed to generate the channel. The streamlines generated by the fish in an otherwise quiescent fluid are shown in the channel colored by local velocity magnitude (red: high; blue: low). Dashed and solid lines are mirroring planes for the method of images, the pattern for which continues *ad infinitum*.

where $n$ is a non-negative integer representing the $n$ -th set of images. Subscripts “<” and “>” correspond to position vectors of the images at $y < 0$ and $y > h$ , respectively. Likewise, superscript “±” denotes the orientation of the image dipole as $\pm θ_{f}$ ; that is, a position vector with superscript “+” indicates that the associated image has the same orientation as the fish.

The potential function for a given image is found by replacing ${\vec{r}}_{f}$ in Equation 1 with its position vector from Equation 2d and adjusting the sign of $θ_{f}$ in Equation 1 to match the superscript of its vector. The potential field at $\vec{r}$ due to the image dipoles is

ϕ_{w} (\vec{r}, {\vec{r}}_{f}, θ_{f}) = \sum_{n = 0}^{\infty} (ϕ_{f} (\vec{r}, {\vec{r}}_{<, n}^{+}, θ_{f}) + ϕ_{f} (\vec{r}, {\vec{r}}_{<, n}^{-}, - θ_{f}) + ϕ_{f} (\vec{r}, {\vec{r}}_{>, n}^{+}, θ_{f}) + ϕ_{f} (\vec{r}, {\vec{r}}_{>, n}^{-}, - θ_{f})) .

Thus, the velocity field due to the wall is computed as ${\vec{u}}_{w} = \nabla ϕ_{w}$ , and the overall velocity field induced by the fish is ${\vec{u}}_{f} + {\vec{u}}_{w}$ . (A closed-form expression for the series in terms of trigonometric and hyperbolic functions is presented in Appendix 1) Overall, the presence of the walls distorts the flow generated by the dipole, both compressing the streamlines between the fish and the walls in its proximity and creating long-range swirling patterns in the channel (Figure 2).

The presence of a background flow in the channel is modelled by superimposing a weakly rotational flow,

{\vec{u}}_{b} (\vec{r}) = U_{0} (1 - 4 ϵ {(\frac{y}{h} - \frac{1}{2})}^{2}) \hat{i},

which has speed U₀ at the channel centerline and $U_{0} (1 - ϵ)$ at the walls, $ϵ$ being a small positive parameter. As $ϵ \to 0$ , a uniform (irrotational) background flow is recovered: such a flow is indistinguishable from the one in Figure 2, provided that the observer is moving with the background flow.

For $ϵ ≪ 1$ , the imposed velocity profile approximates that of a turbulent channel flow, wherein a modest degree of velocity profile curvature is present near the channel centerline. We note that this velocity profile does not satisfy the no-slip boundary condition (zero velocity on the walls), and the flow is entirely described by only two parameters (U₀ and $ϵ$ ). For $ϵ ≃ 1$ , the profile approaches that of a laminar flow with parabolic dependence on the cross-stream coordinate. The overall fluid flow in the channel is ultimately computed as $\vec{u} = {\vec{u}}_{f} + {\vec{u}}_{w} + {\vec{u}}_{b}$ .

The circulation in a region $ℛ$ in the flow field centered at some location $y$ is $Γ = \int_{ℛ} ω d A$ , where $ω = (\nabla \times \vec{u}) \cdot \hat{k}$ is the local fluid vorticity ( $\hat{k} = \hat{i} \times \hat{j}$ ). For the considered flow field, we determine

ω (\vec{r}) = \frac{8 U_{0} ϵ}{h} (\frac{y}{h} - \frac{1}{2}),

whereby the irrotational component of the flow field does not contribute to the circulation, and the circulation at a point (per unit area) is equivalent to the local vorticity.

Numerical validation of the dipole model

Despite the success of dipole-based models in the study of fish swimming (Filella et al., 2018; Gazzola et al., 2016; Porfiri et al., 2021; Tchieu et al., 2012), their accuracy against complete Navier-Stokes simulations remains elusive. The potential flow framework in which these models are grounded neglects boundary layers and the resulting wakes that emerge from viscous effects. Quantifying the extent to which these effects influence the flow field generated by the fish is part of this study.

Specifically, computational fluid dynamics (CFD) simulations were conducted to detail the flow field around a fish during steady swimming. The simulation setup was based upon a giant danio of body length $l = 7.3 cm$ in a channel of width $h = 15.0 cm$ . The length of the simulation domain was $L = 50.0 cm$ ( $\sim 6.8 l$ ) with the fish model placed at the channel centerline $20 cm$ ( $\sim 2.7 l$ ) downstream of the inlet. The body undulation of the giant danio was imposed a priori in the simulation, based on data from Najafi and Abtahi, 2022. The time-resolved flow field around the fish was quantified by solving the incompressible Navier-Stokes equations. Details on the setup of the numerical framework and convergence analysis supporting its accuracy are included in Appendix 2.

The mean velocity field averaged over a tail beating cycle is displayed in Figure 3(a). The predominant flow feature observed in the mean field is a flow circulation from the head to the tail of the fish with left-right symmetry and compression of the streamlines near the channel walls. The highest velocity is found at the head of the fish with a thrust wake and recirculation region downsteam of the animal – both at a lower velocity than the anterior flow. The largest velocity in the wake is less than 20% of the peak values recorded ahead of the fish. Additional simulation results are included in Appendix 2. The flow field predicted by the dipole model is in good agreement with numerical simulations, as shown in Figure 3. The dipole model is successful in capturing the circulation from the head to the tail and the compression of the streamlines near the walls. These features are expected to be the main drivers of the interaction between the fish and the channel walls, thereby supporting the value of a dipole model for a first-order analysis of the hydrodynamics of rheotaxis.

Figure 3

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Velocity field around a swimming fish from computational fluid dynamics.

(a) Mean velocity field around the steady swimming giant danio relative to the background flow. (b) Velocity field predicted by a dipole with $θ = π$ located at $0.315 l$ from the fish head along its centerline relative to the background flow. The selection of the dipole location and strength is detailed in Appendix 2.

Model of fish dynamics

From knowledge of the fluid flow in the channel, we compute the advective velocity $\vec{U} ({\vec{r}}_{f}, θ_{f})$ and hydrodynamic turn rate $Ω ({\vec{r}}_{f}, θ_{f})$ at the fish location, which encode the influence of the confining walls and background flow on the translational and rotational motion of the fish, respectively. Neglecting the inertia of the fish so that it instantaneously responds to changes in the fluid flow, we determine (Filella et al., 2018)

{\dot{\vec{r}}}_{f} (t) = \vec{U} ({\vec{r}}_{f} (t), θ_{f} (t)) + {\vec{v}}_{f} (θ_{f} (t)),

{\dot{θ}}_{f} (t) = Ω ({\vec{r}}_{f} (t), θ_{f} (t)) + λ ({\vec{r}}_{f} (t), θ_{f} (t)),

where λ is the feedback mechanism based on the circulation measurement through the lateral line.

The advective velocity is found by de-singularizing the total velocity field $\vec{u}$ at $\vec{r} = {\vec{r}}_{f}$ , which is equivalent to calculating the sum of the velocity due to the walls and the background flow in correspondence of the fish (Milne-Thomson, 1996)

\begin{matrix} \vec{U} ({\vec{r}}_{f}, θ_{f}) = {({\vec{u}}_{w} (\vec{r}, {\vec{r}}_{f}, θ_{f}) + {\vec{u}}_{b} (\vec{r})) |}_{\vec{r} = {\vec{r}}_{f}} \\ = - \frac{π^{2} v_{0} ρ^{2}}{12} [(1 + 3 \csc^{2} (\frac{π y_{f}}{h})) \cos θ_{f} \hat{i} - (1 - 3 \csc^{2} (\frac{π y_{f}}{h})) \sin θ_{f} \hat{j}] \\ + U_{0} (1 - 4 ϵ {(\frac{y_{f}}{h} - \frac{1}{2})}^{2}) \hat{i} . \end{matrix}

Equation (7) indicates that the walls have a retarding effect on the swimming speed of the fish that increases in magnitude the closer the fish gets to either wall of the channel. A fish swimming with orientation $θ_{f} = 0$ at the center of the channel, for example, will swim with velocity ${\dot{\vec{r}}}_{f} (t) = v_{0} (1 - (π^{2} / 3) ρ^{2}) \hat{i} + U_{0} \hat{i}$ . This effect should not be mistaken as traditional viscous drag, which is not included in potential flow theory; rather, it should be intended as the impact of nearby solid boundaries.

Hydrodynamic turn rate is incorporated by considering the difference in velocity experienced by the two constituent vortices comprising the dipole, namely,

\begin{array}{ll} Ω ({\vec{r}}_{f}, θ_{f}) & = - {\hat{v}}_{f} \cdot [\nabla ({\vec{u}}_{w} (\vec{r}, {\vec{r}}_{f}, θ_{f}) + {\vec{u}}_{b} (\vec{r})) |_{\vec{r} = {\vec{r}}_{f}}] {\hat{v}}_{f}^{⊥} \\ = - \frac{π^{3} ρ^{2} v_{0}}{4 h} \cot (\frac{π y_{f}}{h}) \csc^{2} (\frac{π y_{f}}{h}) \cos θ_{f} + \frac{8 U_{0} ϵ}{h} (\frac{y_{f}}{h} - \frac{1}{2}) \cos^{2} θ_{f}, \end{array}

where ${\hat{v}}_{f}^{⟂} = \hat{k} \times {\hat{v}}_{f}$ ; see Materials and methods section for the mathematical derivation. Equation (8) indicates that interaction with the walls causes the fish to turn towards the nearest wall; for example, a fish at $y_{f} = 3 / 4 h$ , will experience a turn rate due to the wall of $(π^{3} ρ^{2} v_{0}) / (2 h) \cos θ_{f}$ , such that it will be rotated counter-clockwise if swimming downstream and clockwise if swimming upstream. On the other hand, the turning direction imposed by the background flow is always positive (counter-clockwise) in the right half of the channel and negative (clockwise) in the left half, irrespective of fish orientation, so that a fish at $y_{f} = 3 / 4 h$ will always be rotated counter-clockwise. As a result, the fish may turn towards or away from a wall, depending on model parameters and orientation.

Based on experimental observations and theoretical insight (Burbano-L and Porfiri, 2021; Oteiza et al., 2017), we hypothesize that hydrodynamic feedback, that is, lateral line measurements of the surrounding fluid that fish can employ to navigate the flow, is related to the measurement of the circulation in a region surrounding the fish. This hypothesis is supported by experimental evidence presented in Oteiza et al., 2017, which indicated the ability of fish to sense variations in the local velocity gradients to perform rheotaxis. Therein, the authors also found that partial ablation of the lateral line leads to the loss of the rheotactic behavior, hinting at the importance of the flow information on both sides of the fish body for the estimation of the flow circulation.¹¹1 Temporal fluctuations, as in turbulent flows, are neglected in our model. As such, we assume time-averaged circulation sensing from the lateral line. We consider a rectangular region $ℛ$ of width r₀ along the fish body length $l$ . For simplicity, we assume a linear feedback mechanism, $λ ({\vec{r}}_{f}, θ_{f}) = K Γ ({\vec{r}}_{f}, θ_{f}),$ where we made evident that circulation is computed about the fish location and $K$ is a non-negative feedback gain. Assuming that the fish size is smaller than the characteristic length scale of the flow, we linearize the vorticity along the fish in Equation 5 as $ω (\vec{r}) \approx ω ({\vec{r}}_{f}) + \nabla ω ({\vec{r}}_{f}) \cdot {\hat{v}}_{f} Δ l$ . By computing the integral from $Δ l = - l / 2$ to $l / 2$ , we obtain

λ ({\vec{r}}_{f}, θ_{f}) = K r_{0} l \frac{8 U_{0} ϵ}{h} (\frac{y_{f}}{h} - \frac{1}{2}) .

Compared to established practice for modeling fish behavior in response to visual stimuli (Calovi et al., 2014; Couzin et al., 2005; Gautrais et al., 2009; Zienkiewicz et al., 2015), the proposed model introduces nonlinear dynamics arising from the bidirectional coupling between the motion of the fish and the flow physics in its surroundings. We note that the employed feedback in Equation 9 neglects additional potential sensing mechanisms, including vision (Lyon, 1904), acceleration sensing through the vestibular system (Pavlov and Tjurjukov, 1995), and pressure sensing through sensory afferents in the fins (Hardy et al., 2016), which might enhance the ability of fish to navigate the flow.

Analysis of the planar dynamical system

Given that the right hand side of equation set Equation 6a and Equation 6b is independent of the streamwise position of the fish, the equations for the cross-streamwise motion and the swimming direction can be separately studied, leading to an elegant nonlinear planar dynamical system. We center the cross-stream coordinate about the center of the channel and non-dimensionalize it with respect to $h$ , introducing $ξ = y_{f} / h - 1 / 2$ . The governing equations become

\dot{ξ} = [1 - \frac{π^{2} ρ^{2}}{12} (3 \csc^{2} (π (ξ + \frac{1}{2})) - 1)] \sin θ_{f},

{\dot{θ}}_{f} = - \frac{π^{3} ρ^{2}}{4} \cot (π (ξ + \frac{1}{2})) \csc^{2} (π (ξ + \frac{1}{2})) \cos θ_{f} + 8 α ξ (\cos^{2} θ_{f} + κ),

where we non-dimensionalized by the time needed for the fish to traverse the channel in the absence of a background flow, that is, $h / v_{0}$ , and introduced $α = U_{0} ϵ / v_{0}$ and $κ = K r_{0} l$ (see Materials and methods section for estimation of these parameters from experimental observations).

In search of the equilibria of the dynamical system, we note that swimming downstream or upstream ( $θ_{f} = 0$ and π, respectively) solves Equation 10a for any choice of the cross-stream coordinate, the value of which is determined from the solution of Equation 10b for the corresponding orientation $θ_{f}$ . In the case of downstream swimming, the only solution of the resulting transcendental equation is $ξ = 0$ . For upstream swimming, depending on the value of the parameter $β = (α (1 + κ)) / ρ^{2}$ , we have one or three solutions: if $β < β^{*} = π^{4} / 32$ , the only solution is $ξ = 0$ , otherwise, in addition to $ξ = 0$ , there are two solutions symmetrically located with respect to the centerline that approach the walls as $β \to \infty$ (Figure 4(a), see Materials and methoods section for mathematical derivations).

Figure 4

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Qualitative dynamics of equation set Equation 10a.

(a) Cross-stream equilibria for upstream swimming as a function of β. (**b,c**) Phase plot for downstream and upstream swimming in the case $α = 0.1$ , $ρ = 0.1$ , and $κ = 1$ , so that $β = 20$ . In all panels, red refers to unstable equilibria and green to stable equilibria.

Local stability of these equilibria is determined by studying the eigenvalues of the state matrix of the corresponding linearized dynamics. For all the considered dynamics, the trace of the state matrix is zero, so that the equilibria can be saddle points (unstable) or neutral centers (stable), if the determinant is negative or positive, respectively (Bakker, 1991; see Materials and methods section for mathematical derivations). In the case of downstream swimming, the determinant is always negative, such that the equilibrium $(θ_{f} = 0, ξ = 0)$ is a saddle point (Figure 4(b)). For upstream swimming, the equilibrium $(θ_{f} = π, ξ = 0)$ is stable if $β > β^{*}$ , leading to periodic oscillations similar to experimental observations (Bak-Coleman et al., 2013; Bak-Coleman and Coombs, 2014; Elder and Coombs, 2015; Figure 1(b)); the other two equilibria located away from the centerline are always unstable (Figure 4(b and c)). Oscillations about the centerline during rheotaxis have a radian frequency $ω_{0} ≃ (π^{2} / 2) ρ \sqrt{β / β^{*} - 1}$ , such that the frequency increases with the square root of β and is zero at $β^{*}$ (see Materials and methods section for the mathematical derivation).

Discussion

There is overwhelming evidence that fish can negotiate complex flow environments by responding to even small flow perturbations (Liao, 2007). However, seldom are these perturbations included in mathematical models of fish behavior, which largely rely on vision cues (Calovi et al., 2014; Couzin et al., 2005; Gautrais et al., 2009; Zienkiewicz et al., 2015). In this paper, we proposed a hydrodynamic model for the bidirectional coupling between fish swimming and fluid flow in the absence of any sensory input but lateral line feedback – encapsulated by a simple linear feedback mechanism. The model reduces to a nonlinear planar dynamical system for the cross-stream coordinate and orientation, of the kind that are featured in nonlinear dynamics textbooks for their elegance, analytical tractability, and broad physical interest (Sastry, 2013).

The planar system anticipates several of the surprising features of rheotaxis. In particular, this study provides some potential answers to the question raised by Coombs et al., 2020: “…what role, if any, do passive (e.g. wind vane) mechanisms play in rheotaxis and how are these influenced by fish factors (e.g. body shape) and flow dynamics?” Through the mathematical analysis of the model, we uncovered an equilibrium at the channel centerline for upstream swimming whose stability is controlled by a single non-dimensional parameter that summarizes flow speed, lateral line feedback, flow gradient, channel width, and fish size. Above a critical value of this parameter, the model predicts that rheotaxis is stable and fish will begin periodic cross-stream sweeping movements whose amplitude can be as large as the channel width. Interestingly, the model anticipates rheotaxis even without sensory feedback, through only passive hydrodynamic mechanisms.

Our mathematical proof of the existence of a nontrivial threshold for β above which upstream swimming becomes stable finds partial support in experimental observations on a number of species in the absence of visual cues (see Appendix 3, where we have performed a bibliographical survey on experimental studies about rheotaxis). Several of these experiments have indicated the existence of a threshold in the flow speed or flow gradient above which fish successfully perform rheotaxis. Importantly, we predict that the presence of channel walls is necessary for the emergence of such a threshold, since for $ρ \to 0$ , $β \to \infty$ , thereby automatically guaranteeing the stability of upstream swimming. Based on our estimation of α and ρ from available data, β can be as small as 10^-1 and exceed 10², thereby encompassing the critical value $β^{*} ≃ 3$ (see Materials and methods section for estimation of model parameters). We should exercise care in drawing comparisons with experiments, which only control for visual feedback, in contrast with the model where we block all sensory modalities except of the lateral line. As reviewed by Coombs et al., 2020, water-motion cues can also be accessible to tactile or other cutaneous senses, beyond the lateral line that is included in our model. In addition, body-motion cues are not limited to visual senses, whereby they can be accessed by tactile and vestibular senses. Hence, a one-to-one comparison between experiments and theory is presently not possible.

The model predicts the emergence of rheotaxis in the absence of any sensory information. Setting $κ = 0$ in our model eliminates hydrodynamic feedback, yet, the fish is able to perform rheotaxis at sufficiently large flow speeds and steep flow gradients. This finding would support the possibility of a completely passive mechanism for rheotaxis. To date, there is no experiment on live animals that can be used to support this claim, owing to the necessity to eliminate all sensory modalities without compromising fish ability to swim. In practice, this may be unfeasible to do. As discussed in Coombs et al., 2020, existing approaches for disabling senses suffer from potential pitfalls, including: (i) unintended effects on the overall fish behavior, which are likely to occur in an effort to block at once vestibular, tactile, and lateral line senses, and (ii) difficulty in guaranteeing complete blockage of a sensory modality, which, like the lateral line, can be distributed throughout the whole body.

A potential line of approach to explore the possibility of a complete passive form of rheotaxis is through experiments with robotic fish ( Duraisamy et al., 2019; Wang et al., 2020; Zhang et al., 2016), mimicking locomotory patterns of live animals and allowing to precisely control sensory input. In this vein, we foresee experiments with robotic fish in a complete open-loop operation that does not utilize any sensory input. The robotic fish developed in our previous study (Kopman and Porfiri, 2013; Kopman et al., 2015) could offer a versatile platform to conduct such an experiment. Such a robot is actuated by a built-in step motor to undertake a periodic tail beating with a predetermined frequency. All its electronics is encased in the frontal section of the robot, so that its size and shape can be readily adjusted though rapid prototyping.

Although free swimming experiments on the robotic fish would be ideal, practicality may suggest to constraint the streamwise and vertical location of the robot while allowing cross-stream motions and heading changes. Such a setup shall also include a load cell to measure the drag on the robot, providing an independent measure to set the tail beat frequency – similar to CFD simulations (see Appendix 2). Also, we would recommend measuring energy expenditure by the robotic fish to gain insight into the hydrodynamic costs and benefits of rheotaxis. Experimental parameters encapsulated in β, including inlet flow speed, channel width, and robot length can be all controlled, and the flow curvature at the centerline can be measured through velocimetry techniques. In the experiments, one shall track the motion of the robotic fish to score conditions in which stable rheotaxis is observed and extract other salient information, such as the frequency of cross-stream sweeping, if present.

The model predicts that increasing κ broadens the stable region, leading to more robust rheotaxis, which is in qualitative agreement with experimental observations – including experiments on animals with intact versus compromised lateral lines (see Appendix 3). The model prediction on the influence of the environment on rheotaxis, including the flow gradient and flow channel size, also parallels the literature on rheotaxis (see Appendix 3). For example, observations by Oteiza et al., 2017 suggest that increasing the flow gradient $ϵ$ enhances hydrodynamic feedback in zebrafish, resulting in improved rheotaxis.

Our analysis also indicates that wider channels should promote rheotaxis by lowering the critical speed above which swimming against the flow becomes a stable equilibrium. This mathematical finding is indirectly supported by experimental observations (see Appendix 3), and bears relevance in the design of experimental protocols for the study of rheotaxis. Confining the subject in a narrow channel will promote bidirectional hydrodynamic interactions with the walls, so that small movements of the animal will reverberate into sizeable changes in the flow physics that will mask the gradient of the background flow. Similarly, in partial alignment with experimental observations, the model predicts a lower threshold for longer fish, owing to a magnification of the hydrodynamic feedback received by a longer body (see Appendix 3). Again, we warn care in drawing comparisons due to the presence of other senses in real experiments, which are not modelled in our work.

Finally, the model anticipates the onset of periodic cross-stream sweeping, which has been studied in some experiments on fish swimming in channels without vision (Coombs et al., 2020). While there is not conclusive experimental evidence regarding the dependence of the frequency of oscillations on flow conditions, the model is in qualitative agreement with experiments by Elder and Coombs, 2015, showing a sublinear dependence on the flow speed. Therein, it is shown that the radian frequency has a weak positive tendency with respect to the flow speed for Mexican tetra swimming with or without cues from the lateral line. Above $2 cm s^{- 1}$ , the animals can successfully perform rheotaxis and display sweeping oscillations at about three cycles per minute and increase to about four cycles per minute at $12 cm s^{- 1}$ . These correspond to a radian frequency on the order of $0.1 rad s^{- 1}$ , which is similar to what we would predict for β ranging from 10⁰ to 10¹ and ρ of the order of $10^{- 1}$ (recall that the time is scaled with respect to time required by the animal to traverse the channel from wall to wall in the absence of a background flow). We acknowledge that the current model does not describe contact and impact with the walls of the channel, which could be important in further detailing the onset of cross-sweeping motions that could involve stick-and-slip at the bottom of the channel (Van Trump and McHenry, 2013).

Just as other minimal models of fish swimming have helped resolve open questions on scaling laws (Gazzola et al., 2014), gait (Gazzola et al., 2015), and drag (Sánchez-Rodríguez et al., 2020), the proposed effort addresses some of the baffling aspects of rheotaxis through a transparent and intuitive treatment of bidirectional hydrodynamic interactions between fish and their surroundings. The crucial role of these bidirectional interactions hints that active manipulation of their surroundings by fish offers them a pathway to overcome sensory deprivation and sustain stable rheotaxis.

The proposed model is not free of limitations, which should be addressed in future research. The current model neglects the elasticity and inertia of the fish, which might reduce the accuracy in the prediction of rheotaxis, especially transient phenomena. Future research should refine the dipole paradigm toward a dynamic, unsteady model that accounts for added mass effects and distributed elasticity, similar to those used in the study of swimming robots (Colgate and Lynch, 2004; Sfakiotakis et al., 1999). The model could also be expanded to account for additional sensory modalities, such as vision, vestibular system, and tactile sensors on the fish body surface. We argue that pursuing any of these extensions shall require detailed experimental data, beyond what the literature can currently offer. Experiments are also needed to refine the linear hydrodynamic feedback mechanism that we hypothesized for the lateral line; in this vein, future experiments could be designed to parametrically vary the flow speed and quantify the activity level of lateral line nerve fibers through neurophysiological recordings (Mogdans, 2019). Beyond the inclusion and refinement of individual sensory modalities, we envision research toward the incorporation of a multisensory framework, as the one introduced by Coombs et al., 2020. Such a framework identifies several motorsensory integration sites in the central nervous system that could contribute to rheotaxis, thereby calling for modeling efforts at the interface of neuroscience and fluid mechanics.

Despite its limitations, the proposed minimalistic model is successful in anticipating some of the puzzling aspects of rheotaxis and points at the possibility of attaining rheotaxis in a purely passive manner, without any sensory input. Most importantly, the model brings forward a potential methodological oversight of laboratory practice in the study of rheotaxis, caused by bidirectional hydrodynamic interactions between the swimming fish and the fluid flow. To date, there is no gold standard for the selection of the size of the swimming domain, which is ultimately chosen on the basis of practical considerations, such as facilitating behavioral scoring and creating a laminar background flow. The model demonstrates that the width of the channel has a modulatory effect on the threshold speed for rheotaxis and the cross-stream swimming frequency, which challenges the comparison of different experimental studies and confounds the precise quantification of the role of individual sensory modalities on rheotaxis. Overall, our effort warrants reconsidering the behavioral phenotype of rheotaxis, by viewing fish as an invasive sensor that modifies the encompassing flow and hydrodynamically responds to it.

Materials and methods

Derivation of the turn rate equation for the fish dynamics

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The expression for the turn rate in Equation 8 is obtained from the original finite-dipole model by Tchieu et al., 2012, in the limit of small distances between the vortices in the pair ( $r_{0} \to 0$ ).

Specifically, eqution (2.11) from Tchieu et al., 2012, adapted to the case of a single dipole reads

{\dot{θ}}_{f} = R e [\frac{(U ({\vec{r}}_{f, r}) - i V ({\vec{r}}_{f, r})) - (U ({\vec{r}}_{f, l}) - i V ({\vec{r}}_{f, l}))}{r_{0}} e^{i θ_{f}}],

where subscript $l$ and $r$ refer to the left and right vortices forming the pair and $\vec{U} = U \hat{i} + V \hat{j}$ is the advective velocity field acting on the dipole. The advective field consists of the interactions with the walls and the background flow, so that $\vec{U} (\vec{r}) = {\vec{u}}_{w} (\vec{r}, {\vec{r}}_{f}, θ_{f}) + {\vec{u}}_{b} (\vec{r})$ ; in the case of Tchieu et al., 2012, such a field encompasses the velocity field induced by any other dipole in the plane. Left and right vortices are defined so that ${\vec{r}}_{f, l} = {\vec{r}}_{f} + r_{0} {\hat{v}}_{f}^{⟂} / 2$ and ${\vec{r}}_{f, r} = {\vec{r}}_{f} - r_{0} {\hat{v}}_{f}^{⟂} / 2$ , which yields ${\vec{r}}_{f, l} - {\vec{r}}_{f, r} = {\hat{v}}_{f}^{⟂} r_{0}$ .

By carrying out the complex algebra in Equation 11, we determine

{\dot{θ}}_{f} = (\frac{\vec{- U} ({\vec{r}}_{f, l}) + \vec{U} ({\vec{r}}_{f, r})}{r_{0}}) \cdot {\hat{v}}_{f},

which supports the intuition that the dipole will turn counter-clockwise if the right vortex would experience a stronger velocity along the swimming direction. Upon linearizing the term in parenthesis in the neighborhood of ${\vec{r}}_{f}$ , this expression becomes

{\dot{θ}}_{f} = - \nabla \vec{U} (\vec{r_{f}}) {\hat{v}}_{f}^{⊥} \cdot {\hat{v}}_{f} .

The chosen approach is consistent from the standpoint of vortex dynamics, by which each vortex in the pair advects in response to local fluid velocity. In this vein, the fish is interpreted as a bluff body, which rotates according to a difference in the drag experienced by its left and right sides. Such a difference is amplified by the pectoral fins, which enhance the effect of any left-to-right asymmetry in the surrounding fluid flow. In the literature, this description is termed T-dipole, in opposition to the so-called A-dipole that introduces two fiducial points along the direction of motion of the dipole that govern its turning (Kanso and Cheng Hou Tsang, 2014). Whether one representation is superior to the other in terms of accuracy is yet to be clarified; our choice of using a T-dipole is based on its theoretical consistency and intuition on the underlying flow physics. Potential avenues for resolution include detailed CFD simulations of free swimming fish or experiments with robotic fish. For completeness, in Appendix 4, we report model predictions based on the A-dipole.

Determination of the equilibria of the planar dynamical system

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By setting $θ_{f} = 0$ or $θ_{f} = π$ in equation set (Equation 10a, Equation 10b), we determine that ξ should be equal to some constant, which is a root of the following transcendental equation:

\frac{π^{3}}{32} \cot (π (ξ + \frac{1}{2})) \csc^{2} (π (ξ + \frac{1}{2})) = \pm β ξ,

where the positive sign corresponds to $θ_{f} = 0$ and the negative sign to $θ_{f} = π$ . Here, $β = α (1 + κ) / ρ^{2}$ as introduced from the main text.

As shown in Figure 5, for $θ_{f} = 0$ , there is only one root of the equation ( $ξ = 0$ ; see the intersection between the solid red line and the solid black curve), while up to three roots can rise for $θ_{f} = π$ depending on the value of β. For β smaller than a critical value $β^{*}$ , only $ξ = 0$ is a solution (see the intersection between the solid blue line and the solid black curve), while for $β > β^{*}$ two additional solutions, symmetrically located with respect to the origin emerge (see the intersections between the dashed blue line and the solid black curve). The critical value $β^{*}$ is identified by matching the slope of the black curve at $ξ = 0$ , so that $β^{*} = π^{4} / 32$ . Notably, the two solutions symmetrically located with respect to the centerline approach the walls as $β \to \infty$ .

Figure 5

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Visual illustration of the process of determining the roots of Equation 14.

(a) Plot of the function $\frac{π^{3}}{32} \cot (π (ξ + \frac{1}{2})) \csc^{2} (π (ξ + \frac{1}{2}))$ (black), superimposed with three lines of different slope: 200 (red), -200 (dashed blue), and -2 (solid blue). (b) Zoomed-in view of the curves in (a) showing that the blue line can only intersect the black curve at the origin.

Local stability analysis of the planar dynamical system

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To examine the local stability of the equilibria of the planar dynamical system, we linearize equation set (Equation 10a, Equation 10b). The state matrix of the linearized dynamics, $A$ , describes the local behavior of the nonlinear system when perturbed in the vicinity of the equilibrium, that is,

\dot{δ q} (t) = A δ q (t),

where $δ q = [δ ξ, δ θ_{f}]^{T}$ is the variation about the equilibrium. The eigenvalues of the $A$ are indicative of local stability about each equilibrium.

For $θ_{f} = 0$ and $ξ = 0$ , the state matrix is given by

A = [\begin{matrix} 0 & 1 - \frac{π^{2} ρ^{2}}{6} \\ 8 (1 + κ) α + \frac{π^{4} ρ^{2}}{4} & 0 \end{matrix}] .

Given that the trace of the matrix is zero ( $tr A = 0$ ), the analysis of the stability of the equilibrium resorts to ensuring the sign of the determinant to be positive ( $det A > 0$ ). Specifically, if the determinant is positive, the eigenvalues are imaginary and the equilibrium is a neutral center (stable, although not asymptotically stable), otherwise one of the eigenvalues is positive and the equilibrium is a saddle point (unstable) (Bakker, 1991). Hence, stability requires that

\frac{1}{24} (- 6 + π^{2} ρ^{2}) (32 α (1 + κ) + π^{4} ρ^{2}) > 0.

Since the first factor is always negative ( $ρ ≪ 1$ ) and the second is positive, the inequality is never fulfilled and the equilibrium is a saddle point (unstable) (Figure 4(a and b)).

For $θ_{f} = π$ and $ξ = 0$ , the state matrix is given by

A = [\begin{matrix} 0 & - 1 + \frac{π^{2} ρ^{2}}{6} \\ 8 (1 + κ) α - \frac{π^{4} ρ^{2}}{4} & 0 \end{matrix}] .

Similar to the previous case, stability requires that $det A > 0$ , that is,

\frac{1}{24} (- 6 + π^{2} ρ^{2}) (- 32 α (1 + κ) + π^{4} ρ^{2}) > 0.

Due to the sign change in the first summand appearing in the second factor with respect to the previous case, stability becomes possible. Specifically, the equilibrium is a neutral center (stable) for $β > β^{*} = π^{4} / 32$ , which is also the necessary condition for the existence of the two equilibria symmetrically located with respect to the channel centerline (Figure 4(a and c)).

When $β > β^{*}$ , we register the presence of two more equilibria at $\pm ξ \neq 0$ . The state matrix takes the form

A = [\begin{matrix} 0 & - 1 - \frac{π^{2} ρ^{2}}{12} + \frac{1}{4} π^{2} ρ^{2} \sec^{2} (π ξ) \\ 8 (1 + κ) α - \frac{1}{4} π^{4} ρ^{2} (2 - \cos (2 π ξ)) \sec^{4} (π ξ) & 0 \end{matrix}],

Also in this case, stability requires that $det A > 0$ , that is,

\frac{1}{48} (- 12 + 3 π^{2} ρ^{2} \sec^{2} (π ξ) - π^{2} ρ^{2}) (- 32 α (1 + κ) + π^{4} ρ^{2} (2 - \cos (2 π ξ)) \sec^{4} (π ξ)) > 0

Once again, for $ρ ≪ 1$ , we can assume that the first factor in parenthesis is negative. (This assumption is grounded upon Equation 14, which yields that $(ξ \pm 1 / 2) = O (ρ^{2 / 3})$ ; since $\cos (π ξ)^{2} = O ((ξ \pm 1 / 2)^{2})$ , we have that $ρ^{2} \sec^{2} (π ξ) \to 0$ as $ρ \to 0$ .) Hence, we obtain

β > \frac{π^{4}}{32} (2 - \cos (2 π ξ)) \sec^{4} (π ξ),

which is not satisfied for any choice of $β > β^{*}$ . Thus, the two equilibria away from the channel centerline, close to the walls are always saddle points (unstable) (Figure 4(a and c)).

We comment that the local stability analysis requires only knowledge of the curvature of the flow field at the centerline of the channel. Hence, should one contemplate alternative profiles for the background flow, linear stability results shall not change. Higher-order parameterizations for the flow profile will result into nonlinear dependencies on ξ that do not affect the linear analysis. Likewise, while we considered a linear feedback mechanism to integrate lateral information via a simple gain, one may explore nonlinear relationships between λ and $Γ$ . The linear stability analysis shall not change, whereby these nonlinear forms will result into dependencies on higher powers of ξ.

Frequency of cross-stream sweeping

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The linearized planar system about the stable focus in Equation 18 is equivalent to a classical second-order system in terms of the cross-stream coordinate, similar to a mass-spring model. Hence, the radian resonance frequency of the system is

ω_{0} = \sqrt{det A} ≃ \frac{π^{2}}{2} ρ \sqrt{\frac{β}{β^{*}} - 1} .

where the last approximation holds for $ρ ≪ 1$ . Equation (23) shows that, close to the threshold, the frequency of oscillations is small and it increases with β and ρ.

Estimation of model parameters

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In a typical experimental setup on rheotaxis, the width of the channel, $h$ , is on the order of three to ten times the body length of the animal, $l$ . For example, experiments from Elder and Coombs, 2015 on Mexican tetras of $l = 8.3 cm$ were conducted in a channel with $h = 25 cm$ . Similarly, in the experiments on adult zebrafish from Burbano-L and Porfiri, 2021, $l = 3.6 cm$ and $h = 13.8 cm$ , and in the experiments on zebrafish larvae from Oteiza et al., 2017, $l = 4.2 mm$ (inferred from the animals’ age) and $h = 1.27$ – $4.76 cm$ . The distance between the vortices simulating a fish, r₀, should be on the order of a tail beat, which has a typical value of $0.2 l$ (Gazzola et al., 2014). As a result, it is tenable to assume that $ρ^{2}$ is between $10^{- 4}$ and $10^{- 2}$ .

A safe estimation of the velocity of the animal in the absence of the background flow, v₀, would be on the order of few body lengths per second (Gazzola et al., 2014). The speed used for the background flow across experiments, U₀, tend to be of the same order as the magnitude of v₀, leaning toward values close to one body length per second (Coombs et al., 2020). For instance, data on zebrafish from Burbano-L and Porfiri, 2021 suggest $v_{0} = 5.7 cm s^{- 1}$ and $U_{0} = 3.2 cm s^{- 1}$ . The estimation of the non-dimensional parameter $ϵ$ associated with the shear in the flow is more difficult, since data on the velocity profiles are seldom reported. That being said, for channel flow of sufficiently high Reynolds number, the velocity profile in the channel is expected to be blunt, approximating a uniform flow profile near the channel center (White, 1974). Thus, it is tenable to treat $ϵ$ as a small parameter, between 10^-2 and 10^-1. For flow of low Reynolds number (Oteiza et al., 2017) ( $R e < 100$ ), the velocity gradient in the channel has been observed to be large, corresponding to $ϵ$ values in the range of 10^-1 and 1. By combining these estimations, we propose that α ranges between 0 and 1.

An estimation of κ is difficult to offer, whereby feedback from the lateral line has only been included in few studies (Burbano-L and Porfiri, 2021; Chicoli et al., 2015; Colvert and Kanso, 2016; Oteiza et al., 2017). Using the data-driven model from Burbano-L and Porfiri, 2021, it is tenable to assume values on the order of 10¹ for individuals showing high rheotactic performance. This gain can also be estimated by comparing the threshold speeds of fish, $U_{c}$ , with and without the lateral line, through $\frac{U_{c} (LL -)}{U_{c} (LL +)} = 1 + κ$ , according to Equation 29 in Appendix 3. The significant increase in the threshold speed following lateral line ablation in Baker and Montgomery, 1999 indicates that $κ \in [2, 7]$ , while the indistinguishable threshold speed between LL+ and LL- fish in a few other studies (Bak-Coleman and Coombs, 2014; Elder and Coombs, 2015; Van Trump and McHenry, 2013) may suggest that $κ \sim 0$ . In Table 1, we summarize the model parameters identified from data in the experimental studies detailed in Appendix 3.

Table 1

Estimation of model parameters from data in the literature.

Reference	$ρ$	$ϵ$	$α$	$κ$	$β$
Bak-Coleman et al., 2013	$\sim 0.05$	$[10^{- 2}, 10^{- 1}]$	$[0, 0.17]$	—	—
Bak-Coleman and Coombs, 2014	$\sim 0.04$	$[10^{- 2}, 10^{- 1}]$	$[0, 0.16]$	$\sim 0$	$[0, 100]$
Baker and Montgomery, 1999 and Montgomery et al., 1997	$\sim 0.1$	$[10^{- 2}, 10^{- 1}]$	$^{*} [0, 0.32]$	$[2, 7]$	$[0, 256]$
Elder and Coombs, 2015	$\sim 0.066$	$[10^{- 2}, 10^{- 1}]$	$^{*} [0, 0.24]$	$\sim 0$	$[0, 55]$
Kulpa et al., 2015	$\sim 0.04$	$\sim 1$ near center of jet	$\sim 1.3$	—	—
Oteiza et al., 2017	$[0.018, 0.066]$	$[0.20, 0.82]$	—	—	—
Peimani et al., 2017	$\sim 0.044$	$\sim 1$	—	—	—
Suli et al., 2012	$\sim 0.018$	$[0.1, 1]$	—	—	—
Van Trump and McHenry, 2013	$[0.055, 0.127]$	$[10^{- 2}, 10^{- 1}]$	$^{*} [0, 0.32]$	$\sim 0$	$[0, 106]$

LL+ cavefish swimming speed $v_{0} \sim 5 c m / s$ in zero background flow in Bak-Coleman and Coombs, 2014 is used to estimate α.

Appendix 1

Complete expression for the velocity field caused by image dipoles

The velocity field ${\vec{u}}_{f} = u_{f} \hat{i} + v_{f} \hat{j}$ at $\vec{r}$ induced by the single dipole at ${\vec{r}}_{f}$ , given by the potential function in Equation 1, is

u_{f} (\vec{r}, {\vec{r}}_{f}, θ_{f}) = r_{0}^{2} v_{0} (\frac{({(x - x_{f})}^{2} - {(y - y_{f})}^{2}) \cos θ_{f} + 2 (x - x_{f}) (y - y_{f}) \sin θ_{f}}{{({(x - x_{f})}^{2} + {(y - y_{f})}^{2})}^{2}}),

v_{f} (\vec{r}, {\vec{r}}_{f}, θ_{f}) = r_{0}^{2} v_{0} (\frac{- ({(x - x_{f})}^{2} - {(y - y_{f})}^{2}) \sin θ_{f} + 2 (x - x_{f}) (y - y_{f}) \cos θ_{f}}{{({(x - x_{f})}^{2} + {(y - y_{f})}^{2})}^{2}}) .

The potential function describing the image vortex system for a dipole in a channel presented in Equation 3 can be simplified using Mathematica, yielding

\begin{array}{ll} ϕ_{w} (\vec{r}, {\vec{r}}_{f}, θ_{f}) & = \frac{r_{0}^{2} v_{0}}{4} [4 \frac{(x - x_{f}) \cos θ_{f} + (y - y_{f}) \sin θ_{f}}{(x - x_{f})^{2} + (y - y_{f})^{2}} \\ - \frac{π e^{- i θ_{f}}}{h} (e^{2 i θ_{f}} (\coth (π A) + \coth (π B^{*})) + \coth (π A^{*}) + \coth (π B))], \end{array}

where $A = ((x - x_{f}) + i (y - y_{f})) / (2 h)$ , $B = ((x - x_{f}) + i (y + y_{f})) / (2 h)$ , $i = \sqrt{- 1}$ , and a superscript * indicates complex conjugate. The velocity field at due to the walls, is

\begin{array}{ll} v_{w} = \frac{r_{0}^{2} v_{0}}{4} [\frac{π^{2} e^{- i θ_{f}}}{2 h^{2}} (e^{2 i θ_{f}} (c s c h^{2} π A + c s c h^{2} π B^{*}) + (c s c h^{2} π A^{*} + c s c h^{2} π B)) \\ + \frac{4 \cos θ_{f}}{(x - x_{f})^{2} + (y - y_{f})^{2}} - \frac{8 (x - x_{f}) ((x - x_{f}) \cos θ_{f} + (y - y_{f}) \sin θ_{f})}{((x - x_{f})^{2} + (y - y_{f})^{2})^{2}}] . \end{array}

\begin{array}{ll} v_{w} = \frac{r_{0}^{2} v_{0}}{4} [\frac{i π^{2} e^{- i θ_{f}}}{2 h^{2}} (e^{2 i θ_{f}} (c s c h^{2} π A - c s c h^{2} π B^{*}) - (c s c h^{2} π A^{*} + c s c h^{2} π B)) \\ + \frac{4 \sin θ_{f}}{(x - x_{f})^{2} + (y - y_{f})^{2}} - \frac{8 (y - y_{f}) ((x - x_{f}) \cos θ_{f} + (y - y_{f}) \sin θ_{f})}{((x - x_{f})^{2} + (y - y_{f})^{2})^{2}}] . \end{array}

Superimposing the velocity fields from the dipole and its images and setting $y = 0$ (or $y = h$ ) yields $v_{f} + v_{w} = 0$ , thereby confirming that the walls of the channel are streamlines.

Appendix 2

Computational fluid dynamics

Framework

To quantify the flow around the swimming fish, we solved the incompressible Navier-Stokes equations numerically in the commercial software COMSOL Multiphysics (version 5.6). We focused on the steady swimming of a giant danio exhibiting a carangiform swimming pattern, consisting of large body undulations in the posterior of the animal and minimal lateral movement in the anterior portion. The lateral movement of a giant danio was mathematically described through a local coordinate system, $x^{'}$ - $y^{'}$ , such that the undeformed fish aligns its centerline along the $x^{'}$ -axis with head at $x^{'} = 0$ and tail at $x^{'} = l$ (see Appendix 2—figure 1a). The lateral movement were described as a traveling wave from the head to the tail as (Najafi and Abtahi, 2022).

y^{'} = [c_{1} (x^{'} - 0.3 l) + c_{2} {(x^{'} - 0.3 l)}^{2}] \sin [k_{L} (x^{'} - 0.3 l) - 2 π f t]

where c₁ and c₂ are two constants that describe the shape of the undulation envelope, $k_{L}$ is the wavenumber, and $f$ is the tail beating frequency. The values of $l$ , c₁, c₂, and $k_{L}$ are taken from Najafi and Abtahi, 2022, and the value of $f$ is taken from Zhang et al., 2019; these parameters are summarized in Appendix 2—table 1. For the chosen tail beat frequency, the oscillatory Reynolds number (Gazzola et al., 2014) is $S w = \frac{2 π C f l}{ν} = 8, 100$ , where $C$ is the tail beat amplitude, given as $C = 0.7 \times c_{1} l + 0.49 \times c_{2} l^{2}$ , and ν is the kinematic viscosity of water at room temperature ( $ν = 1.0 \times 10^{- 6} m^{2} s^{- 1}$ ).

The undeformed giant danio body shape was approximated as a NACA0013 airfoil, which has a maximum thickness-to-chord length matching that of the animal in Zhang et al., 2019. A NACA airfoil offers a reasonable approximation of the fish body in terms of its streamlined shape and its ability to emulate thrust production of a swimming fish (Lucas et al., 2020). The movement of the fish body was imposed in the numerical simulations using a moving boundary. No-slip boundary conditions was set on the fish body, whereas the channel walls satisfied only the no-penetration boundary condition, that is, they were treated as slip walls. In the simulations, we set a uniform flow with speed U₀ at the inlet, imposed a zero pressure boundary condition at the outlet, and fixed the axial location of the fish at the channel centerline.

Appendix 2—figure 1

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Details about the implementation of the computational fluid dynamics simulations.

(a) Mesh implemented in the simulations, with definitions of coordinate systems and a zoomed-in view of the refined mesh around the fish. (b) Mesh convergence analysis, showing the mean drag as a function of number of elements in the simulation.

The fluid domain was discretized using triangular elements, as illustrated in Appendix 2—figure 1a, and was allowed to deform in time to accommodate the body undulations. A grid convergence study was performed to ensure the solution was independent of the mesh. As shown in Appendix 2—figure 2b, a total number of $76 k$ elements were sufficient to guarantee the mesh independence of the simulations, such that implementing a higher number of $122 k$ elements introduced negligible variation in the mean drag prediction on the fish. As a result, all simulations were conducted using $76 k$ elements. A total of 10 tail beating cycles were simulated in each simulation, which was sufficiently long for the flow in the channel to fully develop. All simulations were conducted on 12 Intel Xeon Platinum 8268 CPUs with a base frequency of $2.90 GHz$ and a total of $48 GB$ memory. A typical simulation required approximately $6 h$ computational time to complete.

To represent the realistic swimming condition, the imposed inlet flow speed, U₀, should match the fish swimming speed, v₀, which depends on the body undulations described by (27). To identify the value of v₀, we conducted a series of preliminary simulations by varying U₀ until the time-averaged total drag on the fish, ${\bar{F}}_{D}$ was zero. That is, the drag experienced by the fish exactly balanced the thrust generated by the body undulations. The resulting swimming speed was determined to be $v_{0} = 19.74 cm / s$ . The resulting Reynolds number based upon channel width is $Re = \frac{h U_{0}}{ν} = 29, 600$ .

Results

The instantaneous velocity fields in the vicinity of the giant danio relative to the background flow are presented at five time instants during half of a tail beating cycle in Appendix 2—figure 2. In comparison with the mean flow shown in Figure 3, we observe distortions of the streamlines, with a left-right asymmetry caused by the body undulations. We also identify a series of alternating vortices generated through tail beating that form the wake. The magnitude of the wake flow decays as it is advected downstream.

CFD results are also useful to quantify the thickness of the boundary layer along the animal and offer support in favor of the proposed inviscid model for the study of the interactions between a fish and the channel walls. The thickness of the boundary layer can be quantified from the flow velocity component along the $x$ -direction, $u_{t}$ , in the presence of the background flow. As shown in Appendix 2—figure 3, the value of $u_{t}$ is zero at the body surface due to the no-slip boundary condition. A large gradient is observed within a thin layer at the boundary, in which $u_{t}$ rapidly increases to v₀. The boundary layer thickness can be estimated by identifying the location at which $u_{t}$ reaches 99% of its asymptotic value away from the fish body. During a tail beating cycle, the boundary layer thickness ranged between 2.8% and 15.7% of the fish body length, thereby supporting the feasibility of neglecting the influence of the viscous boundary layers as a first-order approximation.

Appendix 2—figure 2

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Instantaneous velocity fields around a swimming fish relative to the background flow from computational fluid dynamics.

(a) – (e) correspond to $t = 0$ , $T / 8$ , $T / 4$ , $3 T / 8$ , and $T / 2$ , respectively, where $T$ is the period of a tail beat. White curves are streamlines with arrows indicating flow directions.

Appendix 2—figure 3

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Analysis of the boundary layer thickness along a swimming fish.

x-component of the flow velocity, $u_{t}$ , extracted across the half-length of the fish body. The values of $u_{t}$ are measured in a coordinate system moving at the speed of v₀ along the fish swimming direction.

Comparison with the dipole model

The velocity field predicted by the dipole model is validated against the mean velocity quantified through CFD (see Figure 3(a)). Consistent with the fish location and heading direction, we set $y_{f} = h / 2$ and $θ = π$ for the dipole. The axial location, x_f, and the characteristic length scale, r₀, of the dipole are treated as fitting parameters. The velocity field associated with the dipole model in Figure 3(b) corresponds to a set of fitting parameters that minimizes the discrepancy between the model prediction and the simulated simulation. Denoting the model-predicted velocity field as ${\vec{u}}^{dipole}$ and the simulated one as ${\vec{u}}^{CFD}$ , the discrepancy between them is quantified through

E = \sqrt{\frac{\int_{D} {| {\vec{u}}^{d i p o l e} - {\vec{u}}^{C F D} |}^{2} d A}{\int_{D} d A}},

where $D$ is the computational domain. The optimal values of the fitting parameters that minimize $E$ are determined through an exhaustive search of the parameter space, leading to $(x_{f} - x_{s}) = 0.315 l$ and $r_{0} = 0.062 l$ , where x_s is the axial location of the fish head (the origin of the $x^{'}$ - $y^{'}$ coordinate system).

Appendix 2—table 1

Parameters employed in (27) to describe the locomotory pattern of a giant danio.

Parameters	$l$	$c_{1}$	$c_{2}$	$k_{L}$	$f$
Values	$7.3 cm$	0.004	$- 2.33 m^{- 1}$	$78.5 m^{- 1}$	$3 Hz$

Appendix 3

Bibliographical survey

We surveyed over three hundred publications cited by Arnold, 1974 and Coombs et al., 2020 – two review papers on rheotaxis, with the former focusing on early investigations from 1900 s to 1970 s, and the latter highlighting more recent works conducted between 1970 s and 2020. Publications were selected through the following inclusion and exclusion criteria.

Criteria

Inclusion criteria

We selected studies where: (i) the subject animals were fish; (ii) fish demonstrated rheotactic behavior; (iii) no unsteady flow events were present in the swimming domain, such as the wake structure of obstacles; (iv) the sensory cues available to fish could be identified with some confidence; (v) fish behavior was not influenced by social interactions; (vi) fish swam without visual cues; and (vii) the publication was written in English. Within criterion (iii), we focused on experiments with steady flows where the flow gradient is consistent over time, thus excluding swimming in random flow events. Criterion (vi) was introduced to direct our search toward the effects of hydrodynamic cues and lateral line sensing, which limited our search to experiments using blind fish or experiments in the dark. We acknowledge that this condition is not reflective of the model hypotheses, which, in fact, block any sense except for the lateral lines (such as vestibular and tactile senses).

Exclusion criteria

Among studies identified through the selection criteria, we excluded experiments on pleuronectiform flatfishes, which swim on their side and generate propulsive undulations in a vertical plane (Webb, 2002). This locomotory pattern differs fundamentally from the current model, derived on the assumption the fish align their bodies vertically and undulate on a horizontal plane, which is the swimming strategy of the majority of fishes.

Dataset

Appendix 3—table 1 presents data extracted from the selected studies, including the fish species, size of the swimming domain, flow conditions, sensory cues available to the fish, and the measured rheotaxis threshold speed. Swimming domains with rectangular cross-sections are defined by their length ( $L$ ), width ( $h$ ), and depth ( $W$ ), while swimming domains with circular cross-sections by their length and diameter ( $D$ ). Flow conditions are quantified through the flow speed and flow gradient. If information about the flow gradient was not available in a study, we qualitatively estimated its value through the Reynolds number of the flow, defined based on the width (diameter) of the channel and the background flow speed as $Re = \frac{h U_{0}}{ν}$ ( $Re = \frac{D U_{0}}{ν}$ ). For a sufficiently high $Re$ , the flow gradient near the center of the channel is expected to be low.

Comparison against model predictions

The studies identified in Appendix 3—table 1 are utilized to offer some context to the proposed theoretical framework with respect to the rheotaxis stability threshold. We first express the stability threshold $β = β^{*}$ in dimensional form in terms of the rheotaxis threshold speed

U_{c} = \frac{π^{4} r_{0}^{2} v_{0}}{32 h^{2} (1 + K r_{0} l) ϵ},

such that $U_{0} > U_{c}$ corresponds to the stable condition $β > β^{*}$ , and vice versa. From most studies, the values of $U_{c}$ can be identified and its confidence level can be inferred (see Appendix 3—table 1).

As evidenced in Equation 29, a series of parameters could influence the rheotaxis threshold speed, including the lateral line feedback, flow gradient, swimming domain size, and fish body length. Specifically, Equation 29 predicts that increasing the lateral line feedback, flow gradient, and/or width of swimming channel promotes rheotaxis at lower flow speeds, whereas increasing fish size will require higher flow speeds to elicit rheotactic behavior. The effects of these parameters are validated independently in Appendix 3—table 2, where we include experimental evidence garnered within each study and, when possible, carry out a comparison, across them. We compare each of these empirical observations to model predictions, and assess if they support the model, contradict the model, or are inconclusive. An observation is considered supportive of (contradictive to) our model if the measured $U_{c}$ exhibits with statistical significance the same (opposite) dependence on a certain parameter. Data that lack statistical significance are considered inconclusive.

The confidence intervals of the measured $U_{c}$ values were estimated to determine if $U_{c}$ were significantly different across studies. When the mean and standard error of the mean (s.e.m.) of $U_{c}$ were provided, we estimated its 95% confidence interval as $(mean - 1.96 s . e . m ., mean + 1.96 s . e . m .)$ . If the confidence intervals of two $U_{c}$ values did not overlap, we considered them significantly different. For instance, in Bak-Coleman and Coombs, 2014 and Elder and Coombs, 2015, the confidence intervals of $U_{c}$ were determined to be $(0.63, 1.17) cm / s$ and $(1.27, 2.64) cm / s$ , respectively, and thus the $U_{c}$ values were considered significantly different. In several studies, such as Baker and Montgomery, 1999 and Van Trump and McHenry, 2013, the threshold speeds were only estimated as intervals, where fish swimming below a lower bound did not perform rheotaxis, while they exhibited rheotaxis above an upper bound. We treated this speed interval as the confidence interval for $U_{c}$ in our statistical analysis.

Effect of lateral line feedback

Several studies provide some support in favor of the prediction of our model of the beneficial role of lateral line feedback, showing a significant reduction in rheotactic performance when the lateral line is compromised (Kulpa et al., 2015; Oteiza et al., 2017; Suli et al., 2012), see Appendix 3—table 2. In these studies, fish locomotion was measured in steady background flows, so that a fish holding station would experience minimal linear acceleration and marginally engage the vestibular system. Throughout these studies, fish were not observed to make contact with the swim channel, indicating that tactile senses played a negligible role in rheotaxis.

Effect of flow gradient

We identified two studies (Lyon, 1904; Oteiza et al., 2017) that could back the predicted effect of the flow velocity gradient on rheotaxis, as summarized in Appendix 3—table 2. In both studies, fish locomotion was recorded in flows with varying velocity gradients. In qualitative agreement with the proposed model, the rheotaxis performance of zebrafish larvae significantly improved with increasing gradient magnitudes (Oteiza et al., 2017). Similar observations were obtained by Lyon on blind Fundulus (Lyon, 1904), where in a flow with a small gradient, fish performed rheotaxis only when tactile cues were available, while in a jet flow with a large flow gradient, rheotaxis could be elicited solely by the flow. Although qualitatively in line with our predictions, we conservatively considered this study as inconclusive due to a lack of quantitative data for statistical tests.

Effect of size of swimming domain

To elucidate the role of the swimming domain size on rheotaxis threshold speed, we conducted cross-study comparisons as shown in Appendix 3—table 2. As evidenced through comparisons between two experiments on zebrafish larvae (Oteiza et al., 2017; Peimani et al., 2017) in swim channels of drastically different sizes, rheotaxis was elicited at a higher threshold speed in a smaller flow channel, which supports our model prediction. Our model is also qualitatively supported by comparisons between Bak-Coleman and Coombs, 2014 and Baker and Montgomery, 1999, or Bak-Coleman and Coombs, 2014 and Van Trump and McHenry, 2013, where experiments on blind cavefish of comparable body sizes uncovered higher threshold speeds in smaller flow channels. In the experiments of Bak-Coleman and Coombs, 2014, blind cavefish were observed to receive transient tactile senses while swimming, which could have contributed to its lower rheotaxis threshold. As a result, experimental data on blind cavefish were conservatively deemed to be inconclusive.

Effect of fish size

The relationship between the threshold speed and fish body size is less straightforward, as the body size not only determines the value of $l$ , but also influences r₀, which is on the order of the fish tail beat amplitude. We assumed $r_{0} = 0.2 l$ , which is a typical tail-beat-amplitude-to-body-length ratio (Gazzola et al., 2014). For fish with functional lateral lines that produce positive feedback, $K > 0$ , we obtain $U_{c} \sim 1 - \frac{1}{1 + 0.2 K l^{2}}$ . For fish with disabled lateral line, $K = 0$ , we find $U_{c} \sim l^{2}$ . In both cases, the model predicts that $U_{c}$ is larger for fish with larger body length. Some evidence can be garnered by contrasting a pair of studies by Bak-Coleman and Coombs, 2014 and Elder and Coombs, 2015, where experiments were conducted on fish of the same species (Astyanax mexicanus) in swim tunnels of the same size, and tested in flows at a similar range of speeds. The high flow speeds in both studies suggest that the flow gradients in these experiments were small. We assume that the lateral line feedback were equivalent in both studies, as the subjects were conspecific. Although the tactile cues present in the experiments by Bak-Coleman and Coombs, 2014 hinder our ability to reach a definitive conclusion on the effect of fish body size, the higher threshold speed observed in larger fish qualitatively supports our model prediction. The paucity of data for validation of the effect of fish size is a result of a lack of studies with matching experimental conditions, including dimensions of the flow facilities, flow conditions, and functionality of the lateral line.

In summary, we identified a total of five sets of experiments in support of our model, and nine sets of studies that offer inconclusive evidence. None of the data contradicted predictions from the proposed model.

Most experiments used in our comparison listed in Appendix 3—table 1 were conducted in the past 25 years, and only two studies date back to before 1970. This disparity is attributed to an evolution of the methodologies for the study of rheotaxis over time. Among the earlier efforts, a large portion relied on observations of fish behavior in the field (Arnold, 1974). Although these studies minimized the introduction of external stimuli stemming from human presence and unfamiliar environments that could alter the behavior of fish in the wild, a lack of flexibility in the design of controlled experiments in the field, together with an insufficient measurement resolution, has led to only a limited number of works that could distinguish the impact of one sensory cue from another. As a result, a large number of earlier efforts do not meet our inclusion criteria.

Likely, the interest in fish rheotaxis was recently reignited owning to the advancements in technologies that could selectively deactivate specific fish sensory organs, thereby allowing for the targeted investigation of the role of each sensory cue in rheotaxis. For instance, pharmacological methods that could disable the lateral line led to studies (Baker and Montgomery, 1999; Montgomery et al., 1997) challenging the long-standing perception that the lateral line could not mediate rheotaxis. In addition, the development of high speed cameras with infra-red sensing capabilities enabled precise measurements of fish behavior in the dark, allowing for the elimination of visual cues from the study of lateral line functionality in rheotaxis.

Some early experiments that have been considered in the past as evidence against the role of the lateral line are not listed in Appendix 3—table 1 due to a lack of a controlled experimental design in the field setting. For example, some species of salmonids, including salmon and trout, were observed to swim against the current in the day and rest on the bottom of a stream at night (Davidson, 1949; Edmundson et al., 1968; Gibson, 1966), leading to a conclusion that the lateral line played a minimal role in rheotaxis (Arnold, 1974). However, we did not include these experiments for our model validation due to confounding factors posed by the field settings, such as variations in water temperature (Edmundson et al., 1968; Fraser et al., 1993; Needham and Jones, 1959) and current speeds at different hours of the day. Daily fluctuations in the availability of food (Waters, 1962; Elliott, 1965) is another factor that could influence the activity levels of fish at night, as observed in white bass (McNaught and Hasler, 1961) and trout (Elliott, 1965). Another class of experiments that led to the previous rejection of lateral line was the demonstration of the imperative role of vision in rheotaxis. Experiments on salmon (Hoar, 1954) and herring (Brawn, 1960) showed a reduction in rheotaxis when vision was obscured in the dark or in muddy water, conflating the role of visual cues in rheotaxis. Again, these observations do not directly contradict the proposed model, which suggests that in the absence of visual cues, rheotaxis could still manifest provided that the flow speed is sufficiently high.

Appendix 3—table 1

Relevant publications on fish rheotaxis in the absence of visual cues, identified through literature review.

Reference	Fish		Swimming domain	Flow properties		*Sensory cues	Rheotaxis threshold speed
Reference	Species	Length	Swimming domain	Flow speed	Flow gradient	*Sensory cues	Rheotaxis threshold speed
Bak-Coleman et al., 2013	Giant danio (Devario aequipinnatus)	6.0 –7.3 cm	Flow tank of $25 \times 25 \times 25 c m$ ( $L \times h \times W$ )	0, 3, and $7 cm / s$	$Re \sim 7500$ at LL+ threshold speed; flow gradient expected to be small near center of tank	LL+/LL-	$\leq 3 cm / s$
Bak-Coleman and Coombs, 2014	blind cavefish (Astyanax mexicanus)	4.2 –5.0 cm	Flow tank of $25 \times 25 \times 25 c m$ ( $L \times h \times W$ )	0, 1, 2, 3, 4, 7 and $8 cm / s$	$Re \sim 2000$ at LL+ threshold speed; flow gradient expected to be small near center of tank	LL+/LL-; fish made transient contacts with substrate	LL+: $0.90 c m / s$ ; LL-: $0.54 c m / s$
^†Baker and Montgomery, 1999	blind cavefish (Astyanax fasciatus)	4 –7 cm	Flow tank of $51 \times 9 \times 20 c m$ ( $L \times h \times W$ )	0, 2, 3, 5, 9 and $16 cm / s$	$Re \sim 2000$ at LL+ threshold speed; flow gradient expected to be small near center of tank	LL+/LL-; tactile senses	LL+: 2– $3 cm / s$ ; LL-: 9– $16 cm / s$
Elder and Coombs, 2015	Mexican tetras (Astyanax mexicanus)	$8.3 cm$	Flow tank of $25 \times 25 \times 25 c m$ ( $L \times h \times W$ )	0, 1, 2, 4, 7, and $12 cm / s$	$Re \sim 5000$ at threshold speed; flow gradient expected to be small near center of tank	LL+/LL-	$\sim 2 cm / s$ for LL+ and LL-
Kulpa et al., 2015	blind cavefish (Astyanax mexicanus)	4.4 –5.3 cm	Flow tank of $25 \times 25 \times 10 c m$ ( $L \times h \times W$ )	Maximum speed of $8 cm / s$	Jet flow across center of tank; flow gradient expected to be large	LL+/LL-	$\leq 8 cm / s$
^‡Lyon, 1904	blind Fundulus	unspecified	Trough with unspecified dimensions; tideway leading to pond	“not too strong current” in trough and current with “more or less eddy and irregularity” in tideway	Flow gradient expected to be small	LL+; some fish gained tactile senses	Not measured; rheotaxis elicited only by tactile cues
^‡Lyon, 1904	blind Fundulus	unspecified	Trough with unspecified dimensions	flow “gushing rather violently”	Jet flow; flow gradient expected to be large	LL+	Not measured; rheotaxis elicited by flow
^†Montgomery et al., 1997	blind cavefish (Astyanax fasciatus)	4 –7 cm	^§Flow tank of $51 \times 9 \times 20 c m$ ( $L \times h \times W$ )	0, 2, 3, 5, 9, and $16 cm / s$	$Re \sim 2000$ at LL+ threshold speed; flow gradient expected to be small near center of tank	LL+/LL-; tactile senses	LL+: 2–3 cm/s; LL-: 9–16 cm/s
Oteiza et al., 2017	zebrafish (Danio rerio) larva 5–7 days post fertilization (dpf)	unspecified	13 cm-long circular tube with diameter 1.27– $4.76 c m$	0.2–0.8 cm/s	Low to high flow gradients identified through particle image velocimetry	LL+/LL-	LL+: rheotaxis observed as low as $0.2 cm / s$
Peimani et al., 2017	zebrafish (Danio rerio) larva 5–7 dpf	estimated $\sim 0.35 c m$	Flow channel of $63.3 \times 1.6 \times 0.55 m m$ ( $L \times h \times W$ )	0.95–3.8 cm/s	$Re \sim 10$ at threshold speed; flow gradient expected to be large	LL+	$0.95 cm / s$
Suli et al., 2012	zebrafish (Danio rerio) larva 5 dpf	$\sim 0.33 cm$	Flume of $110 \times 3.7 \times 2.8 c m$ ( $L \times h \times W$ )	0.075, 0.15, $0.2 cm / s$	$R e < 75$ ; flow gradient expected to be large	LL+/LL-	Not quantified
Van Trump and McHenry, 2013	blind Mexican cavefish (Astyanax fasciatus)	3 –7 cm	Cylindrical channel of $150 \times 11 c m$ ( $L \times D$ )	0, 1, 2, 4, 6, 8, 10, 13, $16 cm / s$	$R e > 2000$ at threshold speed; flow gradient expected to be small near center of tank	LL+/LL-	2–4 cm/s

*

LL+: lateral line enabled; LL−: lateral line disabled
†

Data are extracted from the same set of experiments
‡

Two experiments are considered from the same paper
§

Data are from Baker and Montgomery, 1999.

Appendix 3—table 2

Results of the bibliographical research on fish rheotaxis in the absence of visual cues, used to validate the proposed model.

Reference	Fish species	*Evidence	Comparison with model
Reference	Fish species	*Evidence	Supportive	Inconclusive
Within studies
Effect of lateral line
Bak-Coleman et al., 2013	Giant danio (Devario aequipinnatus)	No significant difference in fish heading angle against current was detected between LL+ and LL-		×
Bak-Coleman and Coombs, 2014	blind cavefish (Astyanax mexicanus)	Rheotaxis threshold speed was slightly (but not significantly) lower in LL- condition		×
Baker and Montgomery, 1999 and Montgomery et al., 1997	blind cavefish (Astyanax fasciatus)	Rheotaxis threshold speed was significantly higher in LL- condition; fish received intermittent tactile senses		×
Elder and Coombs, 2015	Mexican tetras (Astyanax mexicanus)	No significant influence of LL condition was detected on rheotactic performance		×
Kulpa et al., 2015	blind cavefish (Astyanax mexicanus)	Significantly higher rheotaxis index in LL+ fish than LL- fish in jet stream	×
Oteiza et al., 2017	zebrafish (Danio rerio) larva 5–7 dpf	Posterior lateral line ablation or chemical neuromast ablation severely reduced rheotaxis	×
Suli et al., 2012	zebrafish (Danio rerio) larva 5 dpf	LL hair cell damage led to a significant decrease in rheotaxis; regeneration of LL hair cells restored rheotaxis	×
Van Trump and McHenry, 2013	blind Mexican cavefish (Astyanax fasciatus)	In LL+ and LL-, fish exhibited statistically indistinguishable rheotaxis behavior		×
Effect of flow gradient
Lyon, 1904	blind Fundulus	In a flow with small gradient, rheotaxis was elicited only when fish received tactile cues; in jet flow with large gradient, rheotaxis was elicited by flow without tactile cues. Lack of data on statistical significance		×
Oteiza et al., 2017	zebrafish (Danio rerio) larva 5–7 dpf	Rheotaxis of fish improved with increasing gradient magnitudes	×
Across studies
Effect of channel width
Bak-Coleman and Coombs, 2014; Baker and Montgomery, 1999	blind cavefish (Astyanax mexicanus); blind cavefish (Astyanax fasciatus)	Significantly different threshold speed for LL+ fish: $0.90 \pm 0.137 cm / s$ (mean ±s.e.m.) in $25 cm$ wide tunnel; between $2 cm / s$ and $3 cm / s$ in $9 cm$ wide tunnel. Tactile cues available to fish in Bak-Coleman and Coombs, 2014		×
Bak-Coleman and Coombs, 2014; Van Trump and McHenry, 2013	blind cavefish (Astyanax mexicanus); blind cavefish (Astyanax fasciatus)	Significantly different threshold speed for LL+ fish: $0.90 \pm 0.137 cm / s$ (mean ±s.e.m.) in $25 cm$ wide tunnel; between $2 cm / s$ and $4 cm / s$ in $\sim 11 cm$ diameter tunnel. Tactile cues available to fish in Bak-Coleman and Coombs, 2014		×
Oteiza et al., 2017; Peimani et al., 2017	zebrafish (Danio rerio) larva 5–7 dpf	Onset of rheotaxis in LL+ fish observed at flow speed $0.95 cm / s$ in $1.6 mm$ wide tunnel; rheotaxis observed in LL+ fish at flow speed $0.2 cm / s$ in $2.22 cm$ diameter tunnel	×
Effect of body length
Bak-Coleman and Coombs, 2014; Elder and Coombs, 2015	blind cavefish (Astyanax mexicanus); Mexican tetras (Astyanax mexicanus)	Significantly different threshold speed for LL+ fish: $0.90 \pm 0.137 cm / s$ (mean ±s.e.m.) for 4.2– $5.0 cm$ long fish; $1.96 \pm 0.350 cm / s$ (mean ±s.e.m.) for $8.3 cm$ long fish. Tactile cues available to fish in Bak-Coleman and Coombs, 2014		×
Total			5	9

*

LL+: lateral line enabled; LL−: lateral line disabled

Appendix 4

Stability analysis of the dynamical system based on the A-dipole

Derivation of the turn rate equation

Different from Equation 8, the A-dipole model treats fish as a slender body, which rotates in response to a gradient in the cross flow along its body. As such, under the A-dipole paradigm, the hydrodynamic turn rate becomes

\begin{matrix} Ω^{(A)} ({\vec{r}}_{f}, θ_{f}) = {\hat{v}}_{f}^{⟂} \cdot [{\nabla ({\vec{u}}_{w} (\vec{r}, {\vec{r}}_{f}, θ_{f}) + {\vec{u}}_{b} (\vec{r})) |}_{\vec{r} = {\vec{r}}_{f}}] {\hat{v}}_{f} \\ = \frac{π^{3} ρ^{2} v_{0}}{4 h} \cot (\frac{π y_{f}}{h}) \csc^{2} (\frac{π y_{f}}{h}) \cos θ_{f} + \frac{8 U_{0} ϵ}{h} (\frac{y_{f}}{h} - \frac{1}{2}) \sin^{2} θ_{f} . \end{matrix}

While the equation for the cross-stream motion of the A-dipole remains the same as Equation 10a, the governing equation for its orientation requires modification. Substituting Equation 30 into Equation 6b yields

{\dot{θ}}_{f} = \frac{π^{3} ρ^{2}}{4} \cot (π (ξ + \frac{1}{2})) \csc^{2} (π (ξ + \frac{1}{2})) \cos θ_{f} + 8 α ξ (\sin^{2} θ_{f} + κ),

which is analogous to Equation 10b for a T-dipole. Equation 10a and Equation 31 constitute the governing equations of the nonlinear planar dynamical system for an A-dipole fish model.

Determination of the equilibria of the dynamical system

Similar to our analysis of the T-dipole, the equilibria of the dynamical system for the A-dipole can be determined by setting $θ_{f} = 0$ and $θ_{f} = π$ in Equation 10a and Equation 31. Analogous to Equation 14, the cross-stream location ξ of the equilibria can be determined through a transcendental equation,

\frac{π^{3}}{32} \cot (π (ξ + \frac{1}{2})) \csc^{2} (π (ξ + \frac{1}{2})) = \mp β^{(A)} ξ,

where the negative sign corresponds to $θ_{f} = 0$ and the positive sign to $θ_{f} = π$ . Similar to the analysis of the T-dipole, here, we introduce a nondimensional parameter $β^{(A)} = α κ / ρ^{2}$ .

For downstream swimming ( $θ_{f} = 0$ ), there exists one or three roots to Equation 32 depending on the value of $β^{(A)}$ . For $β^{(A)}$ smaller than the critical value of $β^{*} = π^{4} / 32$ , $ξ = 0$ is the only solution, while for $β^{(A)} > β^{*}$ , two additional roots symmetrically located with respect to the centerline emerge. On the other hand, for upstream swimming ( $θ_{f} = π$ ), there is only one root at $ξ = 0$ .

Local stability analysis of the dynamical system

Local stability of the equilibria is studied by linearizing Equation 10a and Equation 31 about the equilibria. Specifically, for $θ_{f} = 0$ and $ξ = 0$ , the state matrix reads

A = [\begin{matrix} 0 & 1 - \frac{π^{2} ρ^{2}}{6} \\ 8 κ α - \frac{π^{4} ρ^{2}}{4} & 0 \end{matrix}] .

Stability requires that the determinant of $A$ is positive ( $det A > 0$ ), that is,

\frac{1}{24} (6 - π^{2} ρ^{2}) (π^{4} ρ^{2} - 32 α κ) > 0.

Since the first factor is always positive ( $ρ ≪ 1$ ), the inequality is fulfilled when $β^{(A)} < β^{*}$ . Hence, the system is stable if $β^{(A)} < β^{*}$ and unstable if $β^{(A)} > β^{*}$ .

For $θ_{f} = 0$ and $β^{(A)} > β^{*}$ , we identify two additional equilibria symmetrically located with respect to the centerline. The state matrix for these equilibria reads

A = [\begin{matrix} 0 & 1 + \frac{π^{2} ρ^{2}}{12} - \frac{1}{4} π^{2} ρ^{2} \sec^{2} (π ξ) \\ 8 κ α - \frac{1}{4} π^{4} ρ^{2} (2 - \cos (2 π ξ)) \sec^{4} (π ξ) & 0 \end{matrix}] .

Stability requires that $det A > 0$ , that is,

\frac{1}{48} (12 - 3 π^{2} ρ^{2} \sec^{2} (π ξ) + π^{2} ρ^{2}) (- 32 α κ + π^{4} ρ^{2} (2 - \cos (2 π ξ)) \sec^{4} (π ξ)) > 0.

As demonstrated in Methods and Materials Section, the first factor in Equation 36 can be assumed to be positive. Thus, the inequality in Equation 36 is equivalent to

β^{(A)} < \frac{π^{4}}{32} (2 - \cos (2 π ξ)) \sec^{4} (π ξ),

which is always satisfied for any choice of $β^{(A)}$ . Therefore, the additional equilibria emerging for $β^{(A)} > β^{*}$ at $ξ \neq 0$ are always stable.

For upstream swimming along the centerline ( $θ_{f} = π$ and $ξ = 0$ ), the state matrix is

A = [\begin{matrix} 0 & \frac{π^{2} ρ^{2}}{6} - 1 \\ 8 κ α + \frac{π^{4} ρ^{2}}{4} & 0 \end{matrix}] .

Similarly, stability requires that $det A > 0$ , that is,

\frac{1}{24} (6 - π^{2} ρ^{2}) (32 α κ + π^{4} ρ^{2}) > 0.

Since both the first and the second factors are positive, the condition in Equation 39 is always satisfied and the equilibrium is stable.

Comparing predictions with the T-dipole, results are similar in that there is a critical threshold that modulates the stability of upstream/downstream swimming, with a preference for rheotactic behavior above the threshold. For the T-dipole, below the critical threshold, neither swimming downstream nor upstream along the centerline of the channel are stable, and above the threshold, the latter becomes stable. Put simply, at low flow speed it is difficult for fish to orient in the flow, but they can successfully orient against the flow at high speed. For the A-dipole, below the critical threshold, both swimming downstream and upstream along the centerline of the channel are stable, and above the threshold, only the latter remains stable. In other words, fish can orient in the flow at low speed, without a preference for downstream or upstream swimming, but at high speed only swimming upstream becomes feasible.

Data availability

The authors declare that the data supporting the findings of this study are available within the paper. The Mathematica notebook used to derive the governing equations, study the planar dynamical, and generate associated figures, together with the CFD data discussed in the text, are also available at https://github.com/dynamicalsystemslaboratory/Rheotaxis; (copy archived at swh:1:rev:0c2828a439cb0df9971cdf12dc7dd93d16ce3450).

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Decision letter

Agnese Seminara

Reviewing Editor; University of Genoa, Italy
Aleksandra M Walczak

Senior Editor; CNRS LPENS, France

Our editorial process produces two outputs: (i) public reviews designed to be posted alongside the preprint for the benefit of readers; (ii) feedback on the manuscript for the authors, including requests for revisions, shown below. We also include an acceptance summary that explains what the editors found interesting or important about the work.

Decision letter after peer review:

Thank you for submitting your article "Hydrodynamic model of fish orientation in a channel flow" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Aleksandra Walczak as the Senior Editor. The reviewers have opted to remain anonymous.

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.

Essential revisions:

1) While the attempt to compare predictions with data is clearly valuable, the data appear inconclusive and weaken the results. Please present these data as a supplementary information, de-emphasize the comparison and temper claims about biological relevance.

2) Please discuss the assumptions of the model, and in what parameter regime they are expected to hold. in particular, please provide evidence for adequacy of the dipole model; the rationale for modelling the external flow as a constant + parabolic perturbation; and the rationale for the feedback.

3) Please validate the model, for example with numerical simulations that solve the Navier Stokes equations.

4) Please include a discussion about experiments that could definitively test the hypothesis with real fish, even if you will not perform them.

Reviewer #1 (Recommendations for the authors):

The paper is missing an independent measure of function. Another line of evidence that this phenomenon is actually contributing to rheotaxis would lend strength to their argument. The strength of the theoretical work largely outweighs the support from the biological literature.

As of now, they come up with a model that matches some of what has been shown in the (inconclusive) literature. Open loop robotics is a useful suggestion and should be implemented for conclusive results. At the very least, I would have the authors suggest more concrete experiments, even if they will not do them. This shows a commitment to advancing our understanding of the actual biological phenomenon. Regarding open loop robots, and I would like to see a more detailed description of what results they would expect and how this would strengthen their argument. Likewise, a discussion on how wider flumes are expected to increase rheotaxis should be included, rather than simply mentioning that this is supported in some biological studies.

Table 1 summarizes experiments for rheotactic fish without vision, with some studies supportive and most inconclusive. I found this table marginally useful (the fault of the studies, not the authors) because these experiments have other sensory modalities intact that can generate rheotaxis. To use this to support that fish can use only their lateral line for rheotaxis is misleading, in my opinion. For the importance of a single parameter threshold to be realized, one would observe cross stream sweeping movements at higher flows for a good majority of fish swimming studies, and this is simply not the case. Literature could be better interpreted. Rheotaxis is a multi-modal behavior, so ablation of the lateral line is not sufficient to guarantee that rheotaxis can occur without it.

If improving biological experiments is the goal, then more discussion is warranted. A discussion of reafference and what flow information is incorporated in the model-acceleration, velocity, both? What do larval zfish (superficial neuromasts) behaviors tell us that are consistent (or not) with adult behaviors (canal neuromasts)?

The impact contracts in the face of what can be conclusively supported, leaving the authors to describe their work as rectifying a methodological oversight in laboratory experiments.

Reviewer #2 (Recommendations for the authors):

Please conduct a quantitative validation and sensitivity analysis of the model.

Reviewer #3 (Recommendations for the authors):

I have now read this manuscript on the stability of a fish in a channel flow. As stated in my public review, I think the assumptions of the model are not adequate for the problem studied. For this reason, I believe the manuscript is not publishable as it is. Here is a list of some comments.

- In the introduction, one aspect of fish locomotion seems to be missing: proprioception. Fish sense their surrounding also be sensing how the hydrodynamic forces and moments affect their own shape.

- The dipole model is very crude, is there any experimental evidence that this model would be appropriate to model zebrafish larvae, for instance? I believe not, because zebrafish do not swim continuously and the Reynolds number is far too small for a potential flow assumption. Besides, there is a wake behind a swimming fish that is not captured by the dipole model.

- What is the Reynolds number of the channel flows in the experiments? I believe that superposing a constant flow and a parabolic flow is not the best model for these channel flows. Usually, people use some sort of plug flow instead.

- It is strange to have a mix between a viscous flow for the channel flow and potential flow for the swimmer. What is the rationale for this mix?

- Eq. (8) describes how the potential flow rotates the dipole. I understand that you consider a sort of dumbbell model, with the dumbbell oriented perpendicular to the swimming direction. But fish are elongated in the longitudinal direction, so it seems strange.

- Eq. (9) is not a "rich nonlinear dynamics" as the author state, but simply a linear feedback with the distance from the wall. Most visual models have the same kind of feedback.

- The comparison with experimental results is presented in tables. This is not very clear and the reader is left with the impression that most comparisons are inconclusive.

https://doi.org/10.7554/eLife.75225.sa1

Author response

Essential revisions:

1) While the attempt to compare predictions with data is clearly valuable, the data appear inconclusive and weaken the results. Please present these data as a supplementary information, de-emphasize the comparison and temper claims about biological relevance.

Thank you for the constructive feedback. We acknowledge that most data in the literature only provide inconclusive evidence and have followed your advice to move the data to Appendix 3 to avoid over-emphasizing the biological relevance. Furthermore, we have largely rewritten the Discussion section, focusing on the model results and acknowledging limitations inherent to any comparison with available empirical findings.

2) Please discuss the assumptions of the model, and in what parameter regime they are expected to hold. in particular, please provide evidence for adequacy of the dipole model; the rationale for modelling the external flow as a constant + parabolic perturbation; and the rationale for the feedback.

Thanks for the great suggestion, which has prompted us to significantly expand on the theoretical contribution of the work by performing an original computational validation of the dipole model – which has never been done in the literature. Numerical results are included in the new subsection Numerical Validation of the Dipole Model in the Results section and accompanying Appendix 2. With respect to the rationale for selecting a constant flow + parabolic perturbation, we have added details in the main text. Our assumptions on the flow profile consisting of a uniform flow (plug flow) with a parabolic profile is the simplest form that approximates the mean flow while incorporating vorticity near the channel centerline. Importantly, should one account for more complex velocity profiles, the linear stability analysis will not change, as it is based only on local flow features at the centerline. As a result, our claims regarding the stability of rheotaxis above a critical threshold speed would not be affected by the assumption of a more complex velocity profile. In the same vein, a nonlinear feedback mechanism would not change the results from the linear stability analysis. A paragraph has been added after Equation (22) in the Methods and Materials section.

3) Please validate the model, for example with numerical simulations that solve the Navier Stokes equations.

Once again, thanks a lot for the request that prompted us to undertake the computational simulation of Navier Stokes equations of a fish undulating its body in a channel flow. Numerical simulations demonstrate that the dipole model provides a sufficiently accurate approximation of the mean flow field, capturing the flow circulation from the fish head to the tail and the elongated streamline pattern near the walls. (See the new Numerical Validation of the Dipole Model subsection in the manuscript, with additional details provided in Appendix 2.)

4) Please include a discussion about experiments that could definitively test the hypothesis with real fish, even if you will not perform them.

Thank you for the constructive request. We believe that the best experimental approach to test the hypothesis of passive rheotaxis should actually involve robotic, rather than real, fish. Specifically, robotic fish mimicking the locomotory patterns of live animals and working in open loop (without any sensory input) could be used to test the hypothesis that above a critical flow speed, rheotaxis is stable. We have added two paragraphs in the Discussion section (paragraphs five and six) to detail an experiment that could definitively test the hypothesis of a completely passive hydrodynamic mechanism for rheotaxis. Therein, we also expand on the limitations of existing methods to disable sensory modalities in live animals. We specifically borrow arguments from Coombs et al. (Journal of Experimental Biology, 2020, 223, 223008) to articulate that an attempt to block all sensory modalities may challenge fish ability to swim; for example, disabling vestibular senses may cause inability to maintain an upright posture (see paragraph four of the Discussion section).

Reviewer #1 (Recommendations for the authors):

The paper is missing an independent measure of function. Another line of evidence that this phenomenon is actually contributing to rheotaxis would lend strength to their argument. The strength of the theoretical work largely outweighs the support from the biological literature.

As of now, they come up with a model that matches some of what has been shown in the (inconclusive) literature. Open loop robotics is a useful suggestion and should be implemented for conclusive results. At the very least, I would have the authors suggest more concrete experiments, even if they will not do them. This shows a commitment to advancing our understanding of the actual biological phenomenon. Regarding open loop robots, and I would like to see a more detailed description of what results they would expect and how this would strengthen their argument. Likewise, a discussion on how wider flumes are expected to increase rheotaxis should be included, rather than simply mentioning that this is supported in some biological studies.

We agree with the Reviewer on the limited support in the biological literature. In the revised manuscript, we discuss limitations of the existing literature to validate our model (see the fourth paragraph of the Discussion section). We have elaborated on an experimental protocol involving robotic fish operating in open loop that could be performed to validate our model (see paragraphs five and six of the Discussion section). In addition, we have included a more detailed discussion of the role of the channel width (see paragraph eight of the Discussion section).

Table 1 summarizes experiments for rheotactic fish without vision, with some studies supportive and most inconclusive. I found this table marginally useful (the fault of the studies, not the authors) because these experiments have other sensory modalities intact that can generate rheotaxis. To use this to support that fish can use only their lateral line for rheotaxis is misleading, in my opinion. For the importance of a single parameter threshold to be realized, one would observe cross stream sweeping movements at higher flows for a good majority of fish swimming studies, and this is simply not the case. Literature could be better interpreted. Rheotaxis is a multi-modal behavior, so ablation of the lateral line is not sufficient to guarantee that rheotaxis can occur without it.

We thank the Reviewer for the insightful comments on the interpretation of the literature in our manuscript. We agree that most of the studies identified in the literature do not establish an idealized condition where only the lateral line was intact while all other sensory modalities were eliminated, leading to “inconclusive” comparisons for most studies. In the revised manuscript, we have softened and focused all of the claims, moved the validation against the literature to Appendix 3, and have added context to acknowledge limitations of the existing experimental studies (see, for example, paragraphs four and eleven of the Discussion section).

If improving biological experiments is the goal, then more discussion is warranted. A discussion of reafference and what flow information is incorporated in the model-acceleration, velocity, both? What do larval zfish (superficial neuromasts) behaviors tell us that are consistent (or not) with adult behaviors (canal neuromasts)?

The model does not incorporate flow information from acceleration. Information from velocity is encapsulated in the form of the background flow circulation that is sensed through the lateral line, and, original to this work, the bidirectional interaction of the fish with the confined flow. We clarified these aspects when introducing the model, softened biological statements throughout the text, and added additional discussion regarding the model limitations (see the second-to-last paragraph of the Discussion section).

The impact contracts in the face of what can be conclusively supported, leaving the authors to describe their work as rectifying a methodological oversight in laboratory experiments.

In the text, we acknowledged the limited support of the literature and highlighted the value of the conclusions that can be drawn on the basis of a pure fluid mechanics perspective.

Reviewer #2 (Recommendations for the authors):

Please conduct a quantitative validation and sensitivity analysis of the model.

Our two-dimensional numerical validation model was developed by extracting the geometry and body motion of a giant danio from the literature. The numerical model was implemented into a laminar flow channel whose speed was selected such that the net drag on the model was zero. The local and global flow features generated by the numerical fish model were compared with those produced by a dipole model with identical swimming speed. (See the new Numerical Validation of the Dipole Model subsection, with additional details in Appendix 2.)

Reviewer #3 (Recommendations for the authors):

I have now read this manuscript on the stability of a fish in a channel flow. As stated in my public review, I think the assumptions of the model are not adequate for the problem studied. For this reason, I believe the manuscript is not publishable as it is. Here is a list of some comments.

- In the introduction, one aspect of fish locomotion seems to be missing: proprioception. Fish sense their surrounding also be sensing how the hydrodynamic forces and moments affect their own shape.

We thank the Reviewer for highlighting this. We have amended the Introduction to include a more comprehensive list of the sensing modalities employed by swimming fish. (See the added text in the second paragraph of the Introduction.)

- The dipole model is very crude, is there any experimental evidence that this model would be appropriate to model zebrafish larvae, for instance? I believe not, because zebrafish do not swim continuously and the Reynolds number is far too small for a potential flow assumption. Besides, there is a wake behind a swimming fish that is not captured by the dipole model.

In the revised manuscript we have clarified that the entire analysis was not tailored to explore zebrafish larvae motion, which is indeed at a much lower Reynolds number. Furthermore, we have added to the manuscript a comparison of the dipole model with the results from a twodimensional computational fluid dynamics simulation of the flow around a swimming giant danio. Simulation results demonstrate that the dipole model is successful in replicating the global, mean flow features. (See the new Numerical Validation of the Dipole Model subsection, with additional details supplied in Appendix 2.)

- What is the Reynolds number of the channel flows in the experiments? I believe that superposing a constant flow and a parabolic flow is not the best model for these channel flows. Usually, people use some sort of plug flow instead.

The Reynolds numbers for the experiments, which are reported in Appendix 3 Table 1, span a broad range from 10 to 10,000. At the low end of the range, a parabolic velocity profile is expected. At the higher end of the spectrum, the velocity profile is expected to be turbulent, resembling a top hat (plug flow). In both cases, near the channel centerline there will be a degree of shear flow, offering some bias to the animal by which it can appraise the flow environment and distinguish downstream from upstream. This is the only information that we utilize in our model and its local stability analysis to demonstrate the existence of a critical flow speed above which fish will perform rheotaxis. (See added text in the Results section after Equation (4) and in the Methods and Materials section after Equation (22).)

- It is strange to have a mix between a viscous flow for the channel flow and potential flow for the swimmer. What is the rationale for this mix?

We apologize for the lack of clarity and have revised the manuscript to rectify this. We are not modeling the channel flow as purely viscous, as this would necessitate satisfaction of the noslip boundary condition (zero velocity on the walls). By superimposing a parabolic (rotational) perturbation to a uniform (irrotational) mean flow we offer an approximation of a turbulent velocity profile with the modest vorticity needed for fish hydrodynamic sensing. This approximation only employs one parameter to capture curvature of the velocity profile near the channel centerline. (See the added text in the Results section after Equation (4).)

- Eq. (8) describes how the potential flow rotates the dipole. I understand that you consider a sort of dumbbell model, with the dumbbell oriented perpendicular to the swimming direction. But fish are elongated in the longitudinal direction, so it seems strange.

We thank the Reviewer for the comment. There are two dipole models for swimming fish in the literature, the so-called A- and T-dipoles. Our model employs the T-dipole, which is consistent from the standpoint of vortex dynamics for the propagation and orientation of a vortex pair (see Equation (12) and associated discussion in the manuscript). In the A-dipole, in contrast, the fiducial points governing the turning of the dipole are along the swimming direction and thus not coincident with the driving vortices. Whether the A- or T-dipole is a better model for a fish is a subject for debate, which we aim to address through the proposed experiments using robotic fish. We note that one interpretation of the T-dipole is that it treats the fish as a bluff body, which rotates according to a gradient in the pressure drag across the width of its body. This torque is amplified by a mismatch in the hydrodynamic drag experienced by the paired pectoral fins of fish. (See the text added in the Derivation of the Turn Rate Equation for Fish Dynamics subsection after Equation (13).)

- Eq. (9) is not a "rich nonlinear dynamics" as the author state, but simply a linear feedback with the distance from the wall. Most visual models have the same kind of feedback.

We apologize for the overstatement and have revised the terminology in the manuscript.

- The comparison with experimental results is presented in tables. This is not very clear and the reader is left with the impression that most comparisons are inconclusive.

We acknowledge that most data in the literature only provide inconclusive evidence. In the revised manuscript, we have moved the literature review to Appendix 3 to de-emphasize the biological statements. Therein, we also reorganized the text into paragraphs to facilitate the interpretation of existing literature in the context of the proposed model.

[Editors' note: we include below the reviews that the authors received from another journal, along with the authors’ responses.]

Reviewer #1 (Remarks to the Author):

This is an interesting and potentially significant modelling evaluation of the possibility of rheotaxis behaviour in the absence of sensory information. However, several aspects are problematic need to be clearly addressed and/or clarified:

1. In the discussion, the authors quote Lyon (1904): “It is equally absurd to imagine a fish in the Gulf Stream to be stimulated and oriented by a uniform forward motion of the water. Whether orientation be a simple reflex or a conscious process, points of reference – i.e., points relatively at rest – are necessary.” And they go on to say “It is the gradient of the flow that creates hydrodynamic points of reference for a fish to undertake rheotaxis in the dark, even without access to sensory information through the lateral line”. The importance of this flow non-uniformity needs to be more apparent in the summary. It needs to be clearly stated that in uniform flow “points relatively at rest are necessary” but that in non-uniform flow other options may be available.

Thank you for the suggestion. We modified the text accordingly.

2. The summary makes the claim: of ”the existence of a critical flow speed for fish to successfully orient without access to sensory information”. And the introduction expands on this…….”While offering an elegant pathway to explain rheotaxis, the framework of Oteiza et al. does not include a way for rheotaxis to be performed in the absence of information about the local vorticity field. Several experimental studies have shown that fish can perform rheotaxis even when their lateral line is partially or completed ablated, provided that the flow speed is sufficiently large. There are at least 2 problems here.

Firstly, the authors have not adequately examined the biological literature (which I admit is complex). Most (if not all) of the studies in the review they cite, that show rheotaxis in LL- fish apply to fish that are benthic, or maintain contact with the base of walls of the tank, which of itself provides tactile means of maintaining rheotaxis. The rheotaxis thresholds in the Coombs etc. table most likely occur at a threshold for slip detection.

We expanded on the biology literature and commented on the possibility that fish with a compromised lateral line may rely on tactile sensing. However, the claim of the Reviewer that the “rheotaxis thresholds in the Coombs etc. table most likely occur at a threshold for slip detection” is a conjecture, which we find unlikely, since rheotaxis in the absence of visual cues therein is accompanied by periodic cross-section sweeping -- a locomotory pattern also observed in a midwater swimming species, giant danio (Bak-Coleman et al., 2013, JEB 216, 4011-4024) -- which would be difficult to justify through slip detection. Should rheotaxis be a sole outcome of slip detection, the fish would either stay in place or erratically swim in the channel, without exhibiting the regular cross-sweeping motion that is observed.

Through our literature review, we identified a total of eight experiments that explored the role of lateral line in rheotaxis, as shown in Table 1 in the Results section. These experiments were conducted either using blind fish or fish in the dark, such that visual cues were not accessible. We intentionally excluded pleuronectiform flatfishes, including the benthic fish plaice, which were frequently referred to by Coombs et al. (see the Methods Section for the exclusion criteria). Among the identified studies, we found three in support of our model, showing a significant decrease in rheotaxis performance when the lateral line was disabled. The rest were found to be inconclusive, where fish were observed to either receive tactile information or failed to exhibit statistically significant differences in threshold speed. No dataset was found to contradict our model. Through our literature review, we also discovered that the rheotaxis threshold speeds for zebrafish larvae and blind cavefish were larger in thinner channels. If the rheotaxis threshold was solely determined by tactile senses, we should expect the threshold speed to be independent of the channel width.

Secondly, and perhaps more problematic for this manuscript is that the example they use in Figure 1 as their illustration of the problem is in fact a LL+ fish (see Elder, J. and Coombs, S. The influence of turbulence on the sensory basis of rheotaxis. Journal of Comparative Physiology A 201, 667–680 (2015) the start of Figure legend 7 “Figure 7 Behavioral results from a single LL+ fish exposed to the TGS+ condition in the dark at 4 cm/s current speed).

We confirm that we used Figure 7 in which fish have a lateral line. The only purpose of using Figure 7 was to illustrate the concept of cross-sweep motions during rheotaxis. That being said, rheotactic accuracy and index are marginally affected by the presence of the lateral line as evinced by comparing the black curves in Figures 4b and 4d with those in 4a and 4c of the same paper, respectively. We apologize if we have given an incorrect impression and, in agreement with Reviewer 2, we opted for a schematic rather than showing experimental data.

Also, the boundary layer profile, shown in (a) in this figure doesn’t adequately represent the profile for these flow speeds in this tank size, and indeed the example they refer to has a turbulencegenerating structure present.

We reiterate that Figure 1a was intended as a schematic of a fish swimming in a generic channel and 1b as a representative illustration of the phenomenon based on the literature (this was indeed among the very few trajectory data publicly available).

3. How does the model reflect normal fish experiments (flows, gradients, habitats etc)? The use of a non-dimensionalized model may well be fully appropriate, but does make relevant comparisons between behavioural experiments and the model non-trivial. Without a more detailed description of how the model equates to observed behaviour, it is difficult to agree with the discussion statement “In agreement with experimental observations, we uncovered an equilibrium at the channel centerline for upstream swimming whose stability is controlled by a single nondimensional parameter that summarizes flow speed, flow gradient, lateral line feedback, fish size, and channel width. Above a critical value of this parameter, rheotaxis is stable and fish will begin periodic cross-stream sweeping movements whose amplitude can be as large as the channel width.” This is particularly so as the comparisons are again referenced to rheotaxis thresholds that are thought to be a result of edge contract and slip detection. Without further justification and biologically relevant validation of the model I am unable to agree with the conclusions stated in this paper. So in summary, I think the model is potentially interesting, but given the concerns raised above do not think that it takes us beyond the Oteiza et al. “elegant hydrodynamic mechanism for fish to actively perform rheotaxis”, and the currently understood complexity of multisensory contributions, including vision, lateral line, tactile, and vestibular sensing.

Thank you for the detailed feedback. In addition to reporting our main claim in nondimensional form, we included results in dimensional form along with a detailed comparison with specific biology literature. In the Results section, we explicitly expressed the fish rheotaxis threshold speed as a function of its lateral line feedback, flow gradient, swimming domain size, and fish body length. At the time of the initial submission, we focused the presentation on the model development more than its biological value. We improved the biological relevance of our study and performed an extensive bibliographical survey that resulted in a database of experimental results that help validate our claims and better frame them in the biology literature on multisensory orientation. For example, the collected data indicate that the rheotactic threshold increases with the size of the fish and decreases with the curvature of the flow and the ablation of the lateral line: all these results are in agreement with our theory. To address the concern raised by the Reviewer on the reference to benthic fishes that depend on tactile senses to perform rheotaxis, in these tables we excluded studies where the subjects were benthic flatfish and considered “inconclusive” studies in which tactile cues were available.

Reviewer #2 (Remarks to the Author):

Porfiri and Peterson describe a mathematical model of rheotaxis in swimming animals. Their calculations suggest that fish may orient swimming against flow through an interaction between the self-generated dipole flow field from swimming and spatial gradients in the free stream flow.

I found this paper difficult to follow and I therefore do not understand the reasoning that underlies their authors’ arguments that they have resolved a centuries-long mystery about rheotaxis. I have itemized some of the instances were the authors have failed to define key terms, did not offer a justification for their decisions for the model design, and did not offer a clear basis for their statements of findings. Someone with a fluid dynamics background who is familiar with related models could probably decode the meaning of this study from the equations alone, but the broad readership of this journal requires a more clear explanation.

We apologize for not having made the model more readily digestible to a broad readership. We revised the language to improve readability for people outside fluid dynamics and dynamical systems.

Specific Comments

L30 – Hair cells do not “comprise” the lateral line system. They are essential components, but the lateral line includes other features (e.g. neuromast cupulae and afferent and efferent neurons).

Thank you for the suggestion. We clarified the text accordingly.

L54 – “different answers” — Different from what?

We deleted the confusing statement.

L55-63 – It is not clear to me what specific intent there is that motivates this modeling. A statement of a hypothesis, question, or aim would help.

The proposed model aims to unveil the implications of a fish being an invasive sensor that actively augments the background flow and responds to it. We clarified throughout the manuscript its objective.

L81 – Please explain on what basis the wall may be modeled by the mirror image of the fish. It might help to include streamlines (perhaps in gray) for the mirror-image fish in Figure 2.

The method of images is a classical method of treating walls in potential flows; we added a reference to the text in the Results section.

Please explain where the boundary layer flow depicted in Figure 1a is designed by the equations.

We clarified this in the caption of Figure 1.

L112 – Please explain the purpose of equations 6a and 6b.

We amended the text to improve its clarity.

L115 – I am not sure that I follow the logic here. I would expect greater resistance to swimming in the center of the channel.

We clarified the physical explanation behind equation 7. We note that the expression does not represent "drag" on the fish in the traditional sense of viscous flows, which would depend on the relative speed of the fish with respect to the background; rather, it is a non-viscous effect from the interaction with the walls.

L118+ – Please explain the meaning of “Hydrodynamic turn rate is incorporated...” What is HTR? What is it incorporated into?

We have added explanation for this at the beginning of the subsection, as detailed in our reply above.

L122 – On what basis? Through an algorithm of motor control, or by passive dynamics?

This is entirely passive hydrodynamics. In this sentence, we have changed “rotate” to “be rotated” to emphasize it is passive dynamics.

L128 – Please define “hydrodynamic feedback”

We added a definition to the sentence.

L132 – Please give the justification for these calculations.

We added justifications for the need to linearize dynamics in the study of stability.

L137 – Please use words to explain the meaning of “the right hand side of (6)”.

We added text.

L192 – I am not sure I agree that the present model resolves this dilemma: doesn’t the model assume boundary layer flow, instead of the laminar flow referred to in the quote? I also don’t follow the meaning of “hydrodynamic points of reference”.

The model does not assume boundary layer flow: we have a uniform (potential) flow with zero boundary layer thickness on which we superimpose a small spatial gradient to the mean flow that is reminiscent of a “laminar flow”. We reworded the text pertaining to hydrodynamic points of reference explaining that these are regions with distinctive flow features from the background.

Figure 1b – I do not think it is necessary to publish a figure from another study here, particularly because that data is not presently used.

We agree with the Reviewer and have replaced the figure with a schematic, which also addresses the concerns of Reviewer 1.

Reviewer #3 (Remarks to the Author):

Key results: The authors devise a mathematical model that explains key features observed in a common behavior in fishes, the ability to orient into a current (rheotaxis). Their demonstration that active manipulation of the fluid, through coupled Fluid-Structure Interactions, can overcome sensory deprivation is novel and of broad interest.

Validity: The major flaw as I see it is in a misrepresentation, albeit not intentional, of the biological literature. The basis for their systems dynamics explaining the “puzzling aspect” of rheotaxis, the need for a critical flow speed in order for rheotaxis to operate absent of sensory stimuli, is based ultimately on one paper, included in their cited review but tracked down here as Bak-Coleman et al. JEB 2013. In Bak-Coleman’s paper, fish had a block of the lateral line, but not of other sensory modalities that can contribute to rheotaxis. Most importantly, the vestibular system in the inner ear can sense changes in body acceleration, which would certainly be the case if the onset of faster flow would case the animal to surge backwards. This would elicit a compensatory movement forward, temporarily or otherwise (it is hard to tell because this level of experiment is difficult to achieve). At the very least, the authors would need to revise their statement on how their model can account for upstream movement, not in the absence of all sensory stimuli, but only in the absence of lateral line stimuli. This distinction is made in line 198, but missing in other sections, misleading the reader to think that fish can perform rheotaxis in the absence of ANY sensory cues (line 15, 27). This sets up a strawman hypothesis. The authors should acknowledge the contribution of the vestibular system, potential auditory cues that accompany faster flows, and the presence of pressure sensors along the skin and fins of fishes. This would take the form of dorsal root ganglion cells and Rohon Beard cells, as well as sensory afferents in the fins, as documented by Melina Hale’s group. Currently, there is no biological experiment where all stimuli from rheotaxis can be abolished.

We apologize for the unintentionally misleading statements that could send mixed messages to the reader regarding the mechanisms underlying rheotaxis. We carefully revised the text and amended the Results and Discussion sections to clarify the possible involvement of other sensory cues in rheotaxis, including vision, vestibular system, and pressure sensing afferents in the fins.

That being said, the authors have demonstrated a unique contribution of bi-directional coupling to ease the need for sensory inputs. I am just doubtful that it has the relevance they propose for real biological systems. I would be more excited about their contributed if they limited it to a purely theoretical paper. Additionally, their claim that the onset of another behavior, crossstream sweeping movements, is not an inherent part of the rheotactic response as they proclaim. This could be an exploratory behavior observed in the one study they cite (and could be a speciesdependent behavior), but the long history of rheotaxis work does not include this as part of this innate behavior, which is simply the orientation of the fish upstream in the presence of a current. I found the writing vague and over-stepping at points.

Thank you for the excellent suggestion. We emphasized the paper contribution as a theoretical investigation of the effect of bidirectional coupling between fish and the surrounding flow, apt at demonstrating the potential consequences of constraining a fish in a water channel to study the principles of rheotaxis. At the same time and compatibly with the requests of the other Reviewers, we focused the writing to avoid overstepping and reinforced the biological framing of the paper. We acknowledge the Reviewer’s comment that cross-stream sweeping is not an inherent locomotory pattern of rheotaxis, and we have revised the text to indicate that this behavior has only been observed in some fish species (for example, cavefish and giant danio). We believe that now the paper makes a compelling case for an overlooked phenomenon that has never been studied (bidirectional interactions), irrespective of the senses that fish may use during orientation.

Originality and significance: The conclusion that Fluid Structure Interactions can obviate the need for sensory inputs is original and very interesting. However, the claim that the behavior of the real animal occurs in the absence of all sensory stimuli is not well-supported, and thus the house of cards crumbles and the interest level to the field wanes.

By refocusing the paper on the bidirectional coupling as the Reviewer suggests, we believe this concern has been addressed. Whether a fish uses none, one, or multiple senses, bidirectional interactions with the surrounding fluid flow remain: our paper demonstrates the consequences of this coupling. As detailed in our reply to your first comment, we amended the Results and Discussion sections to comment on the potential influence of other sensory modalities, including vision, vestibular system, and tactile sensors on the fish body surface.

Data and methodology: The model itself seems appropriate, that hydrodynamic feedback is related to the local circulation around a fish. Small assumptions that could lead to biologically disparate results include (1) a linear hydrodynamic feedback mechanism and (2) neglecting the inertia of the fish (fish cannot respond instantaneously to changes in fluid flow).

We added a paragraph in the Discussion section to acknowledge the main limitations of the model, including those you have identified.

Appropriate use of statistics and treatment of uncertainties: No statistical tests were conducted. Inclusion of a statistical treatment of the occurrence of the cross-stream behavior (from the original biological paper) modeled in Figure 1 would be especially useful.

Based on feedback from other Reviewers, we replaced Figure 1b with a schematic. In this revision, we conducted an extensive literature review and collated a table of experimental results that help validate our claims and frame them in the context of other sensory modalities. We identified several datasets indicating that the rheotactic performance decreases with the ablation of the lateral line and that the rheotaxis threshold decreases with the curvature of the flow and width of the channel -- all in agreement with our theory.

Conclusions: The model itself is of interest, but its relevance to the biological example selected is problematic. This is discussed elsewhere in this review, but an example of over-stating the problem is found in line 189 in Lyon’s quote. Reference points could be visual, magnetic or hydrodynamic (not just hydrodynamic). Again, in line 218 the authors describe a “counter-intuitive” conclusion of active manipulation, but this has long been discovered for the lateral line wallfollowing abilities of the blind cavefish.

Not only did we reinforce the biological basis, but also we refocused the work on the fundamental problem of bidirectional coupling as you suggested. We amended the text following the quotation of Lyon to resolve the over-statement by pointing out possible points of references.

Suggested improvements: I would suggest that the premise of the manuscript be altered to de-emphasize the biological relevance of the work. The argument that fish can orient upstream without the contribution of sensory information is built on shaky ground. My advice would be to re-orient the paper to ask how the model eases the task of sensory computation, rather than proposing a purely physical method of rheotaxis inherent in Fluid-Structure Interactions. Furthermore, a clearer distinction should be made on how this work builds on slender body theory of Lighthill and Taylor. The distinction from Oteiza’s work, which requires flow gradient from walls to make left-right comparisons, could be clearer (particularly Equation 7, line 115—the “retarding effect of the wall”).

We are deeply appreciative of the suggestion, which we have followed (compatibly with the requests by the other Reviewers), along with providing more details on the model. We emphasize that the current minimal model is built upon the finite-dipole framework, which does not rely on the slender body assumption.

References: Line 38—Several experiments are cited as evidence that rheotaxis occurs in the absence of lateral line information—this is a review paper that specifically demonstrates that rheotaxis is a multi-modal behavior, so ablation of one sensory modality is not sufficient to guarantee that rheotaxis can occur in the absence of sensory inputs. Several biological references should be included along the ones from Coombs—among them the authors Montgomery, Windsor, McHenry, Van Netten ,Chagnaud, Bleckmann, Hale, Liao, Trapani, Hudspeth, Kindt and Raible—each of these authors develops work on the lateral line or other relevant sensory modality that would influence these authors and their understanding of how the lateral line and other senses can be effectively ablated.

We strengthened the biological relevance of the work through an extensive literature review, as detailed in the Results and Methods Section. We identified several studies that demonstrated the role of lateral line in the absence of visual and tactile senses, as summarized in Table 1.

Treating the fish as an “invasive” sensor is an important approach, and I agree to the importance of this addition (line 48), but I found line 58 and 61 vague in terms of what this current manuscript offers. Some specificity would be useful here.

The proposed model unveils the crucial role of bidirectional coupling between fish and the surrounding fluid in rheotaxis, which has been overlooked in existing experimental and theoretical frameworks for the study of fish rheotaxis. We clarified the contribution of the manuscript in the Abstract and Discussion sections of the revised manuscript.

Clarity and context: The abstract, Intro and Discussion is largely accessible, but over-reaches. The manuscript is one where a good deal of theoretical work has been done that supports some observations during biological rheotaxis, of which there could be more parsimonious reasons other than the one the authors champion.

Thank you for the comment. We believe that addressing the comments above has provided a clearer focus for the proposed model, along with a stronger biological context upon which claims can be drawn.

Response to the second round of review

Reviewer #1 (Remarks to the Author):

As stated in my original review “This is an interesting and potentially significant modelling evaluation of the possibility of rheotaxis behaviour in the absence of sensory information. However, several aspects are problematic need to be clearly addressed and/or clarified”. In my view the author’s rebuttal does not address these issues and in some respects exacerbates them.

So I still disagree with the some of the fundamental claims of this manuscript:

The abstract states: “we make an essential step to elucidate the hydrodynamic underpinnings of rheotaxis” Whereas, in my view, the manuscript does not elucidated the hydrodynamics of rheotaxis per se, – but shows the theoretical possibility of bidirectional coupling as a possible orientation mechanism under conditions of no sensory input. It is clear from the modelling, that “a fish as an invasive sensor” may theoretically face upstream and move from in a sweeping motion. But the biological arguments to support the statement that fish, in fact, do this are flawed.

The abstract further states that their proposal “captures many of the puzzling aspects of rheotaxis, from the existence of a critical flow speed for fish to successfully orient, to the onset of crossstream sweeping movements while swimming against the flow observed in some fish species”

The statement below quoted from Bak-Colman et al. 2013 contradicts this. The sweeping movements cease with lateral line deprivation. “When deprived of vision, fish move further upstream, but the angular accuracy of the upstream heading is reduced. In addition, visually deprived fish exhibit left/right sweeping movements near the upstream barrier at low flow speeds. Sweeping movements are abolished when these fish are additionally deprived of lateral line information.” [Bak-Coleman, J., Court, A., Paley, D. A., and Coombs, S. (2013). The spatiotemporal dynamics of rheotactic behavior depends on flow speed and available sensory information. Journal of Experimental Biology, 216(21), 4011-4024.]

Furthermore, If you look at the V-/T- (bottom panel) of their Figure 10, Elder and Coombs show that cross-stream sweeping movements occur in LL+ fish in the centre of the test space – but with LL- fish the cross-stream movements occur at the inlet side of the space corresponding with the statement above and probably mediated by tactile sensing. “In particular, fish without visual cues exhibited cross-stream sweeping behaviors similar to those observed in visually-deprived giant danio (Devario aequipinnatus) (Bak-Coleman et al. 2013). This sweeping behavior could represent an active, compensatory strategy for, e.g., trying to make tactile contact with an upstream object to maintain position, or it could represent a passive loss in the ability to hold cross-stream position.” [Elder, J., and Coombs, S. (2015). The influence of turbulence on the sensory basis of rheotaxis. Journal of comparative physiology A, 201(7), 667-680.]

So my view remains that this paper is an interesting modelling illustration of potential ‘invasive sensing’, but that it falls short of demonstrating that the biological evidence supports the case that fish actually do this. In a general sense, understanding animal orientation requires a physically plausible mechanism, but requires behavioural demonstration of the actual use of this in a biologically relevant way. The paper would be better framed to state the case for this possibility and layout the behavioural tests that would demonstrate (or not) its biological relevance.

Before explaining for the sake of an intellectual argument the reason why we believe the statements are flawed, let us acknowledge that in this revision we have further deemphasized statements on cross-sweeping movements, a phenomenon that is quite secondary to our main claims. Practically, the whole reference to this behavior is in a paragraph in the Discussion. Also, we have added text to inform new experimental research at the interface between biology and robotics.

Reviewer 1 is, in our view, cherry-picking statements without correctly connecting them to our model. The evidence they point to does not detract from the model, but rather it reinforces its predictive value. Let us start with the 2013 paper by Coombs and colleagues. The fact that abolishing the lateral line causes the experimental animals to lower cross-sweeping movements is in agreement with our model and not in contradiction. In fact, if you look at Figure 3a in our paper, the locations of the two equilibria with non-zero heading is varying with β/β^*. The better the animal performs rheotaxis (β/β^* >>1), the closer the points are to the walls, thereby affording wider sweeps. For animals that have worse rheotaxis performance, β/β^* ~1 so that the two unstable equilibria will be closer to the origin and cross-sweeping movements will be reduced.

Moving to the 2015 paper by Elder and Coombs, the Reviewer is using the bottom panels of Figure 10 from this 2015 paper (V-/T-/LL+ with V-/T-/LL-) to argue that tactile sensing is the dominant mechanism underlying cross-sweeping movements for subjects with a compromised lateral line.

The circumstantial argument is based on the fact that the heat maps suggest that at high speed there is a tendency of fish with a compromised lateral line to swim more toward the inlet (right hand side). Such an argument has several flaws. First, the animals do not maintain continuous contact with the inlet and it is difficult from the heat maps to objectively argue about even a preference for the inlet. In fact, experiments in the 2013 paper above that detail the stream-wise position of animals for different flow conditions do not point at any difference in spatial preference along the flow direction. Figure 10 from the 2013 paper, shows that animals in the dark (black lines) do not change their streamwise position if their lateral line is compromised (right versus left) for any flow speed (zero, low, and high from top to bottom).

Second, the cross-stream position of these fish is closer the mid-section than those with intact lateral line, in agreement with our predictions (see the point above on the 2013 paper) that the range of cross-stream sweeps becomes wider for larger value of β/β*, that is, for as for increasing feedback from the lateral line. This evidence is even made clearer in Figure 8b from the same 2015 paper, which shows that V-/T-/LL+ has less crosstream positional variability than V-/T-/LL-. Finally, the companion figure, Figure 8a, shows other two key pieces of information that reinforce the idea that hydrodynamic coupling is a viable mechanism for cross-stream movements for animals deprived of vision: sweeps are periodic and their oscillation frequency increases with the flow speed, all in agreement with our model. The last point is explicitly reinforced by the claim made by the authors in the text: "there is a clear emergence of sweep behavior at flow speeds above 2 cm/s.… irrespective of the TGS condition or availability of lateral line information."

Hence, not only does this Reviewer fail to offer compelling evidence to dispute the model (all the presented evidence is in fact supporting our model), but also they focus all of their destructive efforts on a secondary element of the model, which we explicitly acknowledge as a topic that has yet to gather thorough and conclusive empirical observations (L312). We have constructed the entire validation effort on the rheotaxis threshold, for which we have inspected 300-400 papers and created a valuable dataset that can be used for validation. We do not fully understand the frustration of the Reviewer and their perceived hostility, maybe the root cause is our original reply to their comment #2 where we used an excessively forceful language, for which we apologize: "the claim of the Reviewer that the “rheotaxis thresholds in the Coombs etc. table most likely occur at a threshold for slip detection” is a conjecture. " Likely, this reply prompted such a passionate and rushed review of our work, which does not contain any of the manuscript beyond page 2.

Other comments:

L 32 Do fish sense the flow and actively perform rheotaxis accordingly, or can rheotaxis be achieved passively? Biology often demonstrates redundancy so the answer to the above question is not an either/or.

We reworded the text accordingly.

L38 Several modern studies have unveiled the critical role of the lateral line system, an array of mechanosensory receptors located on the surface of fish body, in their ability to orient against a current hinting at a hydrodynamics-based rheotactic mechanism that has not been fully elucidated. I think that this is an interesting point – that adds significantly to the Oteiza et al.

approach.

We agree that this is a key point of novelty and we have edited the text to make it clearer.

Reviewer #2 (Remarks to the Author):

My concerns about this manuscript have been addressed by this revision by the authors.

Reviewer #4 (Remarks to the Author):

To investigate the fish orientation against a flow is a very interesting topic. We have noticed there are some recent studies combining hydrodynamics and biosensors. In a tube flow, it is shown that the rheotaxis behavior of fish is a significant phenomenon. In the present manuscript, the authors tried to illustrate that the rheotaxis exits even without a perceptual system, using a simple hydrodynamic model. This model introduced a bidirectional coupling between the motion of the fish (a dipole-like model) and the flow physics in its surroundings (walls and shearing flow). According to the stability analysis of this dynamic system, they found the critical speed and stability threshold reported in previous studies, and the cross-stream sweeping movements while swimming against the flow. This dynamic process can be independent of the feedback mechanism (based on the circulation measurement through the lateral line), which is a periodic solution. That means, the fish swimming against the flow in a tube is a hydrodynamic behavior, which will help the fish with weak or damaged biosensors swim in a specified tube.

Some suggestions are listed as follows,

Modify the title, including the keywords “tube” and “shear flow”.

We changed the title accordingly.

As a widely accepted conclusion, the rheotaxis behavior is the result of fish’s control by relying on the feedback of various sensors (vision, vestibular system, tactile sensors, lateral line system, etc.). The authors proposed a specific swimming scene that can reduce the dependence on sensors. It is necessary to rewrite the introduction, which will help the readers to understand the relationship between hydrodynamics and biology.

We edited the introduction to clarify the specific conditions we are focusing on.

About the invasive sensor, there is a lack of definition and deep discussion.

We added context throughout.

https://doi.org/10.7554/eLife.75225.sa2

Article and author information

Author details

Maurizio Porfiri
1. Department of Biomedical Engineering, New York University, New York, United States
2. Department of Mechanical and Aerospace Engineering, New York University, New York, United States
3. Center for Urban Science and Progress, New York University Tandon School of Engineering, New York, United States
Contribution
Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, M.P. conceived the study, developed the theoretical model and performed data analysis, wrote a first draft of the manuscript, which was consolidated in its present form by all the authors., Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing

For correspondence
mporfiri@nyu.edu

Competing interests
No competing interests declared

"This ORCID iD identifies the author of this article:" 0000-0002-1480-3539
Peng Zhang
1. Department of Mechanical and Aerospace Engineering, New York University, New York, United States
2. Center for Urban Science and Progress, New York University Tandon School of Engineering, New York, United States
Contribution
Data curation, Investigation, Methodology, P.Z. conducted the literature review and performed the model validation. The manuscript was consolidated in its present form by all the authors., Validation, Writing – original draft

Competing interests
No competing interests declared

"This ORCID iD identifies the author of this article:" 0000-0001-8237-1259
Sean D Peterson

Mechanical and Mechatronics Engineering Department, University of Waterloo, Waterloo, Canada

Contribution
Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, S.D.P. conceived the study, developed the theoretical model and performed data analysis, wrote a first draft of the manuscript, which was consolidated in its present form by all the authors., Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing

For correspondence
peterson@uwaterloo.ca

Competing interests
No competing interests declared

"This ORCID iD identifies the author of this article:" 0000-0001-8746-2491

Funding

National Science Foundation (CMMI-1901697)

Maurizio Porfiri

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

The authors acknowledge financial support from the National Science Foundation under Grant No. CMMI-1901697. The authors acknowledge Alain Boldini and Simone Macrì for useful discussions.

Senior Editor

Aleksandra M Walczak, CNRS LPENS, France

Reviewing Editor

Agnese Seminara, University of Genoa, Italy

Version history

Received: November 3, 2021
Preprint posted: November 12, 2021 (view preprint)
Accepted: May 31, 2022
Accepted Manuscript published: June 6, 2022 (version 1)
Version of Record published: July 18, 2022 (version 2)

Copyright

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.