In Press
Kabelik D, Weitekamp CA, Choudhury SC, Hartline JT, Smith AN, Hofmann HA. Neural activity in the social decision-making network of the brown anole during reproductive and agonistic encounters. Hormones and Behavior [Internet]. In Press. Publisher's VersionAbstract
Animals have evolved flexible strategies that allow them to evaluate and respond to their social environment by integrating the salience of external stimuli with internal physiological cues into adaptive behavioral responses. A highly conserved social decision-makingnetwork (SDMN), consisting of interconnected social behavior and mesolimbic reward networks, has been proposed to underlie such adaptive behaviors across all vertebrates, although our understanding of this system in reptiles is very limited. Here we measure neural activation across the SDMN and associated regions in the male brown anole (Anolis sagrei), within both reproductive and agonistic contexts, by quantifying the expression density of the immediate early gene product Fos. We then relate this neural activity measure to social context, behavioral expression, and activation (as measured by colocalization with Fos) of different phenotypes of ‘source’ node neurons that produce neurotransmittersand neuropeptides known to modulate SDMN ‘target’ node activity. Our results demonstrate that measures of neural activation across the SDMN network are generally independent of specific behavioral output, although Fos induction in a few select nodes of the social behavior network component of the SDMN does vary with social environment and behavioral output. Under control conditions, the mesolimbic reward nodes of the SDMN actually correlate little with the social behavior nodes, but the interconnectivity of these SDMN components increases dramatically within a reproductive context. When relating behavioral output to specific source node activation profiles, we found that catecholaminergic activation is associated with the frequency and intensity of reproductive behavior output, as well as with aggression intensity. Finally, in terms of the effects of source node activation on SDMN activity, we found that Ile8-oxytocin (mesotocin) populations correlate positively, while Ile3-vasopressin (vasotocin), catecholamine, and serotonin populations correlate negatively with SDMN activity. Taken together, our findings present evidence for a highly dynamic SDMN in reptiles that is responsive to salient cues in a social context-dependent manner.
Solomon-Lane TK, Hofmann HA. Early-life social environment alters juvenile behavior and neuroendocrine function in a highly social cichlid fish. 2018.Abstract
Early-life experiences can shape adult behavior, with consequences for fitness and health, yet fundamental questions remain unanswered about how early social environments and experiences are translated into variation in brain and behavior. The African cichlid fish Astatotilapia burtoni, a model system in social neuroscience, is well known for its highly plastic social phenotypes in adulthood. Here, we rear juveniles in either social groups or pairs to investigate the effects of early-life social environments on behavior and neuroendocrine gene expression. We find that both juvenile behavior and neuroendocrine function are sensitive to early-life social effects. Behavior robustly co-varies across multiple contexts (open field, social cue investigation, and dominance behavior assays) to form a behavioral syndrome. Rearing environment shifts pair-reared juveniles towards the end of syndrome that is less active and socially interactive. Pair-reared juveniles also submit more readily as subordinates. In a separate cohort, we then measured neural expression for stress and sex hormone genes, signaling systems known to be developmentally plastic and involved in translating environmental conditions into biological responses and regulating adult social behavior. Rearing environment causes striking differences in neuroendocrine gene co-expression networks. Specifically, expression was tightly integrated in pair-reared juveniles, but not group-reared or isolated juveniles. Glucocorticoid receptor subtypes 1a, 1b, and 2, as well as androgen receptor , drive the significant differences between treatment groups, which supports a highly conserved role for the stress axis mediating early-life effects. Together, this research demonstrates the important developmental origins of behavioral phenotypes and identifies potential behavioral and neuroendocrine mechanisms.
Goldsby HJ, Young RL, Schossau J, Hofmann HA, Hintze A. Serendipitous scaffolding to improve a genetic algorithm's speed and quality. Genetic and Evolutionary Computation Conference. 2018.
Renn SCP, Machado HE, Duftner N, Sessa AK, Harris RM, Hofmann HA. Gene expression signatures of mating system evolution. Genome [Internet]. 2018. 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.

Wylie DC, Hofmann HA, BV Z. SArKS: Discovering gene expression regulatory motifs and domains by suffix array kernel smoothing. PLOS Computational Biology [Internet]. 2018. Publisher's VersionAbstract

 Experiments designed to assess differential gene expression represent a rich resource for discovering how DNA regulatory sequences influence transcription. Results derived from such experiments are usually quantified as continuous scores, such as fold changes, test statistics and p -values. We present a de novo motif discovery algorithm, SArKS, which uses a nonparametric kernel smoothing approach to identify promoter motifs correlated with elevated differential expression scores. SArKS has the capability to smooth over both motif sequence similarity and, in a second pass, over spatial proximity of multiple motifs to identify longer regions enriched in correlative motifs. We applied SArKS to simulated data, illustrating how SArKS can be used to find motifs embedded in random background sequences, and to two published RNA-seq expression data sets, one probing S. cerevisiae  transcriptional response to anti-fungal agents and the other comparing gene expression profiles among cortical neuron subtypes in M. musculus. For both RNA-seq sets we successfully identified motifs whose kernel-smoothed scores were significantly elevated compared to the permutation-estimated background distributions. We found strong similarities between these identified motifs and known, biologically meaningful sequence elements which may help to provide additional context for the results previously published regarding these data sets. Finally, because eukaryotic transcription regulation is highly combinatorial, we also outline how SArKS methods might be extended to discover synergistic motifs

Harris RM, Kao H-Y, Alarcon JM, Hofmann HA, Fenton AA. Analysis of hippocampal transcriptomic responses to technical and biological perturbations. Hippocampus [Internet]. 2018. Publisher's VersionAbstract

Cost-effective next-generation sequencing has made unbiased gene expression analysis possible. Single-neuron gene expression studies may be especially important for understanding nervous system structure and function because of the neuron-specific functionality and plasticity that defines functional neural circuits. Cellular dissociation is a prerequisite technical manipulation for single-cell and single cell-population studies, but the extent to which the cellular dissociation process cells affects neural gene expression has not been determined, nor has it been determined how gene expression is altered by the stress that accompanies many of the behavioral manipulations that are required to study learning and memory and other cognitive functions. Here, we determined to which extent cellular dissociation-induced changes in hippocampal gene expression might confound studies on the behavioral and physiological functions of the hippocampus. We processed tissue punch samples from the dentate gyrus (DG), CA3, and CA1 hippocampus subfields using either a tissue homogenization protocol or a cellular dissociation protocol in preparation for RNA sequencing analysis to evaluate the impact of the tissue preparation. Then, we evaluated the effect of stressful experience and cognitive training on hippocampus subfield specific gene expression and determined to which extent these response overlap with the cellular dissociation response. Finally, we assessed the extent to which the subfield-specific gene expression patterns are consistent with those identified in a recently published hippocampus subfield-specific gene expression database. We report substantial differences in baseline subfield-specific gene expression, that 1% of the hippocampal transcriptome is altered by the process of cellular dissociation, that an even weaker alteration is detected 24 h after stressful experience, and that while these alterations are largely distinct from the subfield specific response of the hippocampus transcriptome to cognitive training, there is nonetheless some important confounding overlap. These findings of the concordant and discordant effects of technical and behavioral manipulations should inform the design of future neural transcriptome studies and thus facilitate a more comprehensive understanding of hippocampal function.

Goldsby HJ, Young RL, Hofmann HA, Hintze A. Increasing the complexity of solutions produced by an evolutionary developmental system. Genetic and Evolutionary Computation Conference. 2017.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 ; 2017. 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]. 2017;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. 2017 :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. 2017;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. 2017;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. 2017. 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. 2017;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 ; 2017. 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]. 2017;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 ; 2017. 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]. 2016;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]. 2016;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]. 2016;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.