Chromosomal Polymorphism in the White-Throated Sparrow, Zonotrichia albicollis (Gmelin)

Allele-specific cis-regulatory methylation of the gene for vasoactive intestinal peptide in white-throated sparrows

White-throated sparrows (Zonotrichia albicollis) offer a unique opportunity to connect genotype with behavioral phenotype. In this species, a rearrangement of the second chromosome is linked with territorial aggression; birds with a copy of this "supergene" rearrangement are more aggressive than those without it. The supergene has captured the gene VIP, which encodes vasoactive intestinal peptide, a neuromodulator that drives aggression in other songbirds. In white-throated sparrows, VIP expression is higher in the anterior hypothalamus of birds with the supergene than those without it, and expression of VIP in this region predicts the level of territorial aggression regardless of genotype. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of VIP both in breeding adults, which exhibit morph differences in territorial aggression, and in nestlings, before territorial behavior develops. We extracted and bisulfite-converted DNA from samples of the hypothalamus in wild-caught adults and nestlings and used high-throughput sequencing to measure DNA methylation of a region upstream of the VIP start site. We found that the allele inside the supergene was less methylated than the alternative allele in both adults and nestlings. The differential methylation was attributed primarily to CpG sites that were shared between the alleles, not to polymorphic sites, which suggests that epigenetic regulation is occurring independently of the genetic differentiation within the supergene. This work represents an initial step toward understanding how epigenetic differentiation inside chromosomal inversions leads to the development of alternative behavioral phenotypes.

Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.

Immunoecology of Species with Alternative Reproductive Tactics and Strategies

Alternative reproductive tactics and strategies (ARTS) refer to polymorphic reproductive behaviours in which in addition to the usual two sexes, there are one or more alternative morphs, usually male, that have evolved the ability to circumvent direct intra-sexual competition. Each morph has its own morphological, ecological, developmental, behavioural, life-history, and physiological profile that shifts the balance between reproduction and self-maintenance, one aspect being immunity. Immunoecological work on species with ARTS, which is the topic of this review, is particularly interesting because the alternative morphs make it possible to separate the effects of sex per se from other factors that in other species are inextricably linked with sex. We first summarize the evolution, development, and maintenance of ARTS. We then review immunoecological hypotheses relevant to species with ARTS, dividing them into physiological, life-history, and ecological hypotheses. In context of these hypotheses, we critically review in detail all immunoecological studies we could find on species with ARTS. Several interesting patterns emerge. Oddly, there is a paucity of studies on insects, despite the many benefits that arise from working with insects: larger sample sizes, simple immune systems, and countless forms of alternative reproductive strategies and tactics. Of all the hypotheses considered, the immunocompetence handicap hypothesis has generated the greatest amount of work, but not necessarily the greatest level of understanding. Unfortunately, it is often used as a general guiding principle rather than a source of explicitly articulated predictions. Other hypotheses are usually considered a posteriori, but perhaps they should take centre stage. Whereas blanket concepts such as “immunocompetence” and “androgens” might be useful to develop a rationale, predictions need to be far more explicitly articulated. Integration so far has been a one-way street, with ecologists delving deeper into physiology, sometimes at the cost of ignoring their organisms’ evolutionary history and ecology. One possible useful framework is to divide ecological and evolutionary factors affecting immunity into those that stimulate the immune system, and those that depress it. Finally, the contributions of genomics to ecology are being increasingly recognized and sometimes applied to species with ARTS, but we must ensure that evolutionary and ecological hypotheses drive the effort, as there is no grandeur in the strict reductionist view of life.

A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes

How locally adapted ecotypes are established and maintained within a species is a long-standing question in evolutionary biology. Using forest and prairie ecotypes of deer mice (Peromyscus maniculatus), we characterized the genetic basis of variation in two defining traits-tail length and coat color-and discovered a 41-megabase chromosomal inversion linked to both. The inversion frequency is 90% in the dark, long-tailed forest ecotype; decreases across a habitat transition; and is absent from the light, short-tailed prairie ecotype. We implicate divergent selection in maintaining the inversion at frequencies observed in the wild, despite high levels of gene flow, and explore fitness benefits that arise from suppressed recombination within the inversion. We uncover a key role for a large, previously uncharacterized inversion in the evolution and maintenance of classic mammalian ecotypes.

Supergenes on steroids

At the birth of supergenes, the genomic landscape is dramatically re-organized leading to pronounced differences in phenotypes and increased intrasexual diversity. Two of the best-studied supergenes in vertebrates are arguably the inversion polymorphisms on chromosomes 2 and 11 in the white-throated sparrow (Zonotrichia albicollis) and the ruff (Calidris pugnax), respectively. In both species, regions of suppressed recombination determine plumage coloration and social behavioural phenotypes. Despite the apparent lack of gene overlap between these two supergenes, in both cases the alternative phenotypes seem to be driven largely by alterations in steroid hormone pathways. Here, we explore the interplay between genomic architecture and steroid-related genes. Due to the highly pleiotropic effects of steroid-related genes and their universal involvement in social behaviour and transcriptomic regulation, processes favouring their linkage are likely to have substantial effects on the evolution of behavioural phenotypes, individual fitness, and life-history strategies. We propose that inversion-related differentiation and regulatory changes in steroid-related genes lie at the core of phenotypic differentiation in both of these interesting species. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.

Inversion breakpoints and the evolution of supergenes

The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.

Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

Much of our knowledge on regulatory impacts of DNA methylation has come from laboratory‐bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally‐occurring variation in DNA methylation in a wild avian species, the white‐throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a nonrecombining chromosome pair linked to both plumage and behavioural phenotypes. Using novel single‐nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was concentrated in the nonrecombining chromosome pair. Interestingly, a large number of CpGs on the nonrecombining chromosome, localized to transposable elements, have undergone dramatic loss of DNA methylation since the split of the ZAL2 and ZAL2^m chromosomes. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome‐wide DNA methylation that are associated with development and with specific functional categories of genes in white‐throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population.

see also the Perspective by Jordan A. Anderson and Jenny Tung.

Behavioral Genetics: Dissecting a Supergene to Understand Behavior

New research shows how alternative 'supergene' alleles of Estrogen Receptor 1 are differentially expressed in specific brain nuclei causing aggressive behavior in the white-throated sparrow.

Inside the supergene of the bird with four sexes

The white-throated sparrow (Zonotrichia albicollis) offers unique opportunities to understand the adaptive value of supergenes, particularly their role in alternative phenotypes. In this species, alternative plumage morphs segregate with a nonrecombining segment of chromosome 2, which has been called a 'supergene'. The species mates disassortatively with respect to the supergene; that is, each breeding pair consists of one individual with it and one without it. This species has therefore been called the "bird with four sexes". The supergene segregates with a behavioral phenotype; birds with it are more aggressive and less parental than birds without it. Here, we review our efforts to identify the genes inside the supergene that are responsible for the behavioral polymorphism. The gene ESR1, which encodes estrogen receptor α, differs between the morphs and predicts both territorial and parental behavior. Variation in the regulatory regions of ESR1 causes an imbalance in expression of the two alleles, and the degree to which this imbalance favors the supergene allele predicts territorial singing. In heterozygotes, knockdown of ESR1 causes a phenotypic switch, from more aggressive to less aggressive. We recently showed that another gene important for social behavior, vasoactive intestinal peptide (VIP), is differentially expressed between the morphs and predicts territorial singing. We hypothesize that ESR1 and VIP contribute to behavior in a coordinated way and could represent co-adapted alleles. Because the supergene contains more than 1000 individual genes, this species provides rich possibilities for discovering alleles that work together to mediate life-history trade-offs and maximize the fitness of alternative complex phenotypes.

A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird

Behavioral evolution relies on genetic changes, yet few behaviors can be traced to specific genetic sequences in vertebrates. Here we provide experimental evidence showing that differentiation of a single gene has contributed to the evolution of divergent behavioral phenotypes in the white-throated sparrow, a common backyard songbird. In this species, a series of chromosomal inversions has formed a supergene that segregates with an aggressive phenotype. The supergene has captured ESR1, the gene that encodes estrogen receptor α (ERα); as a result, this gene is accumulating changes that now distinguish the supergene allele from the standard allele. Our results show that in birds of the more aggressive phenotype, ERα knockdown caused a phenotypic change to that of the less aggressive phenotype. We next showed that in a free-living population, aggression is predicted by allelic imbalance favoring the supergene allele. Finally, we identified cis-regulatory features, both genetic and epigenetic, that explain the allelic imbalance. This work provides a rare illustration of how genotypic divergence has led to behavioral phenotypic divergence in a vertebrate.

Stopover refuelling, movement and departure decisions in the white-throated sparrow: The influence of intrinsic and extrinsic factors during spring migration

Differential migration timing between sex or age classes is an example of how migratory movement strategies can differ among subgroups within a population. However, in songbirds, evidence for intrinsic differences in en route migratory behaviour is often mixed, suggesting that the local environmental context may play a role in accentuating or diminishing patterns. We evaluated how multiple intrinsic and extrinsic variables influenced refuelling rates, local movement behaviour and departure decisions in the white-throated sparrow Zonotrichia albicollis during spring migration. This species exhibits a unique genetically based plumage dimorphism, providing a unique class of individual in which to evaluate patterns and processes of differential migration, in addition to sex, age and migration distance. At a migratory stopover site, plasma metabolite analysis was used to quantify individual variation in stopover refuelling rate. In after second year adults, automated and manual radio telemetry was used to quantify daily activity timing, daily movement distances, stopover duration and departure time. Arrival timing to the stopover site was determined using capture data. Non-breeding and previous breeding/natal latitude were determined using analysis of hydrogen isotopes in claws and feathers. Males arrived at the stopover site 11 days on average before females, but no difference in migration timing was observed between plumage morph or age classes. After second year, adults with more southern previous breeding latitudes arrived at stopover earlier, whereas second year birds making their first return migration arrived at stopover in an inverse relationship to non-breeding latitude. Stopover refuelling rate did not differ between ages, sexes or plumage morphs, and daily departure probability of adults was higher under warmer temperatures and favourable tailwinds. White-striped morphs moved greater distances during stopover, initiated daily activity earlier in the morning and departed for migration earlier in the evening than tan-striped morphs. Our results show that while individual phenotype can influence some aspects of local stopover-scale movement behaviour, evidence for differential stopover behaviour was weak. Differential migration timing is unlikely to result from intrinsic differences in en route refuelling rate and departure decisions, especially because the latter is strongly influenced by meteorological conditions.

Experimental Malaria Infection Affects Songbirds' Nocturnal Migratory Activity

Migratory animals encounter multiple parasite communities, raising concerns that migration may aid transport of infectious disease. How migration affects disease spread depends fundamentally on how disease affects migration, specifically whether infection alters individuals' migratory physiology and behavior. We inoculated white-throated sparrows (Zonotrichia albicollis) with avian malaria parasites (Plasmodium sp.), monitored parasite loads for 5 wk as the birds reached spring migratory condition, and compared nocturnal migratory restlessness (Zugunruhe), body composition (fat, lean, and whole-body mass), and hematocrit among experimentally infected birds, sham-inoculated birds, and birds that were exposed to parasites but resisted infection. Migratory restlessness increased over time in the study, but the rate of change varied between sham (control) birds, infected birds, and birds that resisted infection. We were unable to detect any effects of malaria exposure on body condition. Our findings suggest that encountering parasites affects migratory activity, regardless of whether infection occurs or is resisted.

Parent and offspring genotypes influence gene expression in early life

Parents can have profound effects on offspring fitness. Little, however, is known about the mechanisms through which parental genetic variation influences offspring physiology in natural systems. White-throated sparrows (Zonotrichia albicollis, WTSP) exist in two genetic morphs, tan and white, controlled by a large polymorphic supergene. Morphs mate disassortatively, resulting in two pair types: tan male × white female (T × W) pairs, which provide biparental care and white male × tan female (W × T) pairs, which provide female-biased care. To investigate how parental composition impacts offspring, we performed RNA-seq on whole blood of WTSP nestlings sampled from nests of both pair types. Parental pair type had a large effect on nestling gene expression, with 881 genes differentially expressed (DE) and seven correlated gene coexpression modules. The DE genes and modules expressed at higher levels in W × T nests with female-biased parental care function in metabolism and stress-related pathways resulting from the overrepresentation of proteolysis and stress-response genes (e.g., SOD2, NR3C1). These results show that parental genotypes and/or associated behaviours influence nestling physiology, and highlight avenues of further research investigating the ultimate implications for the maintenance of this polymorphism. Nestlings also exhibited morph-specific gene expression, with 92 differentially expressed genes, comprising immunity genes and genes encompassed by the supergene. Remarkably, we identified the same regulatory hub genes in these blood-derived expression networks as were previously identified in adult WTSP brains (EPM2A, BPNT1, TAF5L). These hub genes were located within the supergene, highlighting the importance of this gene complex in structuring regulatory networks across diverse tissues.

A chromosomal inversion predicts the expression of sex steroid-related genes in a species with alternative behavioral phenotypes

In white-throated sparrows, a chromosomal rearrangement has led to alternative phenotypes that differ in sex steroid-dependent behaviors. The rearrangement has captured the genes estrogen receptor alpha and 5-alpha reductase, making these genes strong candidates for mediating the behavioral phenotypes. We report here that of the two genes, expression of estrogen receptor alpha mRNA differs between the morphs and predicts behavior to a much greater extent than does expression of 5-alpha reductase mRNA. Differentiation of estrogen receptor alpha, therefore, is likely more important for the behavioral phenotypes. We also found that in some brain regions, the degree to which testosterone treatment affects the expression of steroid-related genes depends strongly on morph. A large morph difference in estrogen receptor alpha mRNA expression in the amygdala appears to be independent of plasma testosterone; this difference persists during the non-breeding season and is detectable in nestlings at post-hatch day seven. The latter result suggests a substrate for organizational effects of hormones during development.

Polymorphism of Sooty-fronted Spinetail (Synallaxis frontalis Aves: Furnariidae): Evidence of chromosomal rearrangements by pericentric inversion in autosomal macrochromosomes

The Passeriformes is the most diverse and cytogenetically well-known clade of birds, comprising approximately 5,000 species. The sooty-fronted spinetail (Synallaxis frontalis Aves: Furnariidae) species, which belongs to the order Passeriformes, is typically found in South America, where it is widely distributed. Polymorphisms provide genetic variability, important for several evolutionary processes, including speciation and adaptation to the environment. The aim of this work was to analyze the possible cytotypes and systemic events involved in the species polymorphism. Of the sampled 19 individuals, two thirds were polymorphic, an event supposedly linked to mutations resulting from genomic evolution that can be transmitted hereditarily. A chromosomal polymorphism was detected between the 1st and 3rdpairs of autosomal macrochromosomes. This type of polymorphism is related to a pericentric inversion in regions involving chromosomal rearrangements. Differently from other polymorphism studies that report a link between polymorphic chromosomes and phenotypic changes, S. frontalis did not present any morphological variation in the sampled individuals.

Actuarial senescence in a dimorphic bird: different rates of ageing in morphs with discrete reproductive strategies

It is often hypothesized that intra-sexual competition accelerates actuarial senescence, or the increase in mortality rates with age. However, an alternative hypothesis is that parental investment is more important to determining senescence rates. We used a unique model system, the white-throated sparrow (Zonotrichia albicollis), to study variation in actuarial senescence. In this species, genetically determined morphs display discrete mating strategies and disassortative pairing, providing an excellent opportunity to test the predictions of the above hypotheses. Compared to tan-striped males, white-striped males are more polygynous and aggressive, and less parental. Tan-striped females receive less parental support, and invest more into parental care than white-striped females, which are also more aggressive. Thus, higher senescence rates in males and white-striped birds would support the intra-sexual competition hypothesis, whereas higher senescence rates in females and tan-striped birds would support the parental investment hypothesis. White-striped males showed the lowest rate of actuarial senescence. Tan-striped females had the highest senescence rate, and tan-striped males and white-striped females showed intermediate, relatively equal rates. Thus, results were inconsistent with sexual selection and competitive strategies increasing senescence rates, and instead indicate that senescence may be accelerated by female-biased parental care, and lessened by sharing of parental duties.

Chromosomal polymorphism and comparative chromosome painting in the rufous-collared sparrow (Zonotrichia capensis)

Zonotrichia capensis is widely distributed in the Neotropics. Previous cytogenetic studies demonstrated the presence of polymorphisms in two chromosome pairs (ZCA2 and ZCA4). Here, we report results based on comparative chromosome painting, using probes derived from Gallus gallus and Leucopternis albicollis, focused on characterizing the chromosome organization of Z. capensis. Our results demonstrate the conservation of ancestral syntenies as observed previously in other species of passerine. Syntenies were rearranged by a series of inversions in the second chromosome as described in other Passeriformes, but in this species, by using probes derived from L. albicollis we observed an extra inversion in the second chromosome that had not previously been reported. We also report a paracentric inversion in pair 3; this chromosome corresponds to the second chromosome in Zonotrichia albicollis and may indicate the presence of ancestral inversions in the genus. The chromosomal inversions we found might be important for understanding the phenotypic variation that exists throughout the distribution of Z. capensis.

Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations?

Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations.

Sociability in Fruit Flies: Genetic Variation, Heritability and Plasticity

Sociability, defined as individuals' propensity to participate in non-aggressive activities with conspecifics, is a fundamental feature of behavior in many animals including humans. However, we still have a limited knowledge of the mechanisms and evolutionary biology of sociability. To enhance our understanding, we developed a new protocol to quantify sociability in fruit flies (Drosophila melanogaster). In a series of experiments with 59 F1 hybrids derived from inbred lines, we documented, first, significant genetic variation in sociability in both males and females, with broad-sense heritabilities of 0.24 and 0.21 respectively. Second, we observed little genetic correlation in sociability between the sexes. Third, we found genetic variation in social plasticity among the hybrids, with a broad-sense heritability of ~0.24. That is, genotypes differed in the degree of sociability after experiencing the same relevant social experience. Our data pave the way for further research on the mechanisms that underlie sociability as well as its ecological and evolutionary consequences.

Morph-Specific Patterns of Reproductive Senescence: Connections to Discrete Reproductive Strategies

How reproductive strategies contribute to patterns of senescence in natural populations remains contentious. We studied reproductive senescence in the dimorphic white-throated sparrow, an excellent species for exploring this issue. Within both sexes the morphs use distinct reproductive strategies, and disassortative pairing by morph results in pair types with distinct parental systems. White morph birds are more colorful and aggressive than tan counterparts, and white males compete for extrapair matings, whereas tan males are more parental. Tan males and white females share parental care equally, whereas white males provide little parental support to tan females. We found morph-specific patterns of reproductive senescence in both sexes. White males exhibited greater reproductive senescence than tan males. This result likely reflects the difficulty of sustaining a highly competitive reproductive strategy as aging progresses rather than high physiological costs of competitiveness, since white males were also long-lived. Moreover, morph was not consistently related to reproductive senescence across the sexes, arguing against especially high costs of the traits associated with white morph identity. Rather, tan females exhibited earlier reproductive senescence than white females and were short-lived, perhaps reflecting the challenges of unsupported motherhood. Results underscore the importance of social dynamics in determining patterns of reproductive senescence.

Negative-Assortative Mating in the White-Throated Sparrow

Nonrandom mating based on phenotype has been observed in a number of organisms, but a very high proportion of these examples are of assortative mating. The strongest example of negative-assortative mating is for white-striped versus tan-striped crown in the white-throated sparrow, where about 98% of the observed pairings (mated pairs or social pairs) are between mates with different phenotypes and the correlation between mating types is -0.964. Although nonrandom mating has been explored theoretically for decades, these models have generally not focused on specific well-documented examples. Here we have developed a model to investigate the dynamics and equilibrium of this iconic example. The observed pattern of mating appears to be the result of 96% negative-assortative mating and a 17% advantage of W (white) male × T (tan) female matings compared to the reciprocal T male × W female matings. The equilibrium heterozygosity given these values is 0.500, very close to the 0.501 observed in our large sample of pairings, and this heterozygosity has been maintained for the 29 years from 1988 to 2016. In addition, the equilibrium frequency of 2m inversion determining the white-striped phenotype has been maintained at a frequency very close to its equilibrium frequency of 0.25. Overall, this model demonstrates how evolutionary genetic models can be used to understand negative-assortative mating.

Rapid effects of estradiol on aggression depend on genotype in a species with an estrogen receptor polymorphism

The white-throated sparrow (Zonotrichia albicollis) represents a powerful model in behavioral neuroendocrinology because it occurs in two plumage morphs that differ with respect to steroid-dependent social behaviors. Birds of the white-striped (WS) morph engage in more territorial aggression than do birds of the tan-striped (TS) morph, and the TS birds engage in more parenting behavior. This behavioral polymorphism is caused by a chromosomal inversion that has captured many genes, including estrogen receptor alpha (ERα). In this study, we tested the hypothesis that morph differences in aggression might be explained by differential sensitivity to estradiol (E2). We administered E2 non-invasively to non-breeding white-throated sparrows and quantified aggression toward a conspecific 10 min later. E2 administration rapidly increased aggression in WS birds but not TS birds, consistent with our hypothesis that differential sensitivity to E2 may at least partially explain morph differences in aggression. To query the site of E2 action in the brain, we administered E2 and quantified Egr-1 expression in brain regions in which expression of ERα is known to differ between the morphs. E2 treatment decreased Egr-1 immunoreactivity in nucleus taeniae of the amygdala, but this effect did not depend on morph. Overall, our results support a role for differential effects of E2 on aggression in the two morphs, but more research will be needed to determine the neuroanatomical site of action.

Multiple signaling functions of song in a polymorphic species with alternative reproductive strategies

Vocal traits can be sexually selected to reflect male quality, but may also evolve to serve additional signaling functions. We used a long-term dataset to examine the signaling potential of song in dimorphic white-throated sparrows (Zonotrichia albicollis). We investigated whether song conveys multifaceted information about the vocalizing individual, including fitness, species identity, individual identity, and morph. We also evaluated whether song traits correlate differently with fitness in the two morphs, as the more promiscuous strategy of white, relative to tan, morph males might impose stronger sexual selection. Males with high song rates achieved higher lifetime reproductive success, and this pattern was driven by white morph males. In addition, males that sang songs with many notes survived longer, but this pattern was less robust. Thus, song traits reflect differences in fitness and may more strongly affect fitness in the white morph. Song frequency was unrelated to fitness, body size, or morph, but was individual specific and could signal individual identity. Songs of the two morphs displayed similar frequency ratios and bandwidths. However, tan morph males sang songs with longer first notes, fewer notes, and higher variability. Thus, song could be used in morph discrimination. Variation in frequency ratios between notes was low and could function in conspecific recognition, but pitch change dynamics did differ between four different song types observed. Our results support a multiple messages model for white-throated sparrow song, in which different song traits communicate discrete information about the vocalizing individual.

The colour of paternity: extra-pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs

In socially monogamous species, individuals can use extra-pair paternity and offspring sex allocation as adaptive strategies to ameliorate costs of genetic incompatibility with their partner. Previous studies on domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic incompatibility between head colour morphs, the effects of which are more severe in female offspring. Domesticated females use differential sex allocation, and extra-pair paternity with males of compatible head colour, to reduce fitness costs associated with incompatibility in mixed-morph pairings. However, laboratory studies are an oversimplification of the complex ecological factors experienced in the wild and may only reflect the biology of a domesticated species. This study aimed to examine the patterns of parentage and sex ratio bias with respect to colour pairing combinations in a wild population of the Gouldian finch. We utilized a novel PCR assay that allowed us to genotype the morph of offspring before the morph phenotype develops and to explore bias in morph paternity and selection at the nest. Contrary to previous findings in the laboratory, we found no effect of pairing combinations on patterns of extra-pair paternity, offspring sex ratio or selection on morphs in nestlings. In the wild, the effect of morph incompatibility is likely much smaller, or absent, than was observed in the domesticated birds. Furthermore, the previously studied domesticated population is genetically differentiated from the wild population, consistent with the effects of domestication. It is possible that the domestication process fostered the emergence (or enhancement) of incompatibility between colour morphs previously demonstrated in the laboratory.

Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae)

Colour polymorphism is known to facilitate speciation but the genetic basis of animal pigmentation and how colour polymorphisms contribute to speciation is poorly understood. Restricted recombination may promote linkage disequilibrium between the colour locus and incompatibility genes. Genomic rearrangement and the position of relevant loci within a chromosome are important factors that influence the frequency of recombination. Therefore, it is important to know the position of the colour locus, gene order and recombination landscape of the chromosome to understand the mechanism that generates incompatibilities between morphs. Recent studies showed remarkable pre- and postzygotic incompatibilities between sympatric colour morphs of the Gouldian finch (Erythrura gouldiae), in which head feather colour is genetically determined by a single sex-linked locus, Red. We constructed a genetic map for the Z chromosome of the Gouldian finch (male-specific map distance=131 cM), using 618 captive-bred birds and 34 microsatellite markers, to investigate the extent of inter- and intraspecific genomic rearrangements and variation in recombination rate within the Z chromosome. We refined the location of the Red locus to a ~7.2-cM interval in a region with a moderate recombination rate but outside the least-recombining, putative centromeric region. There was no evidence of chromosome-wide genomic rearrangements between the chromosomes carrying the red or black alleles with the current marker resolution. This work will contribute to identifying the causal gene, which will in turn enable alternative explanations for the association between incompatibility and colouration, such as fine-scale linkage disequilibrium, genomic rearrangements and pleiotropy, to be tested.

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

A major challenge in biology is to understand the genetic basis of adaptation. One compelling idea is that groups of tightly linked genes (i.e., "supergenes" [1, 2]) facilitate adaptation in suites of traits that determine fitness. Despite their likely importance, little is known about how alternate supergene alleles arise and become differentiated, nor their ultimate fate within species. Herein we address these questions by investigating the evolutionary history of a supergene in white-throated sparrows, Zonotrichia albicollis. This species comprises two morphs, tan and white, that differ in pigmentation and components of social behavior [3-5]. Morph is determined by alternative alleles at a balanced >100-Mb inversion-based supergene, providing a unique system for studying gene-behavior relationships. Using over two decades of field data, we document near-perfect disassortative mating among morphs, as well as the fitness consequences of rare assortative mating. We use de novo whole-genome sequencing coupled with population- and phylogenomic data to show that alternate supergene alleles are highly divergent at over 1,000 genes and that these alleles originated prior to the split of Z. albicollis from its sister species and may be polymorphic in Z. albicollis due to a past hybridization event. We provide evidence that the "white" allele may be degrading, similar to neo-Y/W sex chromosomes. We further show that the "tan" allele has surprisingly low levels of genetic diversity yet does not show several canonical signatures of recurrent positive selection. We discuss these results in the context of the origin, molecular evolution, and possible fate of this remarkable polymorphism.

Genetics of aggressive behavior: An overview

The Research Domain Criteria (RDoC) address three types of aggression: frustrative non-reward, defensive aggression and offensive/proactive aggression. This review sought to present the evidence for genetic underpinnings of aggression and to determine to what degree prior studies have examined phenotypes that fit into the RDoC framework. Although the constructs of defensive and offensive aggression have been widely used in the animal genetics literature, the human literature is mostly agnostic with regard to all the RDoC constructs. We know from twin studies that about half the variance in behavior may be explained by genetic risk factors. This is true for both dimensional, trait-like, measures of aggression and categorical definitions of psychopathology. The non-shared environment seems to have a moderate influence with the effects of shared environment being unclear. Human molecular genetic studies of aggression are in an early stage. The most promising candidates are in the dopaminergic and serotonergic systems along with hormonal regulators. Genome-wide association studies have not yet achieved genome-wide significance, but current samples are too small to detect variants having the small effects one would expect for a complex disorder. The strongest molecular evidence for a genetic basis for aggression comes from animal models comparing aggressive and non-aggressive strains or documenting the effects of gene knockouts. Although we have learned much from these prior studies, future studies should improve the measurement of aggression by using a systematic method of measurement such as that proposed by the RDoC initiative.

The danger within: the role of genetic, behavioural and ecological factors in population persistence of colour polymorphic species

Polymorphic species have been the focus of important work in evolutionary biology. It has been suggested that colour polymorphic species have specific evolutionary and population dynamics that enable them to persist through environmental changes better than less variable species. We suggest that recent empirical and theoretical work indicates that polymorphic species may be more vulnerable to extinction than previously thought. This vulnerability arises because these species often have a number of correlated sexual, behavioural, life history and ecological traits, which can have a simple genetic underpinning. When exacerbated by environmental change, these alternate strategies can lead to conflict between morphs at the genomic and population levels, which can directly or indirectly affect population and evolutionary dynamics. In this perspective, we identify a number of ways in which the nature of the correlated traits, their underpinning genetic architecture, and the inevitable interactions between colour morphs can result in a reduction in population fitness. The principles illustrated here apply to all kinds of discrete polymorphism (e.g. behavioural syndromes), but we focus primarily on colour polymorphism because they are well studied. We urge further empirical investigation of the genetic architecture and interactions in polymorphic species to elucidate the impact on population fitness.

Estrogen Receptor Alpha as a Mediator of Life-History Trade-offs

Trade-offs between competitive and parental strategies often are mediated by sex steroids. The mechanisms underlying steroid signaling and metabolism may therefore serve as targets of disruptive selection that leads to alternative behavioral phenotypes. White-throated sparrows exhibit two color morphs that differ in both competitive and parental behavior; white-striped (WS) birds engage in more territorial singing, whereas tan-striped (TS) birds provision nestlings more often. Although WS birds have higher levels of plasma testosterone (T) and estradiol than do TS birds, experimental equalization of these hormones does not abolish morph differences in singing. Neural sensitivity to sex steroids may differ between the morphs because the gene for estrogen receptor alpha (ERα) has been captured by a chromosomal rearrangement found only in the WS birds. We recently showed that expression of this gene differs between the morphs and may drive the behavioral polymorphism. First, the ERα promoter region contains fixed polymorphisms that affect transcription efficiency in vitro. Second, in a free-living population, local expression of ERα depends strongly on morph and predicts both territorial singing and parental provisioning. Differential ERα expression is particularly striking in the medial amygdala; WS birds have three times more ERα mRNA than do TS birds. This difference persists during the non-breeding season and is unaffected by exogenous T treatment. Finally, preliminary data generated by RNA-seq confirm that ERα expression in MeA is both differentially expressed and correlated with territorial singing. Together, these results suggest that ERα may be a target of disruptive selection that leads to alternative behavioral strategies. Our future directions include a more detailed analysis of the ERα promoter regions to determine the molecular basis of differential expression as well as gene network analyses to identify genes connected to ERα.

New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis

The white-throated sparrow is a promising model for behavioural neuroendocrinology and genetics because behaviour and endocrine function may be linked to a chromosomal rearrangement that determines plumage colour. The notion that the two colour morphs, tan-striped (TS) and white-striped (WS), differ predictably in aggression and parenting has been widely accepted, despite conflicting evidence. It is also hypothesized that morph-typic behaviour is hormone mediated, yet no field study has measured sex steroids and behaviour in the same birds. Here, we re-evaluate the TS and WS phenotypes, describe the conditions under which they differ and investigate relationships between sex steroids and behaviour. We report that (1) during territorial intrusions, WS males were more aggressive than TS birds, but this difference was restricted to singing; WS males sang more than TS males but showed identical levels of physical aggression. WS females sang more than TS females and were also more physically aggressive. (2) TS males provisioned young more frequently than did WS males, but only during first broods. The parental strategy of WS males was flexible, and during replacement broods, WS and TS males provisioned at equal rates. (3) Consistent with previous studies, we detected no morph difference in female provisioning. (4) Plasma testosterone and dihydrotestosterone were higher in WS males than in TS males during periods of peak territorial defence and during first broods; within breeding stages, male androgen levels were positively correlated with singing and negatively correlated with provisioning. Plasma oestradiol levels were higher in WS females than in TS females and higher during peak territorial defence; oestradiol levels tended to be positively correlated with singing. Overall, our results refine the TS and WS phenotypes, show that behavioural differences between them are restricted to periods with relatively high mating opportunity, and demonstrate an association between sex steroids and morph-typic behaviour. These results will inform future studies of this promising model.

Evaluation of reference genes for quantitative real-time PCR in the brain, pituitary, and gonads of songbirds

Quantitative real-time PCR (qPCR) is becoming a popular tool for the quantification of gene expression in the brain and endocrine tissues of songbirds. Accurate analysis of qPCR data relies on the selection of appropriate reference genes for normalization, yet few papers on songbirds contain evidence of reference gene validation. Here, we evaluated the expression of ten potential reference genes (18S, ACTB, GAPDH, HMBS, HPRT, PPIA, RPL4, RPL32, TFRC, and UBC) in brain, pituitary, ovary, and testis in two species of songbirds: zebra finch and white-throated sparrow. We used two algorithms, geNorm and NormFinder, to assess the stability of these reference genes in our samples. We found that the suitability of some of the most popular reference genes for target gene normalization in mammals, such as 18S, depended highly on tissue type. Thus, they are not the best choices for brain and gonad in these songbirds. In contrast, we identified alternative genes, such as HPRT, RPL4 and PPIA, that were highly stable in brain, pituitary, and gonad in these species. Our results suggest that the validation of reference genes in mammals does not necessarily extrapolate to other taxonomic groups. For researchers wishing to identify and evaluate suitable reference genes for qPCR in songbirds, our results should serve as a starting point and should help increase the power and utility of songbird models in behavioral neuroendocrinology.

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel's white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as an important determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

Advancing avian behavioral neuroendocrinology through genomics

Genome technologies are transforming all areas of biology, including the study of hormones, brain and behavior. Annotated reference genome assemblies are rapidly being produced for many avian species. Here we briefly review the basic concepts and tools used in genomics. We then consider how these are informing the study of avian behavioral neuroendocrinology, focusing in particular on lessons from the study of songbirds. We discuss the impact of having a complete "parts list" for an organism; the transformational potential of studying large sets of genes at once instead one gene at a time; the growing recognition that environmental and behavioral signals trigger massive shifts in gene expression in the brain; and the prospects for using comparative genomics to uncover the genetic roots of behavioral variation. Throughout, we identify promising new directions for bolstering the application of genomic information to further advance the study of avian brain and behavior.

Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish

Phenotypic polymorphisms can be applied to study the micro-evolutionary forces that maintain genetic variation and can mediate speciation, but it can be difficult to determine the genetic basis of polymorphisms. Recently, restriction-site-associated DNA (RAD) sequencing has become popular, which can easily produce multiple single nucleotide polymorphisms from whole genomes. Here, we combined RAD sequencing, allele-specific PCR and Sanger sequencing to determine the genetic basis underlying male colour dimorphism of a Lake Tanganyika cichlid fish, Cyprichromis leptosoma. Our analyses using both a cross-family (two parents and 12 F2 males) and 64 wild individuals do not contradict a hypothesis that two alleles of one-locus control male colour dimorphism. Also, the locus may be located on a genome region that experiences reduced levels of recombination. Although more analyses will be needed to conclude these findings, this study is the first to suggest the genetic basis of a colour polymorphism using RAD sequencing.

Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

Background

The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation.

Findings

We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo.

Conclusions

These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.

Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis)

Inversion polymorphisms have been linked to a variety of fundamental biological and evolutionary processes. Yet few studies have used large-scale genomic sequencing to directly compare the haplotypes associated with the standard and inverted chromosome arrangements. Here we describe the targeted genomic sequencing and comparison of haplotypes representing alternative arrangements of a common inversion polymorphism linked to a suite of phenotypes in the white-throated sparrow (Zonotrichia albicollis). More than 7.4 Mb of genomic sequence was generated and assembled from both the standard (ZAL2) and inverted (ZAL2(m)) arrangements. Sequencing of a pair of inversion breakpoints led to the identification of a ZAL2-specific segmental duplication, as well as evidence of breakpoint reusage. Comparison of the haplotype-based sequence assemblies revealed low genetic differentiation outside versus inside the inversion indicative of historical patterns of gene flow and suppressed recombination between ZAL2 and ZAL2(m). Finally, despite ZAL2(m) being maintained in a near constant state of heterozygosity, no signatures of genetic degeneration were detected on this chromosome. Overall, these results provide important insights into the genomic attributes of an inversion polymorphism linked to mate choice and variation in social behavior.

Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis)

Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2(m)) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2(m) polymorphism is a complex inversion spanning > 100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2(m) polymorphism, we generated sequence from 8 ZAL2(m) and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2(m), resulting in uniformly high levels of genetic differentiation (F(ST)=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ~104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2(m) homozygotes are exceedingly rare in the population, occurring at a frequency of < 1%, we detected evidence of historical recombination between ZAL2(m) chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.

Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)

Background

The level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination. Avian karyotypes are typified by large variation in chromosome size and the rate of recombination in birds has been shown to be negatively correlated with chromosome size. It has thus been predicted that nucleotide diversity is negatively correlated with chromosome size in aves. However, there is limited empirical evidence to support this prediction.

Results

Here we sequenced 27 autosomal and 12 sex chromosome-linked loci in the white-throated sparrow (Zonotrichia albicollis) to quantify and compare patterns of recombination, linkage disequilibrium (LD), and genetic diversity across the genome of this North American songbird. Genetic diversity on the autosomes varied up to 8-fold, with the lowest diversity observed on the macrochromosomes and the highest diversity on the microchromosomes. Genetic diversity on the sex chromosomes was reduced compared to the autosomes, the most extreme difference being a ~300-fold difference between the W chromosome and the microchromosomes. LD and population structure associated with a common inversion polymorphism (ZAL2/2^m) in this species were found to be atypical compared to other macrochromosomes, and nucleotide diversity within this inversion on the two chromosome arrangements was more similar to that observed on the Z chromosome.

Conclusions

A negative correlation between nucleotide diversity and autosome size was observed in the white-throated sparrow genome, as well as low levels of diversity on the sex chromosomes comparable to those reported in other birds. The population structure and extended LD associated with the ZAL2/2^m chromosomal polymorphism are exceptional compared to the rest of the white-throated sparrow genome.