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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.

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.

The ultimate-level factors that drive the evolution of mating systems have been well studied, but an evolutionarily conserved neural mechanism involved in shaping behaviour and social organization across species has remained elusive. Here, we review studies that have investigated the role of neural arginine vasopressin (AVP), vasotocin (AVT), and their receptor V1a in mediating variation in territorial behaviour. First, we discuss how aggression and territoriality are a function of population density in an inverted-U relationship according to resource defence theory, and how territoriality influences some mating systems. Next, we find that neural AVP, AVT, and V1a expression, especially in one particular neural circuit involving the lateral septum of the forebrain, are associated with territorial behaviour in males of diverse species, most likely due to their role in enhancing social cognition. Then we review studies that examined multiple species and find that neural AVP, AVT, and V1a expression is associated with territory size in mammals and fishes. Because territoriality plays an important role in shaping mating systems in many species, we present the idea that neural AVP, AVT, and V1a expression that is selected to mediate territory size may also influence the evolution of different mating systems. Future research that interprets proximate-level neuro-molecular mechanisms in the context of ultimate-level ecological theory may provide deep insight into the brain-behaviour relationships that underlie the diversity of social organization and mating systems seen across the animal kingdom.

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.

At menopause, the dramatic loss of ovarian estradiol (E2) necessitates the adaptation of estrogen-sensitive neurons in the hypothalamus to an estrogen-depleted environment. We developed a rat model to test the “critical window” hypothesis of the effects of timing and duration of E2 treatment after deprivation on the hypothalamic neuronal gene network in the arcuate nucleus and the medial preoptic area. Rats at 2 ages (reproductively mature or aging) were ovariectomized and given E2 or vehicle replacement regimes of differing timing and duration. Using a 48-gene quantitative low-density PCR array and weighted gene coexpression network analysis, we identified gene modules differentially regulated by age, timing, and duration of E2 treatment. Of particular interest, E2 status differentially affected suites of genes in the hypothalamus involved in energy balance, circadian rhythms, and reproduction. In fact, E2 status was the dominant factor in determining gene modules and hormone levels; age, timing, and duration had more subtle effects. Our results highlight the plasticity of hypothalamic neuroendocrine systems during reproductive aging and its surprising ability to adapt to diverse E2 replacement regimes.

Social plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and this ability has an impact in their Darwinian fitness. This behavioral plasticity may be achieved either by rewiring or by biochemically switching nodes of the neural network underlying social behavior in response to perceived social information. Independent of the proximate mechanisms, at the neuromolecular level social plasticity relies on the regulation of gene expression, such that different neurogenomic states emerge in response to different social stimuli and the switches between states are orchestrated by signaling pathways that interface the social environment and the genotype. Here, we test this hypothesis by characterizing the changes in the brain profile of gene expression in response to social odors in the Mozambique Tilapia, Oreochromis mossambicus. This species has a rich repertoire of social behaviors during which both visual and chemical information are conveyed to conspecifics. Specifically, dominant males increase their urination frequency during agonist encounters and during courtship to convey chemical information reflecting their dominance status.

The neural and molecular mechanisms underlying social behavior – including their functional significance and evolution – can only be fully understood using data obtained under multiple social, environmental, and physiological conditions. Understanding the complexity of social behavior requires integration across levels of analysis in both laboratory and field settings. However, there is currently a disconnect between the systems studied in the laboratory versus the field. We argue that recent conceptual and technical advances provide exciting new opportunities to close this gap by making non-model organisms accessible to modern approaches in both laboratory and nature.

Neuropeptides modulate many aspects of behavior and physiology in a broad range of animals. Arginine vasotocin (AVT) is implicated in mediating social behavior in teleost fish, although its specific role varies between species, sexes, life stages, and social context. To investigate whether the effects of AVT on behavior depend on social context, we used the African cichlid fish Astatotilapia burtoni, which is well-known for its remarkable behavioral plasticity. We pharmacologically manipulated the AVT system in established socially dominant and subordinate A. burtoni males, as well as in males ascending to dominance status in a socially unstable environment. Our results show that exogenous AVT causes a stress response, as evidenced by reduced behavioral activity and increased circulating levels of cortisol in established dominant and subordinate males. Administration of the AVT antagonist Manning compound, on the other hand, did not affect established subordinate or dominant males. However, AVT antagonist-treated males ascending from subordinate to dominant status exhibited reduced aggressive and increased courtship behavior compared to vehicle-treated animals. Finally, we measured circulating cortisol levels and brain gene expression levels of AVT and its behaviorally relevant V1a2 receptor in all three social phenotypes and found that plasma cortisol and mRNA levels of both genes were increased in ascending males compared to dominant and subordinate males. Our results provide a more detailed understanding of the role of the AVT system in the regulation of complex behavior in a dynamically changing social environment.

Educated by his deep appreciation of nature, Darwin observed that “from so simple a beginning endless forms most beautiful” have arisen throughout the evolutionary history of life on earth (1). The spectacular diversity of orchids (2) and beetles (3) has long fascinated naturalists and casual observers alike. More recently, the adaptive radiations of Hawaiian drosophilids (4), Caribbean Anolis lizards (5), and African cichlid fishes (6) have become prime examples for understanding the mechanisms that enable diversification. Gene duplication and deletion are generally considered important evolutionary mechanisms that give rise to phenotypic diversity (7). Following gene duplication and loss, adaptation and speciation appear to proceed through a combination of both structural and cis-regulatory changes in one or more paralogous genes (8). Recent advances in sequencing technology have enabled researchers to make significant progress in understanding the molecular evolution that has facilitated diversification. In PNAS, Cortesi et al. (9) examine the evolution of vertebrate opsin genes as a spectacular example of how gene duplication and deletion events that affect spectral sensitivity have driven adaptation to diverse light environments and visual displays.

Behavioral studies have often examined parental care by measuring phenotypic plasticity of behavior within a species. Phylogenetic studies have compared parental care among species, but only at broad categories (e.g., care vs. no care). Here we provide a detailed account that integrates phylogenetic analysis with quantitative behavioral data to better understand parental care behavior in the Cuatro Ciénegas cichlid, Herichthys minckleyi. We found that H. minckleyi occurs in a clade of sexually monochromatic or weakly dichromatic monogamous species, but that male and female H. minckleyi have dramatically different reproductive coloration patterns, likely as a result of sexual selection. Furthermore, we found that males are polygynous; large males guard large territories, and smaller males may attempt alternative mating tactics (sneaking). Finally, compared to the closely related monogamous Rio Grande cichlid, H. cyanoguttatus, males of H. minckleyi were present at their nests less often and performed lower rates of aggressive offspring defense, and females compensated for the absence of their mates by performing higher levels of offspring defense. Body color, mating system, and parental care in H. minckleyi appear to have evolved after it colonized Cuatro Ciénegas, and are likely a result of evolution in an isolated, stable environment.