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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.

Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species’ range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species’ distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.

Recently diverged taxa often exhibit heterogeneous landscapes of genomic differentiation, characterized by regions of elevated differentiation on an otherwise homogeneous background. While divergence peaks are generally interpreted as regions responsible for reproductive isolation, they can also arise due to background selection, selective sweeps unrelated to speciation, and variation in recombination and mutation rates. To investigate the association between patterns of recombination and landscapes of genomic differentiation during the early stages of speciation, we generated fine-scale recombination maps for six southern capuchino seedeaters (Sporophila) and two subspecies of White Wagtail (Motacilla alba), two recent avian radiations in which divergent selection on pigmentation genes has likely generated peaks of differentiation. We compared these recombination maps to those of Collared (Ficedula albicollis) and Pied Flycatchers (Ficedula hypoleuca), non-sister taxa characterized by moderate genomic divergence and a heterogenous landscape of genomic differentiation shaped in part by background selection. Although recombination landscapes were conserved within all three systems, we documented a weaker negative correlation between recombination rate and genomic differentiation in the recent radiations. All divergence peaks between capuchinos, wagtails, and flycatchers were located in regions with lower-than-average recombination rates, and most divergence peaks in capuchinos and flycatchers fell in regions of exceptionally reduced recombination. Thus, co-adapted allelic combinations in these regions may have been protected early in divergence, facilitating rapid diversification. Despite largely conserved recombination landscapes, divergence peaks are specific to each focal comparison in capuchinos, suggesting that regions of elevated differentiation have not been generated by variation in recombination rate alone.

High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.

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.

Coloration traits are central to animal communication; they often govern mate choice, promote reproductive isolation and catalyse speciation. Specific genetic changes can cause variation in coloration, yet far less is known about how overall coloration patterns—which involve combinations of multiple colour patches across the body—can arise and are genomically controlled. We performed genome-wide association analyses to link genomic changes to variation in melanin (eumelanin and pheomelanin) concentration in feathers from different body parts in the capuchino seedeaters, an avian radiation with diverse colour patterns despite remarkably low genetic differentiation across species. Cross-species colour variation in each plumage patch is associated with unique combinations of variants at a few genomic regions, which include mostly non-coding (presumably regulatory) areas close to known pigmentation genes. Genotype–phenotype associations can vary depending on patch colour and are stronger for eumelanin pigmentation, suggesting eumelanin production is tightly regulated. Although some genes are involved in colour variation in multiple patches, in some cases, the SNPs associated with colour changes in different patches segregate spatially. These results suggest that coloration patterning in capuchinos is generated by the modular combination of variants that regulate multiple melanogenesis genes, a mechanism that may have promoted this rapid radiation.

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.

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.

Subtropical grasslands are highly susceptible to habitat conversion and number among South America’s most threatened ecosystems. The grasslands of northeastern Argentina have been identified as a priority conservation area for threatened capuchino seedeaters because they constitute the main breeding area of these migratory birds. The Iberá Seedeater (Sporophila iberaensis) is a newly described species in the Iberá Wetlands in Argentina whose biology is still poorly understood. The endangered species inhabits grasslands but has only been reported to breed in the Iberá Wetlands ecoregion of northeastern Argentina. To explore the species’ association with grassland vegetation, we studied the breeding biology (clutch size, hatching success, and fledgling production) of the Iberá Seedeater and the main parameters that influence nest survival and nest-site selection. We conducted nest searches and banded adults and nestlings in Iberá National Park during the breeding seasons of 2016–2018. The breeding season of the Iberá Seedeater was highly synchronous and the cumulative probability of nest survival was 0.16. The daily nest survival rate decreased as the breeding season advanced, survival was lower for nests supported by Rhynchospora corymbosa than Paspalum durifolium, the two main nest substrates, and the main causes of nest failure were nest predation and strong winds. Additionally, the population exhibited male-biased site fidelity and a low female return rate. In contrast to other capuchinos, whose breeding biology is associated with upland grasslands, the Iberá Seedeater nested exclusively in flooded lowland grasslands on marsh plants. Thus, effective lowland grassland management is key to maintain the vegetation structure required for reproduction in the Iberá Seedeater.

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

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.

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.

Scientific writing, while an indispensable step of the scientific process, is often overlooked in undergraduate courses in favor of maximizing class time devoted to scientific concepts. However, the ability to effectively communicate research findings is crucial for success in the biological sciences. Graduate students are encouraged to publish early and often, and professional scientists are generally evaluated by the quantity of articles published and the number of citations those articles receive. It is therefore important that undergraduate students receive a solid foundation in scientific writing early in their academic careers. In order to increase the emphasis on effective writing in the classroom, we assembled a succinct step-by-Step guide to scientific writing that can be directly disseminated to undergraduates enrolled in biological science courses. The guide breaks down the scientific writing process into easily digestible pieces, providing concrete examples that students can refer to when preparing a scientific manuscript or laboratory report. By increasing undergraduate exposure to the scientific writing process, we hope to better prepare undergraduates for graduate school and productive careers in the biological sciences.

Patterns of connectivity between breeding and wintering grounds can have important implications for individual fitness and population dynamics. Using light-level geolocators and stable hydrogen isotopes (δ(2)H) in feathers, we evaluated differential migration of Savannah sparrows (Passerculus sandwichensis) breeding on Kent Island in the Bay of Fundy, New Brunswick, Canada in relation to sex, age, and body size. Based on geolocators recovered from 38 individuals between 2012 and 2014, the winter distribution was centered in North Carolina (median latitude 34°, range 26°-41°), with males overwintering, on average, approximately 275 km further north than females. Based on analyses of tail feather samples collected from 106 individuals from the same population between 2008 and 2012, males and adults had more negative δ(2)H values than females and juveniles, respectively, providing additional evidence that males wintered north of females and that adults wintered north of juveniles. Winter latitude and δ(2)H values within each sex were not found to be related to body size. From geolocator data, males returned to the breeding grounds, on average, 14 days earlier than females. For males, there was some evidence that arrival date on the breeding grounds was negatively correlated with winter latitude and that individuals which arrived earlier tended to breed earlier. Thus, benefits for males of early arrival on the breeding grounds may have contributed to their wintering farther north than females. Social dominance may also have contributed to age and sex differences in winter latitude, whereby dominant males and adults forced subordinate females and juveniles further south.

The evolution of colonial breeding remains an outstanding question in evolutionary biology due to our limited understanding of the costs and benefits of group living. We document 85 cases of Barn Swallows (Hirundo rustica erythrogaster) laying, and subsequently abandoning, eggs in empty, unclaimed nests located adjacent to active nests during a 6 y study. The frequency of this behavior was positively correlated with total available nests, a metric that increases with colony size. In addition, two female swallows were observed alternately incubating multiple clutches after mislaying eggs in neighboring nests. We argue the potential to mislay eggs and allocate parental care across separate nests may represent an overlooked cost of colonial nesting in birds.

The southern capuchino seedeaters constitute a rapid radiation of finch-like birds that inhabit Neotropical grasslands in continental South America. While capuchinos are highly sympatric, the mechanisms allowing them to breed in sympatry, such as patterns of microhabitat use, remain largely unknown. We provide the first nesting account of the Ibera Seedeater (Sporophila iberaensis), a recently discovered capuchino species that breeds exclusively in the Ibera wetlands of northeastern Argentina, and compare its nesting habits to those of other members of the capuchino radiation. From November 2016 to January 2017, we located and monitored 25 Ibera Seedeater nests. The Ibera Seedeater constructs open-cup nests in clumps of grass on the margins of flooded habitat and lays an average of 2 eggs per clutch. Like other capuchino species, females participate in nest construction and incubation, while both sexes provision offspring. Despite similarities in nest architecture, the Ibera Seedeater differs in ...

The correlation between migration and wing pointedness, a pattern generally attributed to the need to reduce drag during powered straight-line flight, is well established in avian ecomorphology. However, most studies investigating this pattern have focused on relatively rounded-wing taxa, which employ different flight modes during foraging and migration. The basic assumption that migrants have comparatively pointed wings has not been questioned by analysing taxa with similar migratory and foraging flight. This study examines the correlation between migration and wing shape in swallows (Hirundinidae), a family with relatively pointed wings in which foraging flight resembles migratory flight. Using a phylogeny-based analysis, we compare the wing shape of species pairs with varying migratory habits in eight swallow genera. Surprisingly, migratory swallows have less pointed wings than sedentary species, and wing pointedness declines linearly with increasing migratory distance. This study represents the first published result documenting a reversal of the correlation between migration and wing pointedness found in other avian taxa. Interpreting this reversal requires a more nuanced understanding of wing ecomorphology; we hypothesize that inclement weather conditions on the breeding grounds and/or the roosting habits of migratory swallows create conflicting selective pressures that increase the cost of wing pointedness in migratory swallows.

The idea that genetic differentiation can proceed despite genetic exchange between divergent lineages is gaining support in evolutionary biology (Nosil 2008). Though theoretically difficult to achieve because interbreeding counteracts population differentiation, divergence with gene flow has shaped the evolutionary histories of diverse organisms including Heliconius butterflies (Martin et al. 2013) and Galapagos finches (de Leon et al. 2010). In some taxa, such as the haplochromine cichlids, hybridization may even have played a creative role, providing the genetic variation necessary to fuel adaptive radiations (Meier et al. 2017). This article is protected by copyright. All rights reserved