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Social behaviors are essential for survival and reproduction and vary within and among species. We integrate single nucleus RNA-sequencing (snRNA-seq), comparative genomics, and automated behavior analysis to investigate a recently-evolved social “bower building” behavior in Lake Malawi cichlid fishes. We functionally profile telencephalic nuclei matched to 38 paired behaving/control individuals. Our data suggest bower behavior has evolved in part through divergence in a gene module selectively expressed in a subpopulation of glia lining the pallium. Downregulation of the module is associated with glial departure from quiescence and rebalancing of neuronal subpopulation proportions in the putative homologue of the hippocampus. We show further evidence that behavior-associated excitation of neuronal populations that project to the putative hippocampus mediate glial function and rebalancing. Our work suggests that bower behavior has evolved through changes in glia and region-specific neurogenesis, and more broadly shows how snRNA-seq can generate insight into uncharted behaviors and species.

In the wild, behaviors are often expressed over long time periods in complex and dynamic environments, and many behaviors include direct interaction with the environment itself. However, measuring behavior in naturalistic settings is difficult, and this has limited progress in understanding the mechanisms underlying many naturally evolved behaviors that are critical for survival and reproduction. Here we describe an automated system for measuring long-term bower construction behaviors in Lake Malawi cichlid fishes, in which males use their mouths to sculpt sand into large species-specific structures for courtship and mating. We integrate two orthogonal methods, depth sensing and action recognition, to simultaneously track the developing bower structure and the thousands of individual sand manipulation behaviors performed throughout construction. By registering these two data streams, we show that behaviors can be topographically mapped onto a dynamic 3D sand surface through time. The system runs reliably in multiple species, across many aquariums simultaneously, and for up to weeks at a time. Using this system, we show strong differences in construction behavior and bower form that reflect species differences in nature, and we gain new insights into spatial, temporal, social dimensions of bower construction, feeding, and quivering behaviors. Taken together, our work highlights how low-cost tools can automatically quantify behavior in naturalistic and social environments over long timescales in the lab.

Encountering and adaptively responding to unfamiliar or novel stimuli is a fundamental challenge facing animals and is linked to fitness. Behavioural responses to novel stimuli can differ strongly between closely related species; however, the ecological and evolutionary factors underlying these differences are not well understood, in part because most comparative investigations have focused on only two species. In this study, we investigate behavioural responses to novel environments, or exploratory behaviours, sampling from a total of 20 species in a previously untested vertebrate system, Lake Malawi cichlid fishes, which comprises hundreds of phenotypically diverse species that have diverged in the past one million years. We show generally conserved behavioural response patterns to different types of environmental stimuli in Lake Malawi cichlids, spanning multiple assays and paralleling other teleost and rodent lineages. Next, we demonstrate that more specific dimensions of exploratory behaviour vary strongly among Lake Malawi cichlids, and that a large proportion of this variation is explained by species differences. We further show that species differences in open field behaviours are explained by microhabitat and by a major evolutionary split between the mbuna and benthic/utaka radiations in Lake Malawi. Lastly, we track some individuals across a subset of behavioural assays and show that patterns of behavioural covariation across contexts are characteristic of modular complex traits. Taken together, our results tie ecology and evolution to natural behavioural variation, and highlight Lake Malawi cichlids as a powerful system for understanding the biological basis of exploratory behaviours.

Lake Malawi cichlid fishes exhibit extensive divergence in form and function built from a relatively small number of genetic changes. We compared the genomes of rock- and sand-dwelling species and asked which genetic variants differed among the groups. We found that 96% of differentiated variants reside in non-coding sequence but these non-coding diverged variants are evolutionarily conserved. Genome regions near differentiated variants are enriched for craniofacial, neural and behavioral categories. Following leads from genome sequence, we used rock- vs. sand-species and their hybrids to (i) delineate the push–pull roles of BMP signaling and irx1b in the specification of forebrain territories during gastrulation and (ii) reveal striking context-dependent brain gene expression during adult social behavior. Our results demonstrate how divergent genome sequences can predict differences in key evolutionary traits. We highlight the promise of evolutionary reverse genetics—the inference of phenotypic divergence from unbiased genome sequencing and then empirical validation in natural populations.

Lake Malawi cichlid fishes exhibit extensive divergence in form and function among closely related species separated by a relatively small number of genetic changes. During the past million years, hundreds of species have diversified along an ecological axis in rock vs. sand habitats. We compared the genomes of rock- and sand-dwelling species and asked which genetic variants in which genes differed among the groups. We found that 96% of differentiated variants reside in non-coding sequence but these non-coding diverged variants are evolutionarily conserved. The majority of divergent coding variants are missense and/or loss of function. Regions near differentiated variants are enriched for craniofacial, neural and behavioral functional categories. To follow up experimentally, we used rock- vs. sand-species and their hybrids to (i) clarify the push-pull roles of BMP signaling andirx1bin the specification of forebrain territories during gastrulation and (ii) reveal striking context-dependent brain gene expression during adult social behavior. Our results suggest compelling ties between early brain development and adult behavior and highlight the promise of evolutionary reverse genetics – the identification of functional variants from genome sequencing in natural populations.

Summary Many behaviors that are critical for survival and reproduction are expressed over extended time periods. The ability to inexpensively record and store large volumes of video data creates new opportunities to understand the biological basis of these behaviors and simultaneously creates a need for tools that can automatically quantify behaviors from large video datasets. Here, we demonstrate that 3D Residual Networks can be used to classify an array of complex behaviors in Lake Malawi cichlid fishes. We first apply pixel-based hidden Markov modeling combined with density-based spatiotemporal clustering to identify sand disturbance events. After this, a 3D ResNet, trained on 11,000 manually annotated video clips, accurately (>76%) classifies the sand disturbance events into 10 fish behavior categories, distinguishing between spitting, scooping, fin swipes, and spawning. Furthermore, animal intent can be determined from these clips, as spits and scoops performed during bower construction are classified independently from those during feeding., Graphical Abstract, Highlights • A dataset of more than 14,000 annotated animal behavior videos was created • 3D residual networks can be used to classify animal behavior • Different intents of similar behavioral actions can be distinguished • A working solution to study long-term behaviors was established, Piscine Behavior; Zoology; Computer Science; Artificial Intelligence

Measuring naturalistic behaviors in laboratory settings is difficult, and this hinders progress in understanding decision-making in response to ecologically-relevant stimuli. In the wild, many animals manipulate their environment to create architectural constructions, which represent a type of extended phenotype affecting survival and/or reproduction, and these behaviors are excellent models of goal-directed decision-making. Here, we describe an automated system for measuring bower construction in Lake Malawi cichlid fishes, whereby males construct sand structures to attract mates through the accumulated actions of thousands of individual sand manipulation decisions over the course of many days. The system integrates two orthogonal methods, depth sensing and action recognition, to simultaneously measure the developing bower structure and classify the sand manipulation decisions through which it is constructed. We show that action recognition accurately (>85%) classifies ten sand manipulation behaviors across three different species and distinguishes between scooping and spitting events that occur during bower construction versus feeding. Registration of depth and video data streams enables topographical mapping of these behaviors onto a dynamic 3D sand surface. The hardware required for this setup is inexpensive (

Encountering and adaptively responding to unfamiliar or novel stimuli is a fundamental challenge facing animals and is linked to fitness. Behavioral responses to novel stimuli, or exploratory behavior, can differ strongly between closely related species; however, the ecological and evolutionary factors underlying these differences are not well understood, in part because most comparative investigations have focused on only two species. In this study, we investigate exploratory behavior across 23 species in a previously untested vertebrate system, Lake Malawi cichlid fishes, which comprises hundreds of phenotypically diverse species that have diverged in the past one million years. We investigate behavioral variation across species, across microhabitats, and across environmental contexts. We find strong species differences in behavior that are associated with microhabitat, demonstrate that intermediate microhabitats are associated with higher levels of exploratory behavior, show that patterns of behavioral covariation across contexts are characteristic of modular complex traits, and contrast Malawi cichlid data with behavioral data from selectively bred high-and low-exploratory zebrafish. Taken together, our results tie ecology to species differences in behavior, and highlight Lake Malawi cichlids as a powerful system for understanding the evolution, ecology, and biology of natural behavioral variation.HighlightsMalawi cichlids exhibit high phenotypic variance in exploratory behaviorsSpecies differences in exploratory behavior are explained by microhabitatRock-dwelling species exhibit strong edge preferences across assaysIntermediate habitats are associated with “high exploratory” open field behaviorPatterns of behavioral covariance across contexts are modular in Malawi cichlids

The telencephalon is the most complex brain region, controlling communication, emotion, movement and memory. Its adult derivatives develop from the dorsal pallium and ventral subpallium. Despite knowledge of genes required in these territories, we do not understand how evolution has shaped telencephalon diversity. Here, using rock- and sand-dwelling cichlid fishes from Lake Malawi, we demonstrate that differences in strength and timing of opposing Hedgehog and Wingless signals establish evolutionary divergence in dorsal-ventral telencephalon patterning. Rock dwellers exhibit early, extensive Hedgehog activity in the ventral forebrain resulting in expression of foxg1 before dorsal Wingless signals, and a larger subpallium. Sand dwellers show rapid deployment of Wingless, later foxg1 expression and a larger pallium. Manipulation of the Hedgehog and Wingless pathways in cichlid and zebrafish embryos is sufficient to mimic differences between rock- versus sand-dweller brains. Our data suggest that competing ventral Hedgehog and dorsal Wingless signals mediate evolutionary diversification of the telencephalon.

The shape of teeth occupies a central position in various biological disciplines, from paleo-ecology to molecular biology to cosmetic and reconstructive dentistry. Despite a long tradition of study in mammals, important questions remain regarding the genetic and developmental basis of differences in tooth shape. Here, we use natural mutants of cichlid fish from East Africa, which exhibit tremendous dental diversity, to help fill the gaps in our understanding of vertebrate odontogenesis. We employ an expanded genetic linkage map to demonstrate that cusp number segregates as a gene of major effect, which explains approximately 40% of the phenotypic variance, on cichlid chromosome 5. Furthermore, we examine patterns of Bmp4 expression in early odontogenesis to address and refine predictions of models linking tooth shape and tooth number. Mutations in the Bmp4 cistron do not control tooth shape in this mapping cross. Our data suggest that the evolution of novelty in the cichlid dentition is galvanized by a small number of genetic changes, echoing similar conclusions from recent studies of other vertebrate adaptive morphologies.

Background Lake Malawi cichlids represent one of a growing number of vertebrate models used to uncover the genetic and developmental basis of trait diversity. Rapid evolutionary radiation has resulted in species that share similar genomes but differ markedly in phenotypes including brains and behavior, nuptial coloration and the craniofacial skeleton. Research has begun to identify the genes, as well as the molecular and developmental pathways that underlie trait divergence. Results We assemble a compendium of gene expression for Lake Malawi cichlids, across pharyngula (the phylotypic stage) and larval stages of development, encompassing hundreds of gene transcripts. We chart patterns of expression in Bone morphogenetic protein (BMP), Fibroblast growth factor (FGF), Hedgehog (Hh), Notch and Wingless (Wnt) signaling pathways, as well as genes involved in neurogenesis, calcium and endocrine signaling, stem cell biology, and numerous homeobox (Hox) factors—in three planes using whole-mount in situ hybridization. Because of low sequence divergence across the Malawi cichlid assemblage, the probes we employ are broadly applicable in hundreds of species. We tabulate gene expression across general tissue domains, and highlight examples of unexpected expression patterns. Conclusions On the heels of recently published genomes, this compendium of developmental gene expression in Lake Malawi cichlids provides a valuable resource for those interested in the relationship between evolution and development.