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Hybridization has important effects on the evolutionary trajectories of natural populations but estimates of this process in the wild and at the individual-level are lacking. Justyn et al. attempted to fill this gap using the citizen science database eBird but there are limitations to this approach. Here, we outline and directly test these limitations using literature searches, case studies, and a comparison between eBird and Birds of North America (BNA), a database that documents hybridization using the scientific literature. We use a hybrid zone between Lazuli and Indigo buntings to highlight the importance of considering geographic range when estimating rates of hybridization and two literature searches to show the importance of considering cryptic hybrids (those that cannot be identified using phenotypic traits) when quantifying these rates. We also use BNA and a case study of hybrid White-faced and Glossy Ibises to show that citizen scientists are underreporting hybrids compared with experts. Justyn et al. highlighted an important gap in the literature, but their results likely represent the lower limit of hybridization between birds and a more nuanced interpretation of their results (e.g., considering extrinsic postzygotic selection) is needed.

Closely related populations often display similar patterns of genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.e., linked negative selection). To date, there have been few direct tests of these competing hypotheses. To determine the relative contributions of background selection and parallel selection to patterns of repeated differentiation, we examined 24 independently derived populations of freshwater stickleback occupying a variety of niches and estimated genomic patterns of differentiation in each relative to their common marine ancestor. Patterns of genetic differentiation were strongly correlated across pairs of freshwater populations adapting to the same ecological niche, supporting a role for parallel natural selection. In contrast to other recent work, our study comparing populations adapting to the same niche produced no evidence signifying that similar patterns of genomic differentiation are generated by background selection. We also found that overall patterns of genetic differentiation were considerably more similar for populations found in closer geographic proximity. In fact, the effect of geography on the repeatability of differentiation was greater than that of parallel selection. Our results suggest that shared selective landscapes and ancestral variation are the key drivers of repeated patterns of differentiation in systems that have recently colonized novel environments.

Hybrid zones are particularly valuable for understanding the evolution of partial reproductive isolation between differentiated populations. An increasing number of hybrid zones have been inferred to move over time, but in most such cases zone movement has not been tested with long-term genomic data. The hybrid zone between Townsend's Warblers (Setophaga townsendi) and Hermit Warblers (S. occidentalis) in the Washington Cascades was previously inferred to be moving from northern S. townsendi southwards towards S. occidentalis, based on plumage and behavioural patterns as well as a 2000-km genetic wake of hermit mitochondrial DNA (mtDNA) in coastal Townsend's Warblers. We directly tested whether hybrid zone position has changed over 2-3 decades by tracking plumage, mtDNA and nuclear genomic variation across the hybrid zone over two sampling periods (1987-94 and 2015-16). Surprisingly, there was no significant movement in genomic or plumage cline centres between the two time periods. Plumage cline widths were narrower than expected by neutral diffusion, consistent with a 'tension zone' model, in which selection against hybrids is balanced by movement of parental forms into the zone. Our results indicate that this hybrid zone is either stable in its location or moving at a rate that is not detectable over 2-3 decades. Despite considerable gene flow, the stable clines in multiple phenotypic and genotypic characters over decades suggest evolutionary stability of this young pair of sister species, allowing divergence to continue. We propose a novel biogeographic scenario to explain these patterns: rather than the hybrid zone having moved thousands of kilometres to its current position, inland Townsend's met coastal Hermit Warbler populations along a broad front of the British Columbia and Alaska coast and hybridization led to replacement of the Hermit Warbler plumage with Townsend's Warbler plumage patterns along this coastline. Hence, hybrid zones along British Columbia and Alaska moved only a short distance from the inland to the coast, whereas the Hermit Warbler phenotype appears stable in Washington and further south. This case provides an example of the complex biogeographic processes that have led to the distribution of current phenotypes within and among closely related species.

Summary Selecting breeding habitats that ameliorate environmental limits on fitness and facilitate successful reproduction should benefit individual animals. This is particularly true in the temperate zone, where breeding early in a season presents a unique series of environmental challenges that can limit an individual's fitness. While many studies document links between habitat quality and reproductive success, few identify the cues used to assess habitat quality or the components of reproduction most influenced by occupying higher quality habitat, particularly during the early breeding season. We used detailed spatial maps and observations of all early season nesting attempts in an insular song sparrow (Melospiza melodia) population over 38 years to estimate the influence of nest-site preference on reproductive success and to test whether relative microclimate or food availability may act as cues for early season site selection. Female sparrows in preferred early season nest sites had earlier laying dates, exhibited more energetically efficient incubation behaviour and produced more offspring that recruited to the population than those nesting in less-preferred sites. Preference for potential nesting sites was positively related to leaf damage by Lepidopteran larvae, an indicator of food abundance, negatively related to early season microclimate, likely due to greater vegetation cover, and unrelated to site-specific plant phenology. Our findings show that breeding in preferred, high-quality habitat may offer females a fitness advantage by facilitating early laying and the production of offspring more likely to recruit to the population at a lower potential reproductive cost to the parent. We provide a clear demonstration of potential links between habitat preference and quality and their contributions to the ecology and life history of animals in seasonal environments.

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.

Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this ‘sweep-before-differentiation’ model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions. © 2016 John Wiley Sons Ltd

Frequent copulation is assumed to be an important male reproductive strategy for paternity assurance in species with female sexual promiscuity. However, the empirical evidence supporting this hypothesis is limited. We examined copulation behaviour in relation to within-pair paternity in the socially monogamous tree swallow, Tachycineta bicolor, a passerine bird species with frequent copulation, a lack of mate guarding and high levels of extrapair paternity. We found that the frequency of within-pair copulation attempts increased and peaked just before the appearance of the first egg. A marked drop in the frequency of copulation attempts was observed once the first egg was laid. Furthermore, the frequency of successful within-pair copulations was highly repeatable for particular pairs within the 3 days prior to appearance of the first egg. Finally, males that obtained a higher number of successful within-pair copulations during this time also sired a larger proportion of the offspring in their own brood. Our findings suggest that frequent copulations just before the start of egg laying is an adaptation to decrease the risk of being cuckolded in the presence of sperm competition, and thus provide empirical support for the paternity assurance hypothesis. Crown Copyright 2008 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour. All rights reserved. Paternity assurance is critical to male fitness, particularly in species in which females frequently participate in extrapair copulations (EPCs) and males provide costly parental care. In response to fitness loss due to cuckoldry, several types of paternity assurance behaviour have evolved across taxa. One strategy is constant mate guarding by following, as males can protect their paternity by ensuring that no other male has an opportunity to mate with their paired female (Moller & Birkhead 1991). However, for some species, constant mate guarding may be constrained by territory protection or other activities. The paternity assurance hypothesis (Moller 1987; Simmons 1990), also known as the paternity confidence hypothesis (Eens & Pinxten 1995) and the sperm competition hypothesis (Birkhead et al. 1987), suggests that for species in which EPCs are common, males copulate frequently with their pair females to avoid being cuckolded. Males may minimize cuckoldry through frequent copulation by devaluing EPCs that their mates

Migratory divides are contact zones between breeding populations that use divergent migratory routes and have been described in a variety of species. These divides are of major importance to evolution, ecology and conservation but have been identified using limited band recovery data and/or indirect methods. Data from band recoveries and mitochondrial haplotypes suggested that inland and coastal Swainson's thrushes (Catharus ustulatus) form a migratory divide in western North America. We attached light-level geolocators to birds at the edges of this contact zone to provide, to our knowledge, the first direct test of a putative divide using data from individual birds over the entire annual cycle. Coastal thrushes migrated along the west coast to Mexico, Guatemala and Honduras. Some of these birds used multiple wintering sites. Inland thrushes migrated across the Rocky Mountains, through central North America to Columbia and Venezuela. These birds migrated longer distances than coastal birds and performed a loop migration, navigating over the Gulf of Mexico in autumn and around this barrier in spring. These findings support the suggestion that divergent migratory behaviour could contribute to reproductive isolation between migrants, advance our understanding of their non-breeding ecology, and are integral to development of detailed conservation strategies for this group.

Ecosystems services are threatened by the rapid degradation of tropical rainforests. In light of these threats, questions remain about how societies on the forest fringe who depend on provisioning services affect plant functional traits. This study assessed the relationship between plant functional traits, forest-dependent societies and provisioning ecosystem services along a forest–agriculture matrix gradient in tropical humid forests of Madagascar. Data were collected for six functional traits and six provisioning services. We evaluated functional diversity (FD) and utilitarian diversity (FD of provisioning services) along disturbance gradients. We also determined the traits most susceptible to loss along the gradient as well as the relationship between functional traits and provisioning services. The results showed that FD, utilitarian diversity and species richness decreased significantly across all modified habitats. There was a distinct suite of traits absent from intensely used habitats and those same traits were associated with the two most important provisioning services in the region (firewood and construction). The activities of people living on the forest fringe seem to be a strong selective force on trait loss in plant communities, which in turn will influence future species assembly and trait diversity and distribution. Moreover, this study suggests that it is possible to predict trait loss from plant communities in forests where degradation is mediated primarily through subsistence agriculture and resource extraction. Conservation efforts should recognize that forest degradation and deforestation are contextually specific, determined mostly by people’s efforts to maintain their basic livelihood, and therefore necessitate local-scale interventions that feed into landscape-scale policy initiatives.