Renn SCP, Machado HE, Duftner N, Sessa AK, Harris RM, Hofmann HA. Gene expression signatures of mating system evolution. Genome [Internet]. Publisher's VersionAbstract

The diversity of mating systems among animals is astounding. Importantly, similar mating systems have evolved even across distantly related taxa. However, our understanding of the mechanisms underlying these convergently evolved phenotypes is limited. Here, we examine on a genomic scale the neuromolecular basis of social organization in Ectodini cichlids from Lake Tanganyika. Using field collected males and females of four closely related species representing two independent evolutionary transitions from polygyny to monogamy, we take a comparative transcriptomic approach to test the hypothesis that these independent transitions have recruited similar gene sets. Our results demonstrate that while lineage and species exert a strong influence on neural gene expression profiles, social phenotype can also drive gene expression evolution. Specifically, 331 genes (~6% of those assayed) were associated with monogamous mating systems independent of species or sex. Among these genes, we find a strong bias (4:1 ratio) toward genes with increased expression in monogamous individuals. A highly conserved nonapeptide system known to be involved in the regulation of social behavior across animals was not associated with mating system in our analysis. Overall, our findings suggest deep molecular homologies underlying the convergent or parallel evolution of monogamy in different lineages of Ectodini cichlids.

Goldsby HJ, Young RL, Hofmann HA, Hintze A. Increasing the complexity of solutions produced by an evolutionary developmental system., in Genetic and Evolutionary Computation Conference (GECCO). Berlin (Germany) ; :57-58.Abstract

Evolutionary computation and neuroevolution seek to create systems of ever increasing sophistication, such that the digitally evolved forms reflect the variety, diversity, and complexity seen within nature in living organisms. In general, most evolutionary computation and neuroevolution techniques do so by encoding the final form without any type of development. This is in contrast to nature, where most complex organisms go through a developmental period. Here we focus on an evolving digital tissues that develop from a single cell and unfold into a complex body plan. It quickly became evident that evolving developing forms is quite challenging. We compare four different techniques that have successfully been employed within evolutionary computation to evolve complex forms and behavior: scaffolding (i.e., gradually increasing the difficulty of the task rewarded by the environment over evolutionary time), stepping stones (i.e., rewarding easier tasks within an environment that can co-opted for the performance of more complex tasks), and island models (i.e., rewarding different fitness functions within different subpopulations with migration). We show the effect of these methods on the evolution of complex forms that develop from a single cell, the rate of adaptation, and different dimensions of robustness and variation among solutions.

Baker MR, Hofmann HA, Wong RY. Neurogenomics of behavioural plasticity in socioecological contexts. In: Encyclopedia of Life Sciences. Chichester: John Wiley & Sons, Ltd. Publisher's VersionAbstract

Social and ecological challenges often elicit behavioural and physiological responses that are adaptive and subject to selection. The varying behavioural states and traits of animals are a direct output of the nervous system and underlying molecular substrates. Changes in gene expression in response to a variety of contexts such as mate choice, aggression and developmental experience can alter a number of cellular and neural pathways that lead to changes in behaviour. A common framework has emerged to understand the role of the transcriptome in animal behaviour. Behavioural plasticity describes both an individual’s ability to modify behavioural states and correlated suites of behaviour in populations, which may constrain variance across contexts. By integrating the study of behavioural plasticity with genome scale, bioinformatics and candidate gene analyses, we are rapidly expanding our understanding of this kind of organismal flexibility, its relationship with the genome and its evolutionary implications.

Rodriguez-Santiago M, Nguyen J, Winton LS, Weitekamp CA, Hofmann HA. Arginine vasotocin preprohormone is expressed in surprising regions of the teleost forebrain. Frontiers in Endocrinology [Internet]. 8. Publisher's VersionAbstract
Nonapeptides play a fundamental role in the regulation of social behavior, among numerous other functions. In particular, arginine vasopressin and its non-mammalian homolog, arginine vasotocin (AVT), have been implicated in regulating affiliative, reproductive, and aggressive behavior in many vertebrate species. Where these nonapeptides are synthesized in the brain has been studied extensively in most vertebrate lineages. While several hypothalamic and forebrain populations of vasopressinergic neurons have been described in amniotes, the consensus suggests that the expression of AVT in the brain of teleost fish is limited to the hypothalamus, specifically the preoptic area (POA) and the anterior tuberal nucleus (putative homolog of the mammalian ventromedial hypothalamus). However, as most studies in teleosts have focused on the POA, there may be an ascertainment bias. Here, we revisit the distribution of AVT preprohormone mRNA across the dorsal and ventral telencephalon of a highly social African cichlid fish. We first use in situ hybridization to map the distribution of AVT preprohormone mRNA across the telencephalon. We then use quantitative real-time polymerase chain reaction to assay AVT expression in the dorsomedial telencephalon, the putative homolog of the mammalian basolateral amygdala. We find evidence for AVT preprohormone mRNA in regions previously not associated with the expression of this nonapeptide, including the putative homologs of the mammalian extended amygdala, hippocampus, striatum, and septum. In addition, AVT preprohormone mRNA expression within the basolateral amygdala homolog differs across social contexts, suggesting a possible role in behavioral regulation. We conclude that the surprising presence of AVT preprohormone mRNA within dorsal and medial telencephalic regions warrants a closer examination of possible AVT synthesis locations in teleost fish, and that these may be more similar to what is observed in mammals and birds.
Weitekamp CA, Nguyen J, Hofmann HA. Neuromolecular Regulation of Aggression Differs by Social Role during Joint Territory Defense. Integrative and Comparative Biology. :1-9.Abstract

In response to a territory intrusion, neighboring males of the African cichlid fish Astatotilapia burtoni engage in aggressive joint territory defense in a manner that depends on their social role. Here, we examine the possible function of several neuroendocrine and neuromodulator pathways previously implicated in the regulation of complex social behavior. We find that the neuromolecular regulation of aggression during joint territory defense is very much dependent on an individual’s role in this context. In neighbors but not in residents, aggression is correlated to gene expression in the medial part of the dorsal telencephalon (area Dm), the putative homolog to the mammalian basolateral amygdala. This correlation is strikingly high for expression of the serotonin receptor 5-HT2c, suggesting the serotonin system is important in regulating context-dependent behavior. Furthermore, by examining candidate gene expression co-variance patterns in area Dm and in the lateral part of the dorsal telencephalon (area Dl), the putative homolog to the mammalian hippocampus, we identify two main patterns: gene expression is co-regulated within, but not across, brain regions, and co-regulation is synergistic rather than antagonistic. Our results highlight the critical effect of social context on both behavior and its neuromolecular basis.

Weitekamp CA, Nguyen J, Hofmann HA. Social context affects behavior, preoptic area gene expression, and response to D2 receptor manipulationduring territorial defense in a cichlid fish. Genes, Brain and Behavior. 16 :601-611.Abstract

Social context often has profound effects on behavior, yet the neural and molecular mechanisms which mediate flexible behavioral responses to different social environments are not well understood. We used the African cichlid fish, Astatotilapia burtoni, to examine aggressive defense behavior across three social contexts representing different motivational states: a reproductive opportunity, a familiar male and a neutral context.To elucidate how differences in behavior across con-texts may be mediated by neural gene expression, we examined gene expression in the preoptic area, a brain region known to control male aggressive and sexual behavior. We show that social context has broad effects on preoptic gene expression. Specifically, we found that the expression of genes encoding nonapeptides and sex steroid receptors are upregulated in the familiar male context. Furthermore, circulating levels of testosterone and cortisol varied markedly depending on social context. We also manipulated the D2 receptor (D2R) ineach social context, given that it has been implicated in mediating context-dependent behavior. We found that a D2R agonist reduced intruder-directed aggression in the reproductive opportunity and familiar male contexts, while a D2R antagonist inhibited intruder-directed aggression in the reproductive opportunity context and increased aggression in the neutral context. Our results demonstrate a critical role for preoptic gene expression, as well as circulating steroid hormone levels, in encoding information from the social environment and in shaping adaptive behavior. In addition, they provide further evidence for a role of D2R in context-dependent behavior.

Liebeskind BJ, Hofmann HA, Hillis DA, Zakon HH. Evolution of Animal Neural Systems. Annual Review of Ecology, Evolution, and Systematics. 48 :377-398.Abstract

Nervous systems are among the most spectacular products of evolution. Their provenance and evolution have been of interest and often the subjects of intense debate since the late nineteenth century. The genomics era has provided researchers with a new set of tools with which to study the early evolution of neurons, and recent progress on the molecular evolution of the first neurons has been both exciting and frustrating. It has become increasingly obvious that genomic data are often insufficient to reconstruct complex phenotypes in deep evolutionary time because too little is known about how gene function evolves over deep time. Therefore, additional functional data across the animal tree are a prerequisite to a fuller understanding of cell evolution. To this end, we review the functional modules of neurons and the evolution of their molecular components, and we introduce the idea of hierarchical molecular evolution.

Dijkstra PD, Maguire SM, Harris RM, Rodriguez AA, DeAngelis RS, Flores SA, Hofmann HA. The melanocortin system regulates body pigmentation and social behaviour in the cichlid fish Astatotilapia burtoni. Proc R Soc B. dijkstra_et_al._2017.pdf
Weitekamp CA, Solomon-Lane TK, Del Valle P, Triki Z, Nugent BM, Hofmann HA. A role for oxytocin-like receptor in social habituation in a teleost. Brain, Behavior, and Evolution. 89 :153-161.Abstract

Oxytocin (OT) mediates social habituation in rodent model systems, but its role in mediating this effect in other vertebrates is unknown. We used males of the African cichlid fish, Astatotilapia burtoni , to investigate two aspects of isotocin (IT; an OT homolog) signaling in social habituation. First, we examined the expression of IT receptor 2 (ITR2) as well as two immediate early genes in brain regions implicated in social recognition. Next, we examined IT neuron activity using immunohistochemistry. Patterns of gene expression in homologs of the amygdala and hippocampus implicate IT signaling in these regions in social habituation to a territorial neighbor. In the preoptic area, the expression of the ITR2 subtype and IT neuron activity respond to the presence of a male, independent of familiarity. Our results implicate IT in mediating social habituation in a teleost.

Harris RM, O'Connell LA, Hofmann HA. Chapter 15: Brain Evolution, Development, and Plasticity. In: Shepherd SV The Wiley Handbook of Evolutionary Neuroscience. 1st ed. John Wiley & Sons, Ltd ; pp. 422-443. harris_et_al_2017.pdf
Weitekamp CA, Hofmann HA. Neuromolecular correlates of cooperation and conflict during territory defense in a cichlid fish. Hormones and Behavior [Internet]. 89 :145-156. Publisher's VersionAbstract

Cooperative behavior is widespread among animals, yet the neural mechanisms have not been studied in detail. We examined cooperative territory defense behavior and associated neural activity in candidate forebrain regions in the cichlid fish, Astatotilapia burtoni. We find that a territorial male neighbor will engage in territory defense dependent on the perceived threat of the intruder. The resident male, on the other hand, engages in defense based on the size and behavior of his partner, the neighbor. In the neighbor, we find that an index of engagement correlates with neural activity in the putative homolog of the mammalian basolateral amygdala and in the preoptic area, as well as in preoptic dopaminergic neurons. In the resident, neighbor behavior is correlated with neural activity in the homolog of the mammalian hippocampus. Overall, we find distinct neural activity patterns between the neighbor and the resident, suggesting that an individual perceives and processes an intruder challenge differently during cooperative territory defense depending on its own behavioral role.

Weitekamp CA, Hofmann HA. Brain Systems Underlying Social Behavior. In: Kaas J Evolution of Nervous Systems. Vol. 1. 2nd ed. Oxford: Elsevier ; pp. 327-334.Abstract

Recent progress in animal behavior research, based on the insight that proximate mechanisms both shape and constrain behavioral responses to natural and sexual selection, has reinforced the importance of knowing the neuromolecular basis of social behavior for understanding its evolution. Here, we review the current state of knowledge of the neural substrates of vertebrate social behavior, with an emphasis on the neuroendocrine and neurochemical pathways involved. Using an integrative perspective, we then discuss the evolution of these mechanisms and highlight several challenges that have hampered progress in this area. Finally, we provide a road map for an integrative evolutionary neuroethology.

Renn SCP, O'Rourke CF, Aubin-Horth N, Fraser EJ, Hofmann HA. Dissecting the transcriptional patterns of social dominance across teleosts. Integrative and Comparative Biology [Internet]. 56 :1250-1265. Publisher's VersionAbstract

In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms. Traditional gene expression analyses are useful for generating candidate gene lists, but are biased by choice of significance cut-offs and difficult to use for between-study comparisons. In contrast, complementary analysis tools allow one to both test a priori hypotheses and generate new hypotheses. Here we employ a meta-analysis of high-throughput expression profiling experiments to investigate the gene expression patterns that underlie mechanisms and evolution of behavioral social phenotypes. Specifically, we use a collection of datasets on social dominance in fish across social contexts, sex, and species. Using experimental manipulation to produce female dominance hierarchies in the cichlid Astatotilapia burtoni, heralded as a genomic model of social dominance, we generate gene lists, and assess molecular gene modules. In the dominant female gene expression profile, we demonstrate a strong pattern of up-regulation of genes previously identified as having male-biased expression and furthermore, compare expression biases between male and female dominance phenotypes. Using a threshold-free approach to identify correlation throughout ranked gene lists, we query previously published datasets associated with maternal behavior, alternative reproductive tactics, cooperative breeding, and sex-role reversal to describe correlations among these various neural gene expression profiles associated with different instances of social dominance. These complementary approaches capitalize on the high-throughput gene expression profiling from similar behavioral phenotypes in order to address the mechanisms associated with social dominance behavioral phenotypes.

Nishi R, Castaneda E, Davis GW, Fenton AA, Hofmann HA, King J, Ryan TA, Trujillo KA. The Global Challenge in Neuroscience Education and Training: The MBL Perspective. Neuron [Internet]. 92 :632-636. Publisher's VersionAbstract

The greatest challenge in moving neuroscience research forward in the 21st century is recruiting, training, and retaining the brightest, rigorous, and most diverse scientists. The MBL research training courses Neurobiology and Neural Systems & Behavior, and the Summer Program in Neuroscience, Excellence, and Success provide a model for full immersion, discovery-based training while enhancing cultural, geographic, and racial diversity.

Goppert C, Harris RM, Theis A, Boila A, Hohl S, Ruegg A, Hofmann HA, Salzburger W, Bohne A. Inhibition of Aromatase Induces Partial Sex Change in a Cichlid Fish: Distinct Functions for Sex Steroids in Brains and Gonads. Sexual Development [Internet]. 10 :97-110. Publisher's VersionAbstract

 Sex steroids are major drivers of sexual development and also responsible for the maintenance of the established gender. Especially fishes exhibit great plasticity and less conservation in sex determination and sexual development compared to other vertebrate groups. In addition, fishes have a constant sex steroid production throughout their entire lifespan, which makes them particularly susceptible to interferences with the endogenous sex steroid system. This susceptibility has recently been used to show that inhibition of the key enzyme of estrogen synthesis, aromatase Cyp19a1, can induce functional sex reversal even in adult fish. Here, we investigated the impact of the aromatase inhibitor (AI) fadrozole in adult females of the East African cichlid fish Astatotilapia burtoni. Using gene expression, phenotypic measurements, behavioral experiments, and hormone measurements, we assessed if females treated with fadrozole develop a male-like phenotype. We found that AI treatment has a different effect on gene expression in the gonad compared to the brain, the 2 tissues mostly implicated in sexual development. In contrast to observations in other gonochoristic species, A. burtoni ovaries cannot be transformed into functional testis by AI. However, rapid changes towards a male-like phenotype can be induced with AI in coloration, hormone levels, and behavior. 

Nugent BM, Stiver KA, Alonzo SH, Hofmann HA. Neuroendocrine profiles associated with discrete behavioural variation in Symphodus ocellatus, a species with male alternative reproductive tactics. Molecular Ecology [Internet]. 25 (20) :5212-5227. Publisher's VersionAbstract

The molecular mechanisms underlying phenotypic plasticity are not well understood. Identifying mechanisms underlying alternative reproductive tactics (ARTs) in species for which the behavioural and fitness consequences of this variation are well characterized provides an opportunity to integrate evolutionary and mechanistic understanding of the maintenance of variation within populations. In the ocellated wrasse Symphodus ocellatus, the behavioural phenotypes of three distinct male morphs (sneakers, satellites and nesting males), which arise from a single genome, have been thoroughly characterized. To determine the neuroendocrine and genomic mechanisms associated with discrete phenotypic variation and ARTs in S. ocellatus in their natural environment, we constructed a whole-brain de novo transcriptome and compared global patterns of gene expression between sexes and male morphs. Next, we quantified circulating cortisol and 11-ketotestosterone (11-kt), mediators of male reproductive behaviours, as well as stress and gonadal steroid hormone receptor expression in the preoptic area, ventral subpallial division of the telencephalon and dorsolateral telencephalon, critical brain regions for social and reproductive behaviours. We found higher levels of 11-kt in nesting males and higher levels of cortisol in sneaker males relative to other male morphs and females. We also identified distinct patterns of brain region-specific hormone receptor expression between males such that most hormone receptors are more highly expressed in satellites and nesting males relative to sneakers and females. Our results establish the neuroendocrine and molecular mechanisms that underlie ARTs in the wild and provide a foundation for experimentally testing hypotheses about the relationship between neuromolecular processes and reproductive success.

Ockendon NF, O'Connell LA, Bush, Stephen J, Monzonsandoval J, Barnes H, Szekely T, Hofmann HA, Dorus S, Urrutia AO. Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes. Molecular Ecology Resources [Internet]. 16 :446-458. Publisher's VersionAbstract

Next-generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a rangeof organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacyand accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustlycharacterized. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melano-gaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methodsand quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analysesdemonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcriptshort reads are aligned directly to the reference genome, significantly outperforms the widely used de novo andguided assembly-based methods in both the quantity and accuracy of gene detection. Our analysis also reveals thatDGM recovers a more representative profile of Gene Ontology functional categories, which are often used to inter-pret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA-seq datademonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy andreduced gene detection associated with sequence divergence thus provides empirically derived guidelines for thedesign of future gene expression studies in species without sequenced genomes.

Jordan LA, Maguire SM, Hofmann HA, Kohda M. The social and ecological costs of an "over-extended" phenotype. Proceedings of the Royal Society B [Internet]. 283 :20152359. Publisher's VersionAbstract

Extended phenotypes offer a unique opportunity to experimentally manipulate and identify sources of selection acting on traits under natural conditions. The social cichlid fish Neolamprologus multifasciatus builds nests by digging up aquatic snail shells, creating an extended sexual phenotype that is highly amenable to experimental manipulation through addition of extra shells. Here, we find sources of both positive sexual selection and opposing natural selection acting on this trait; augmenting shell nests increases access to mates, but also increases social aggression and predation risk. Increasing the attractiveness of one male also changed social interactions throughout the social network and altered the entire community structure. Manipulated males produced and received more displays from neighbouring females, who also joined augmented male territories at higher rates than unmanipulated groups. However, males in more attractive territories received more aggression from neighbouring males, potentially as a form of social policing. We also detected a significant ecological cost of the ‘over-extended' phenotype; heterospecific predators usurped augmented nests at higher rates, using them as breeding sites and displacing residents. Using these natural experiments, we find that both social and ecological interactions generate clear sources of selection mediating the expression of an extended phenotype in the wild.

Liebeskind BJ, Hillis DM, Zakon HH, Hofmann HA. Complex Homology and the Evolution of Nervous Systems. Trends in Ecology and Evolution [Internet]. 31 (2) :127 - 135. Publisher's VersionAbstract

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states.

Hofmann HA, Renn SCP, Rubenstein DR. New Frontiers in the Integrative Study of Animal Behavior: Nothing in Neuroscience Makes Sense Except in the Light of Behavior. Integrative and Comparative Biology [Internet]. :icw127 - icw127. Publisher's Version 2016.hofmann.icb_.pdf