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Despite the increasing feasibility of sequencing whole genomes from diverse taxa, a persistent problem in phylogenomics is the selection of appropriate genetic markers or loci for a given taxonomic group or research question. In this review, we aim to streamline the decision-making process when selecting specific markers to use in phylogenomic studies by introducing commonly used types of genomic markers, their evolutionary characteristics, and their associated uses in phylogenomics. Specifically, we review the utilities of ultraconserved elements (including flanking regions), anchored hybrid enrichment loci, conserved nonexonic elements, untranslated regions, introns, exons, mitochondrial DNA, single nucleotide polymorphisms, and anonymous regions (nonspecific regions that are evenly or randomly distributed across the genome). These various genomic elements and regions differ in their substitution rates, likelihood of neutrality or of being strongly linked to loci under selection, and mode of inheritance, each of which are important considerations in phylogenomic reconstruction. These features may give each type of marker important advantages and disadvantages depending on the biological question, number of taxa sampled, evolutionary timescale, cost effectiveness, and analytical methods used. We provide a concise outline as a resource to efficiently consider key aspects of each type of genetic marker. There are many factors to consider when designing phylogenomic studies, and this review may serve as a primer when weighing options between multiple potential phylogenomic markers.

Reproduction and self-maintenance are energetically costly activities involved in classic life history trade-offs. However, few studies have measured the responses of wild organisms to simultaneous changes in reproductive and self-maintenance costs, which may have interactive effects. In free-living female Barn Swallows (Hirundo rustica), we simultaneously manipulated reproductive costs (by adding or removing two nestlings) and self-maintenance costs (by attaching a ∼ 1 gram weight in the form of a GPS tag to half of our study birds) and measured mass, immune status, blood glucose, feather growth and reproductive output (likelihood of a second clutch, number of eggs, and time between clutches). GPS tags allowed us to analyze how movement range size affected response to brood size manipulation. Tagging altered females’ immune function as evidenced by an elevated heterophil to lymphocyte (H: L) ratio, but all females were equally likely to lay more eggs. There was no evidence of interactive effects of the tagging and brood size treatment. Range size was highly variable, and birds with large ranges grew feathers more slowly, but analyzing the effect of brood size manipulation while accounting for variation in range size did not result in any physiological response. Our results support the theoretical prediction that short-lived vertebrates do face a trade-off between reproduction and self-maintenance and, when faced with increased costs, tend to preserve investment in reproduction at the expense of parental condition. This experiment also helps us to understand how movement patterns may be relevant to life history trade-offs in wild birds.

Migratory divides are contact zones between breeding populations with divergent migratory strategies during the nonbreeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide coinciding with genomic differentiation across a hybrid zone between barn swallow (Hirundo rustica) subspecies in China. Individuals west of the hybrid zone, with H. r. rustica ancestry, had comparatively enriched stable-carbon and hydrogen isotope values and overwintered in eastern Africa, whereas birds east of the hybrid zone, with H. r. gutturalis ancestry, had depleted isotope values and migrated to southern India. The two subspecies took divergent migratory routes around the high-altitude Karakoram Range and arrived on the breeding grounds over 3 weeks apart. These results indicate that assortative mating by timing of arrival and/or selection against hybrids with intermediate migratory traits may maintain reproductive isolation between the subspecies, and that inhospitable geographic features may have contributed to the diversification of Asian avifauna by influencing migratory patterns.

Diversity is a key driver of scientific innovation, yet fields in science, technology, engineering, and mathematics (STEM) have struggled to retain diverse communities. Research suggests that fostering a sense of belonging is critical for retaining diversity. We propose an iterative process that aims to improve sense of belonging among laboratory (lab) members through self-reflection and community collective action.

Abstract Life history theory predicts that increased investment in current offspring decreases future fecundity or survival. Avian parental investment decisions have been studied either via brood size manipulation or direct manipulation of parental energetic costs (also known as handicapping). However, we have limited experimental data on the potential interactive effects of these manipulations on parent behavior. Additionally, we know little about how these manipulations affect spatial foraging behavior away from the nest. We simultaneously manipulated brood size and parental costs (via added weight in the form of a GPS tag) in wild female barn swallows (Hirundo rustica). We measured multiple aspects of parent behavior at and away from the nest while controlling for measures of weather conditions. We found no significant interactive effects of manipulated brood size and parental costs. Both sexes increased their visitation rate with brood size, but nestlings in enlarged broods grew significantly less post-brood size manipulation than those in reduced broods. Foraging range area was highly variable among GPS-tagged females but was unaffected by brood size. As such, increased visitation rate in response to brood size may be more energetically costly for far-ranging females. GPS-tagged females did not alter their visitation rate relative to un-tagged birds, but their mates had higher visitation rates. This suggests that GPS tagging may affect some unmeasured aspect of female behavior, such as prey delivery. Our findings indicate that investigation of foraging tactics alongside visitation rate is critical to understanding parental investment and the benefits and costs of reproduction. Significance statement Avian parental investment decisions have been studied by either brood size manipulation or direct manipulation of parental costs, but rarely both simultaneously. We simultaneously manipulated brood size and parental costs (via addition of a GPS tag) in a wild avian system, allowing us to examine interactive effects of these manipulations. Additionally, studies of parental investment often examine behaviors at the nest, but measurements of parental care behavior away from the nest are rare. Our study is unique in that we measured multiple aspects of parental care, including spatial foraging behavior tracked with GPS tags. We found no interactive effects of manipulated brood size and parental costs on visitation rate or nestling growth, and spatial foraging behavior of females was individually variable. Documenting foraging tactics alongside visitation rate is critical to understanding parental investment because the same visitation rate might be more costly for far-ranging females.

Avian incubation is a highly complex, adjustable behavior essential to embryo development and survival. When incubating, parents face a tradeoff between investing in incubation to maintain optimal temperatures for egg development or in self-maintenance behaviors to ensure their own survival and future reproduction. Because nest ectoparasites are costly and can reduce nestling quality and survival, infections could shift parental investment in current vs. future offspring. However, it is not well understood whether birds change investment in incubation in response to nest ectoparasitism, particularly in the context of other factors that are known to influence incubation behavior, such as ambient temperature, clutch size, and embryo development. We hypothesized that parents could respond to nest parasites by 1) investing more in incubation to promote the development of high-quality offspring to help offset the cost of parasites, 2) investing less in incubation or even abandoning their nest during incubation to save resources for future reproduction, or 3) being unresponsive to parasite infections, as incubation is more constrained by other factors. We tested these hypotheses by experimentally removing and adding mites in barn swallow nests at the start of incubation and deploying thermocouple eggs to measure egg temperatures at one-minute intervals until hatching. We found that while ambient temperature, clutch initiation date, embryo age, and clutch size were the main factors driving variation in egg conditions and parental incubation behavior, parasitized nests had higher mean egg temperatures, which could aid in nestling immune development. However, despite more optimal developmental temperatures, eggs in parasitized nests also had lower hatching success. Our results indicate that incubation is a dynamic behavior that is largely driven by the constraints of maintaining appropriate egg temperatures for development. Although quite costly upon hatching, ectoparasites appear to play a relatively minor role in driving variation in parental incubation investment.LAY SUMMARYIncubation is a complex behavior shaped by both internal and external factors.Ectoparasites often decrease quality and survival of nestlings and could influence investment in incubation because of tradeoffs in how parents spend energy.We manipulated parasites in barn swallow nests and used fake eggs with temperature sensors to collect data on egg temperatures and parental behavior throughout incubation.We found that other factors were the main drivers of variation in incubation behavior, but that eggs in parasite nests were warmer on average, which could help nestlings better cope with parasites upon hatching.Despite more optimal developmental temperatures, eggs in parasitized nests had lower hatching success.Although quite costly to nestlings, ectoparasites played a minor role in shaping parental incubation behavior.

Sex chromosomes often bear distinct patterns of genetic variation due to unique patterns of inheritance and demography. The processes of mutation, recombination, genetic drift and selection also influence rates of evolution on sex chromosomes differently than autosomes. Measuring such differences provides information about how these processes shape genomic variation and their roles in the origin of species. To test hypotheses and predictions about patterns of autosomal and sex-linked genomic diversity and differentiation, we measured population genetic statistics within and between populations and subspecies of the barn swallow (Hirundo rustica) and performed explicit comparisons between autosomal and Z-linked genomic regions. We first tested for evidence of low Z-linked genetic diversity and high Z-linked population differentiation relative to autosomes, then for evidence that the Z chromosome bears greater ancestry information due to faster lineage sorting. Finally, we investigated geographical clines across hybrid zones for evidence that the Z chromosome is resistant to introgression due to selection against hybrids. We found evidence that the barn swallow mating system, demographic history and linked selection each contribute to low Z-linked diversity and high Z-linked differentiation. While incomplete lineage sorting is rampant across the genome, our results indicate faster sorting of ancestral polymorphism on the Z. Finally, hybrid zone analyses indicate barriers to introgression on the Z chromosome, suggesting that sex-linked traits are important in reproductive isolation, especially in migratory divide regions. Our study highlights how selection, gene flow and demography shape sex-linked genetic diversity and underlines the relevance of the Z chromosome in speciation.

Associations between parasite loads and sexual signal expression have long been the focus of research. However, our understanding of how sexual selection operates in the context of multiple parasite infections within the same host is still quite limited. We examined the expression of plumage coloration, which is sexually selected in North American barn swallows, Hirundo rustica erythrogaster, and tail streamer length, which is sexually selected in other barn swallow subspecies, in the context of eight different parasite infections. We found that two parasites, nest mites and Plasmodium, were associated with colour expression, but in opposite directions. Attractive males were less likely to have mites in their nests, but more likely to be infected with Plasmodium. We found that different underlying mechanisms were generating the links between these different parasites and the same colour signal. Males that invested more in colour expression were less likely to survive when infected with Plasmodium, suggesting a physiological mechanism linking colour to Plasmodium infections. However, we found no clear cost to males when examining nest mites, which primarily infect offspring. Instead, using experimental mite manipulations, we provide evidence for a behavioural mechanism, where territorial behaviour and male–male competition likely drive the association between colour expression and nest mite infections. We did not find associations between parasites and streamer length in this subspecies, suggesting that the links between divergent sexual signals and parasites may be quite flexible. These results suggest that the evolution of a single sexual signal can be shaped by several, even opposing, links with different parasite infections.

Urbanization implies a dramatic impact on ecosystems, which may lead to drastic phenotypic differences between urban and nonurban individuals. For instance, urbanization is associated with increased metabolic costs, which may constrain body size, but urbanization also leads to habitat fragmentation, which may favor increases in body mass when for instance it correlates with dispersal capacity. However, this apparent contradiction has rarely been studied. This is particularly evident in China where the urbanization process is currently occurring at an unprecedented scale. Moreover, no study has addressed this issue across large geographical areas encompassing locations in different climates. In this regard, Barn Swallows (Hirundo rustica) are a suitable model to study the impact of urbanization on wild animals because they are a widely distributed species tightly associated with humans. Here, we collected body mass and wing length data for 359 breeding individuals of Barn Swallow (H. r. gutturalis) from 128 sites showing different levels of urbanization around the whole China. Using a set of linear mixed‐effects models, we assessed how urbanization and geography influenced body size measured using body mass, wing length, and their regression residuals. Interestingly, we found that the impact of urbanization was sex‐dependent, negatively affecting males’ body mass, its regression residuals, and females’ wing length. We also found that northern and western individuals were larger, regarding both body mass and wing length, than southern and eastern individuals. Females were heavier than males, yet males had slightly longer wings than females. Overall, our results showed that body mass of males was particularly sensitive trait to urbanization, latitude, and longitude, while it only showed a weak response to latitude in females. Conversely, while wing length showed a similar geographical pattern, it was only affected by urbanization in the case of females. Further research is needed to determine whether these phenotypic differences are associated with negative effects of urbanization or potential selective advantages., Urbanization has become one of the defining questions of the Anthropocene. In China, our results showed that body size of Barn Swallows decreased towards the South and West and with increasing urbanization. This effect was, however, sex‐dependent, affecting wing‐length in females and body mass and body size index in males.

Understanding the patterns and processes related to sexual dimorphism and sex differences in diverse animal taxa is a foundational research topic in ecology and evolution. Within the realm of animal communication, studies have traditionally focused on male signals, assuming that female choice and male–male competition have promoted sex differences via elaboration of male traits, but selection on females also has the potential to drive divergence. Here, we describe female song in barn swallows, Hirundo rustica erythrogaster, for the first time, report rates of female song production and couple song data with plumage data to explore the relative degree to which sex differences in phenotypic traits are consistent with contemporary selection on males versus females. During previous intensive study of male song over 2 years, we opportunistically recorded songs for 15 females, with matched phenotypic and fitness data. We randomly selected 15 high-quality samples from our larger male data set to test whether sex differences in song and plumage are more strongly associated with fledgling success for females or genetic paternity for males. Analyses included 35 potential sexual signals including 22 song parameters and 13 plumage traits. Outcomes indicate that female songs were used in multiple contexts, restricted primarily to the beginning of the breeding season; song traits showed greater sexual differentiation than visual plumage traits; and trait correlations with reproductive success in females, rather than males, predicted sex-based differences in song and plumage. These results are consistent with phylogenetic studies showing that sex-based phenotypic differences are driven by changes in females, highlighting the potential role of female trait evolution in explaining patterns of sexual differentiation. To achieve a better understanding of sex differences and dimorphism, we require comprehensive studies that measure the same traits in males and females and their fitness consequences.

Phenotypic variation is often used to delineate species and subspecies boundaries. Statistical analysis of phenotypic variation within a species is helpful both for understanding biodiversity and for its conservation. At least three named subspecies of barn swallows (Hirundo rustica) have distributions that span China, yet, to date, no systematic study of phenotypic differentiation has been applied to understand the delineation of these subspecies. In this study, we collected 510 samples of barn swallow from 23 populations in China, including two recognized subspecies, H. r. rustica and H. r. gutturalis, and one potential subspecies, H. r. mandschurica. With these samples, we examined and found morphometric and colour differences among different populations. Western Chinese barn swallows (H. r. rustica) have larger body size and could be clearly differentiated from eastern H. r. gutturalis and H. r. mandschurica, while north-eastern populations (named H. r. mandschurica) have darker, redder ventral plumage than H. r. rustica and H. r. gutturalis. However, we inferred that although there were phenotypic differences between H. r. mandschurica and H. r. gutturalis, they were not sufficiently distinct to assign them to separate subspecies based on the 75% rule for defining subspecies.

Many closely related populations are distinguished by variation in sexual signals and this variation is hypothesized to play an important role in reproductive isolation and speciation. Within populations, there is considerable evidence that sexual signals provide information about the incidence and severity of parasite infections, but it remains unclear if variation in parasite communities across space could play a role in initiating or maintaining sexual trait divergence. To test for variation in parasite-associated selection, we compared three barn swallow subspecies with divergent sexual signals. We found that parasite community structure and host tolerance to ecologically similar parasites varied between subspecies. Across subspecies we also found that different parasites were costly in terms of male survival and reproductive success. For each subspecies, the preferred sexual signal(s) were associated with the most costly local parasite(s), indicating that divergent signals are providing relevant information to females about local parasite communities. Across subspecies, the same traits were often associated with different parasites, indicating that parasite-sexual signal links are quite flexible and may evolve relatively quickly. This study provides evidence for (1) variation in parasite communities and (2) different parasite-sexual signal links among three closely related subspecies with divergent sexual signal traits, suggesting that parasites may play an important role in initiating and/or maintaining the divergence of sexual signals among these closely related, yet geographically isolated populations.

Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, it is difficult to test the relative contributions of migratory behaviour vs. other divergent traits to reproductive isolation. Comparing hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behaviour to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive isolation coincided with a migratory divide spanning 20 degrees of latitude. A third subspecies pair exhibited no evidence for a migratory divide and hybridised extensively. Within migratory divides, overwintering habitats were associated with assortative mating, implicating a central contribution of divergent migratory behaviour to reproductive barriers. The remarkable geographic coincidence between migratory divides and genetic breaks supports a long-standing hypothesis that the Tibetan Plateau is a substantial barrier contributing to the diversity of Siberian avifauna.

Twenty years ago, a seminal paper summarized the role of sexual selection in speciation as the coordinated evolution of (male) courtship signals and (female) preferences leading to prezygotic (behavioral) isolation between divergent lineages. Here, we discuss areas of progress that inspire an updated perspective. First, research has identified multiple mechanisms of sexual selection, in addition to female mate choice, that drive the origin and maintenance of species. Second, reviews and empirical data now conclude that sexual selection alone will rarely lead to reproductive isolation without ecological divergence, and we discuss the assumptions and possible exceptions underlying that conclusion. Finally, we consider the variable ways in which sexual selection contributes to divergence according to the spatial, temporal, social, ecological, and genomic context of speciation.

We propose an application of network analysis to determine which traits and behaviors predict fertilizations within and between populations. This approach quantifies how reproductive behavior between individuals shapes patterns of selection and gene flow, filling an important gap in our understanding of the connection between evolutionary processes and emergent patterns.

Choosy females drive isolation Rapid radiations of recently diverged species represent an excellent opportunity for exploring drivers of speciation. The capuchino seedeaters, a group of South American birds, include a number of species that, in the field, are often discernable only through male plumage and song. Turbek et al. used genomes and behavioral experiments to identify potential isolating factors in two members of this group and found that, though entirely sympatric, females mated only with conspecific males and that only a few genes differed between the species (see the Perspective by Jarvis). Thus, a small reshuffling of genes and reinforcement through mate choice has driven divergence in these overlapping and very similar species. Science , this issue p. eabc0256 ; see also p. 1312

Hirundo is the most species-rich genus of the passerine swallow family (Hirundinidae) and has a cosmopolitan distribution. Here we report the complete, annotated mitochondrial genomes for 25 individuals from 10 of the 14 extant Hirundo species; these include representatives from four subspecies of the barn swallow, H. rustica. Mitogenomes were conserved in size, ranging from 18,500 to 18,700 base pairs. They all contained 13 protein-coding regions, 22 tRNAs, a control region, and large and small ribosomal subunits. Phylogenetic analysis resolved most of the relationships between the studied species and subspecies which were largely consistent with previously published trees. Several new relationships were observed within the phylogeny that could have only been discovered with the increased amount of genetic material. This study represents the largest Hirundo mitochondrial phylogeny to date, and could serve as a vital tool for other studies focusing on the evolution of the Hirundo genus.

Assortative social interactions based on (sub)species recognition can be a driving force in speciation processes. To determine whether breeding Barn Swallows Hirundo rustica transitiva in Israel behave differentially towards members of their own subspecies, relative to a different, transient subspecies H. r. rustica and two sympatrically breeding species (Sand Martin Riparia riparia and House Sparrow Passer domesticus), we conducted a territory intrusion experiment near active nests using taxidermy models. Females responded less to the models than males, and the patterns of the recorded behavioral response traits co-varied statistically with sub- or species identity of the models, but none showed patterns of response selectivity for con(sub)specific model types only. These results do not support a role for subspecies recognition in the territorial intrusion responses of H. r. transitiva.

Many sexually selected traits exhibit phenotypic plasticity. Despite a growing appreciation for the ecological context in which sexual selection occurs, and for the role of plasticity in shaping traits associated with local adaptation and divergence, there is an important gap in knowledge about the onset and duration of plasticity in sexual trait expression. Integrating this temporal dimension of plasticity into models of sexual selection informs our understanding of the information conveyed by sexual traits and our predictions related to trait evolution, and is critical in this time of unprecedented and rapid environmental change. We conducted a systematic review of 869 studies to ask how trait modalities (e.g., visual and chemical) relate to the onset and duration of plasticity in vertebrate sexual signals. We show that this literature is dominated by studies of coloration in birds and fish, and most studies take place during the breeding season. Where possible, we integrate results across studies to link physiology of specific trait modalities with the life stage (e.g., juvenile, breeding, or nonbreeding) during which plasticity occurs in well‐studied traits. Limitations of our review included a lack of replication in our dataset, which precluded formal analysis. We argue that the timing of trait plasticity, in addition to environmental context, is critical for determining whether and how various communication signals are associated with ecological context, because plasticity may be ongoing or occur at only one point in an individual's lifetime, and determining a fixed trajectory of trait expression. We advocate for careful consideration of the onset and duration of plasticity when analyzing how environmental variation affects sexual trait expression and associated evolutionary outcomes., Despite a growing appreciation for the ecological context in which sexual selection occurs, there is an important gap in knowledge about the onset and duration of plasticity in sexual trait expression. We conducted a systematic review of 869 studies to ask how trait modalities (e.g., visual and chemical) relate to the onset and duration of plasticity in vertebrate sexual signals. We argue that the timing of trait plasticity, in addition to environmental context, is critical for determining whether and how various communication signals are associated with ecological context, because plasticity may be ongoing or occur at only one point in an individual's lifetime, and determining a fixed trajectory of trait expression.

Animals use morphological signals such as ornamental traits or weaponry to mediate social interactions, and the extent of signal trait elaboration is often positively associated with reproductive success. By demonstrating relationships between signal traits and fitness, researchers often make inferences about how behaviour operates to shape those outcomes. However, detailed information about fine-scale individual behaviour, and its physiological basis, can be difficult to obtain. Here we show that experimental manipulations to exaggerate a signal trait (plumage colour) and concomitant changes in testosterone and stress-induced corticosterone levels altered social interactivity between manipulated males and their social mates. On average, darkened males did not have higher levels of interactivity than unmanipulated males; however, males who experienced a greater shift in colour (pale to dark), a larger, positive change in testosterone levels, and a dampened stress-induced corticosterone response had a larger increase in the number of interactions with their social mate post-manipulation compared to pre-manipulation. This work provides new insights into the integration and real-time flexibility of multivariate phenotypes and direct evidence for the role of social interactions in pair bond maintenance. University of Colorado Innovative Seed Grant; National Science Foundation Postdoctoral Research Fellowship [DBI-1306059] We thank J. Burt for assistance with the tags, S. Turbek, and T. Albrecht for assistance in the field, and Colorado Horse Rescue for access to their barn. A University of Colorado Innovative Seed Grant provided funding for this research and I. Levin was supported by a National Science Foundation Postdoctoral Research Fellowship (DBI-1306059).

Accounting for historical demographic features is vital for many types of evolutionary inferences, including the estimation of divergence times between closely related populations. In barn swallow, Hirundo rustica, inferring historical population sizes and subspecies divergence times can shed light on the recent co-evolution of this species with humans. Pairwise sequentially Markovian coalescent uncovered population growth beginning on the order of one million years ago-which may reflect the radiation of the broader Hirundo genus-and a more recent population decline. Additionally, we used approximate Bayesian computation to evaluate hypotheses about recent timescale barn swallow demography, including population growth due to human commensalism, and a potential founder event associated with the onset of nesting on human structures. We found signal for a bottleneck event approximately 7,700 years ago, near the time that humans began building substantial structures, although there was considerable uncertainty associated with this estimate. Subspecies differentiation and subsequent growth occurred after the bottleneck in the best-supported model, an order of magnitude more recently than previous estimates in this system. We also compared results obtained from whole-genome sequencing versus reduced representation sequencing, finding many similar results despite substantial allelic dropout in the reduced representation data, which may have affected estimates of some parameters. This study presents the first genetic evidence of a potential barn swallow founder effect and subspecies divergence coinciding with the Holocene, which is an important step in analysing the biogeographical history of a well-known human commensal species.

Phenotypic differentiation is common among populations that have large geographic distributions. One proposed mechanism driving phenotype divergence is sexual selection, which predicts that trait differences among closely related populations are underlain by variation in reproductive performance. Here, we examined a population of Asian Barn Swallows (Hirundo rustica gutturalis) in northeastern China. We ask whether traits shown to be under divergent sexual selection in other Barn Swallow populations are under sexual selection in this north Asian population by determining whether two features of phenotype variation, tail streamer length and ventral plumage colouration (including both throat and belly regions), are sexually dimorphic, associated with patterns of assortative mating and predictive of reproductive success. In this population, the length of tail streamers did not correlate with ventral plumage colouration in either males or females. The length of tail streamers was sexually dimorphic, but we did not find assortative mating by tail streamer length. By contrast, we found no sexual dichromatism but we did find assortative mating by throat colouration. Our correlational results indicated that the breeding performance of male Barn Swallows was associated with differences in their ventral plumage colouration, suggesting that ventral plumage colouration is likely a target of sexual selection in this population. Our finding that tail streamer length is unlikely to be under sexual selection is consistent with studies of other H. rustica gutturalis populations. The result that ventral plumage colour is likely to be under sexual selection is partially consistent with previous studies on Japanese H. rustica gutturalis, in which male throat but not belly plumage colour is the sexually selected trait.

Nest-switching is an important breeding strategy for multiple-brooded bird species. When deciding whether or not to switch nests for subsequent breeding attempts, pairs must weigh the costs and benefits of various factors related to the number of fledglings of the first breeding attempt, the likelihood of nest predation, and qualities of the nest environment, such as nest ectoparasites and the age of the nest. In this study, we analyzed the predictors and consequences of nest-switching behavior at 6 breeding sites of North American Barn Swallows (Hirundo rustica erythrogaster), where 60% of pairs that raised 2 broods within a season switched nests for a second breeding attempt. Pairs often reused existing (old) nests constructed during previous years, and pairs that settled in old nests for their first breeding attempt were the most likely to switch nests for a second breeding attempt. Contrary to previous studies, nest predation and nest ectoparasitism had no influence on whether or not pairs sw...

Shen, Sheng-Feng/0000-0002-0631-6343; Karaardic, Hakan/0000-0001-9839-4201; Wilkins, Matthew/0000-0002-3162-6749 WOS: 000429470400011 Divergence in acoustic signals plays an important role in the production and maintenance of biodiversity in numerous taxa. In this study, we assess patterns of acoustic divergence in geographically isolated and sympatric subspecies of barn swallows (Hirundo rustica), including analyses of whether song differentiation varies with geographical isolation, genetic distance and climatic distance. We provide the first description of geographical variation in song among five of six currently recognized barn swallow subspecies. Temporal traits describing terminal trills were the most distinct song traits among subspecies, adding to growing evidence that trills are important in speciation among many birds, insects and fish. Across a similar to 6000 km transect of Russia, acoustic distance was predicted by genetic and geographical distance, but not climatic distance. We also found no reproductive character displacement of song traits in a contact zone between H. r. rustica and H. r. tytleri. Based on patterns discovered in this study, we infer an important role of sexual selection, genetic and/or cultural drift in the gradual build-up of acoustic divergence, which is accelerated in small populations. National Science Foundation Graduate Research Fellowship ProgramNational Science Foundation (NSF); University of Nebraska-Lincoln Population Biology Program of Excellence Postdoctoral Fellowship; University of Colorado Ecology and Evolution Department; American Ornithological Society: Alexander Wetmore Award; National Science FoundationNational Science Foundation (NSF) [DEB-CAREER 1149942] M.R.W. was supported by the National Science Foundation Graduate Research Fellowship Program program, the University of Nebraska-Lincoln Population Biology Program of Excellence Postdoctoral Fellowship, grants from the University of Colorado Ecology and Evolution Department, and the American Ornithological Society: Alexander Wetmore Award. M.R.W., E.S.C.S. and R.J.S. were supported by National Science Foundation DEB-CAREER 1149942 to R.J.S.

Seasonal journeys between breeding and non-breeding habitat are undertaken by a diverse array of animals. Parallel developments in tracking and genomic methods are enabling finer resolution of these movements and their role in the evolutionary process. Evidence from allopatric and co-occurring breeding populations indicates that variation in migratory behavior is often associated with genetic differentiation. While assortative mating and selection against hybrids due to divergent migratory phenotypes can contribute to reproductive isolation, the details of these mechanisms remain unclear. Here we identify gaps in our understanding of the role of seasonal migration in the speciation process and propose a framework to test the relative significance of reproductive barriers associated with variation in migratory behavior that might underlie population differentiation.

Hybrid zones are geographic regions where isolating barriers between divergent populations are challenged by admixture. Identifying factors that facilitate or inhibit hybridization in sympatry can illuminate the processes that maintain those reproductive barriers. We analysed patterns of hybridization and phenotypic variation across two newly discovered hybrid zones between three subspecies of barn swallow (Hirundo rustica). These subspecies differ in ventral coloration and wing length, traits that are targets of sexual and natural selection, respectively, and are associated with genome-wide differentiation in allopatry. We tested the hypothesis that the degree of divergence in these traits is associated with the extent of hybridization in secondary contact. We applied measures of population structure based on >23,000 SNPs to confirm that named subspecies correspond to distinct genomic clusters, and assessed coincidence between geographic clines for ancestry and phenotype. Although gene flow was ongoing across both hybrid zones and pairwise FST between subspecies was extremely low, we found striking differences in the extent of hybridization. In the more phenotypically differentiated subspecies pair, clines for ancestry, wing length and ventral coloration were steep and coincident, suggestive of strong isolation and, potentially, selection associated with phenotype. In the less phenotypically differentiated pair, gene flow and phenotypic variation occurred over a wide geographic span, indicative of weaker isolation. Traits associated with genome-wide differentiation in allopatry may thus also contribute to isolation in sympatry. We discuss potentially important additional roles for evolutionary history and ecology in shaping variation in the extent hybridization between closely related pairs of subspecies.

Because elevated glucocorticoid levels can impair reproduction, populations or species that engage in particularly valuable reproductive attempts may down-regulate the glucocorticoid stress response during reproduction (the brood value hypothesis). It is not clear, however, whether individuals rapidly modulate glucocorticoid responses based on shifting cues about the likelihood of reproductive success. By manipulating brood size to create broods that differed in potential value, we tested whether female barn swallows (Hirundo rustica) rapidly modulated the glucocorticoid stress response to promote investment in high-value broods, and whether nestling phenotype was influenced by treatment. Within-individual changes in female corticosterone, body mass, and measures of oxidative stress were unrelated to brood size treatment. Standard offspring provisioning rate did not differ across treatments; however, in the presence of a model predator, females raising enlarged broods maintained higher offspring feeding rates relative to control broods. Brood size did influence nestling phenotype. Nestlings from enlarged broods had lower body mass and higher baseline corticosterone than those from reduced broods. Finally, in adult females both baseline and stress-induced corticosterone were individually repeatable. Thus, while under moderately challenging environmental conditions brood size manipulations had context-dependent effects on parental investment, and influenced nestling phenotype, maternal glucocorticoid levels were not modulated based on brood value but were individually consistent features of phenotype during breeding.

Sexual selection can drive the evolution of conspicuous visual signals that advertise individual quality to prospective mates. Reproductive strategy can influence the balance between selective pressures and whether sexually selected signals evolve. Alternatively, visual signals can serve other functions, including predator deterrence, species recognition and differentiating genetically determined morphs. In the dimorphic white-throated sparrow, Zonotrichia albicollis, we explored how selection on conspicuous coloration changes with reproductive strategy, and whether visual signals of morph identity are discrete from sexually selected signals of individual quality. In this species, white morph birds have more colourful plumage than tan morph birds, and white males are more promiscuous and aggressive than tan counterparts. White females are also more aggressive than tan females. White males with more contrasting coloration achieved higher lifetime fitness, whereas the opposite relationship occurred among tan males. Linear selection gradients indicated strong, positive selection on plumage contrast in white males, but negative selection on contrast in tan males. For both morphs, relationships between female coloration and fitness were weak. Results demonstrate disruptive selection on a visual signalling trait in a colour-polymorphic species and suggest that signals associated with an aggressive morph can also evolve to indicate individual quality within that morph.

Vaquero-Alba and colleagues published a study in The Auk: Ornithological Advances comparing objective color measurements of plumage taken in the field directly on a bird's body to those taken in the lab on collected feathers arranged to emulate the appearance of a bird's natural plumage. Although the field measures of plumage color were less repeatable than lab measures, the authors concluded that measurements taken in the field were more representative of a bird's “true color.” Accordingly, they recommend that researchers should bring spectrophotometers into the field to measure color on live birds. We question the assumption that their field measurements represent true color and highlight concerns regarding their experimental design and methodology. Because they did not measure color of live birds in the lab or the color of plucked feathers in the field, they cannot directly test whether the assessment of color in the field on a live bird is superior. Also, rather than assume field measures are...

Despite the clear fitness consequences of animal decisions, the science of animal decision making in evolutionary biology is underdeveloped compared with decision science in human psychology. Specifically, the field lacks a conceptual framework that defines and describes the relevant components of a decision, leading to imprecise language and concepts. The 'judgment and decision-making' (JDM) framework in human psychology is a powerful tool for framing and understanding human decisions, and we apply it here to components of animal decisions, which we refer to as 'cognitive phenotypes'. We distinguish multiple cognitive phenotypes in the context of a JDM framework and highlight empirical approaches to characterize them as evolvable traits.

Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, the relative contribution of migratory behavior to reproductive isolation is difficult to test. Comparing reproductive isolation in hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive isolation coincided with an apparent migratory divide spanning 20 degrees of latitude. A third subspecies pair exhibited no evidence for a migratory divide and hybridized extensively. Within migratory divides, migratory phenotype was associated with assortative mating, implicating a central contribution of divergent migratory behavior to reproductive barriers. The remarkable geographic coincidence between migratory divides and genetic breaks supports a longstanding hypothesis that the Tibetan Plateau is a substantial barrier contributing to the diversity of Siberian avifauna.

The field of sexual selection has burgeoned with research into trait evolution in the context of ecology, sociality, phylogeny, natural selection, and sexual conflict. This paper is the product of a “stock-taking” workshop; our aim is to stimulate discussion, not to provide an exhaustive review. We identify outstanding questions organized into four thematic sections. 1) Evolution of mate choice and mating systems. Variation in mate quality can generate mating competition and choice in either sex with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems. Specifically, polyandry evolves in response to the strength of pre- vs. post-copulatory selection. The evolution of polyandry may be related to diversity of pathogens and Major Histocompatibility Complex (MHC) genes. MHC genes are also potential cues of kinship in avoidance of inbreeding. The balance between inbreeding avoidance and inclusive fitness in mating decisions deserves greater attention. 2) Sender and receiver mechanisms shaping signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are a challenge to measure. The neuroethology of sensory and cognitive receiver biases is the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both start and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. 3) Genetic architecture of sexual selection. Despite advances in modern molecular techniques, the number and identity of genes underlying performance remain largely unknown. A combination of genomic techniques and long-term field studies that reveal ecological correlates of reproductive success is warranted. In-depth investigations into the genetic basis of sexual dimorphism will reveal constraints and trajectories of sexually selected trait evolution. 4) Sexual selection and conflict as drivers of speciation. Population divergence and speciation is often driven by an interplay between sexual and natural selection. To what extent sexual selection promotes or counteracts population divergence may differ depending on the genetic architecture of traits as well as covariance between mating competition and local adaptation, if traits have multiple functions and if sensory systems used in mate choice are locally adapted. Also, post-copulatory processes, e.g. selection against heterospecific sperm, may influence the importance of sexual selection. Sexual conflict can shape speciation processes, since mate choice selection on females can restrict gene flow whereas selection on males is permissive. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection.

A goal of many research programmes in biology is to extract meaningful insights from large, complex datasets. Researchers in ecology, evolution and behavior (EEB) often grapple with long-term, observational datasets from which they construct models to test causal hypotheses about biological processes. Similarly, epidemiologists analyse large, complex observational datasets to understand the distribution and determinants of human health. A key difference in the analytical workflows for these two distinct areas of biology is the delineation of data analysis tasks and explicit use of causal directed acyclic graphs (DAGs), widely adopted by epidemiologists. Here, we review the most recent causal inference literature and describe an analytical workflow that has direct applications for EEB. We start this commentary by defining four distinct analytical tasks (description, prediction, association, causal inference). The remainder of the text is dedicated to causal inference, specifically focusing on the use of DAGs to inform the modelling strategy. Given the increasing interest in causal inference and misperceptions regarding this task, we seek to facilitate an exchange of ideas between disciplinary silos and provide an analytical framework that is particularly relevant for making causal inference from observational data.

Evolutionary biologists have long been fascinated by extravagant male traits that abound across the animal kingdom and yet convey no apparent benefits to survival. From isopods to elephants, from armaments to ornaments, researchers have spent decades studying male-male competition and female mate choice in an effort to understand the significance of these secondary sexual characteristics. Among socially monogamous species, a frequently proposed explanation for the existence of male ornaments is that they are indicators of male genetic quality subject to female extra-pair mate choice. However, despite over two decades of extensive research into extra-pair paternity (EPP), the evidence that females actually choose more ornamented extra-pair sires is surprisingly scant. Consequently, whether EPP and female choice have contributed to the evolution of male ornaments in socially monogamous species, and what fitness benefits (if any) they signal to females, remains unclear. Progress in this field has been hampered by the challenge of dissociating clear female choice for ornamentation from confounding factors. In this issue of Molecular Ecology, Whittingham & Dunn (2016) use an experimental approach in a bird species with very high rates of EPP to tease apart these correlative effects. In doing so, they demonstrate clearly that male ornamentation is subject to female extra-pair mate choice. Their findings further suggest that EPP can be adaptive for females, and represent an important step forward in validating the role of EPP as an evolutionary driver of ornamental elaboration in socially monogamous species.

The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related to avian systems. We highlight how genomic tools are advancing research by discussing their contributions to 3 important facets of avian evolutionary history. We focus on (1) general inferences about biogeography and biogeographic history, (2) patterns of gene flow and isolation upon seco...

Nest ectoparasites can impose significant costs to altricial nestlings that are confined to the nest and dependent on parental care. These costs are often passed on to parents who may compensate for, or magnify, the direct costs of parasites on their nestlings through adjustments in parental care behaviour. If the effects of ectoparasites on nestlings vary across development, parents would be expected to dynamically adjust their behaviour across time with the possibility that males and females may vary in their responses. Currently, we lack a complete understanding of the potential sex differences and variation in parental care behaviour across the nestling period as a function of offspring parasite infection. Our experimental study compared disinfected and parasitized treatment groups to examine how northern fowl mites, Ornithonyssus sylviarum, in nests of the North American barn swallow, Hirundo rustica erythrogaster, affect parental care behaviour. Specifically, we addressed how provisioning rates and nest attendance behaviours (time spent at the nest) changed in response to ectoparasite infection early (day 7) and late (day 13) in the nestling period, and between male and female parents. Early in the nestling period, female provisioning rates were lower for parasitized nests than for disinfected nests whereas male provisioning rates did not differ between treatments. However, males of parasitized nests showed higher nest attendance whereas females did not alter their attendance of nestlings as a function of the parasite manipulation. Later in the nestling period, parental care behaviours changed dramatically. Male provisioning rates were higher for parasitized nests than for disinfected nests whereas female provisioning rates did not differ between treatments. Both males and females showed greater nest attendance for parasitized nests compared to disinfected nests on day 13. These findings suggest that parasites do affect provisioning and nest attendance behaviours: parental care responses differ between males and females, and are dynamic across the nestling developmental period.

International audience; According to a recent survey, ecologists and evolutionary biologists feel that theoretical and empirical research should coexist in a tight feedback loop but believe that the two domains actually interact very little. We evaluate this perception using a citation network analysis for two data sets, representing the literature on sexual selection and speciation. Overall, 54%-60% of citations come from a paper's own category, whereas 17%-23% are citations across categories. These cross-citations tend to focus on highly cited papers, and we observe a positive correlation between the numbers of citations a study receives within and across categories. We find evidence that reviews can function as integrators between the two literatures, argue that theoretical models are analogous to specific empirical study systems, and complement our analyses by studying a cocitation network. We conclude that theoretical and empirical research are more tightly connected than generally thought but that avenues exist to further increase this integration.

During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under several evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics. We used these simulations to investigate, in a preliminary way, if and how selected and neutral sites differ in the conditions they require for transitions during speciation. For the parameter combinations we explored, as the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence—and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence—farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of effective gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of Heliconius butterflies. We found that fixation index ( F S T ) outliers and allele-frequency outliers exhibited stronger patterns of within-deme LD than the genomic background, as expected. The statistical characteristics of within-deme LD—likely indicative of the strength of coupling of barrier loci—varied between chromosomes and taxonomic comparisons. Qualitatively, the patterns we observed in the empirical data and in our simulations suggest that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.

During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under different evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics, allowing us to investigate if and how selected and neutral sites differ in the conditions they require for transitions during speciation. As the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence – and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence – farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of Heliconius butterflies. We found that allele-frequency outliers and F ST outliers exhibited stronger patterns of LD than the genomic background, as expected. The statistical characteristics of LD – likely indicative of the strength of coupling of barrier loci – varied between chromosomes and taxonomic comparisons. Broad qualitative agreement between the patterns we observed in the empirical data and our simulations suggests that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.