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Abstract Extra-pair mating is common in avian species and can modulate the strength of sexual selection. Mate searching behavior of female birds may be an important predictor of mating opportunities and extra-pair mating, yet important knowledge is lacking as we have little data on fine-scale movement of females during the peak fertilization period. Accordingly, much is still unknown about whether and how female phenotypes contribute to extra-pair mating. Here, we examined how female space use and female plumage color are associated with extra-pair mating outcomes in wild barn swallows (Hirundo rustica erythrogaster). We tracked 10 females breeding in Colorado, USA with GPS backpack tags for two hours each morning during their fertile period following an experimental nest failure. We then used low-coverage whole-genome sequencing to determine offspring paternity and to quantify extra-pair mating in the removed clutch and the replacement clutch. Plumage and movement did not correlate with changes in paternity between successive clutches, but movement did correlate with paternity in the replacement clutch. Females that spent more time away from the nest had a higher proportion and number of extra-pair offspring in the clutch laid immediately after the tracking period. These results suggest that differences in female space use contribute to differences in extra-pair fertilizations. In contrast to the historic emphasis on male traits, our study highlights female movement behavior as an important variable associated with mating outcomes in natural populations. 

ABSTRACT Disentangling the drivers of genomic divergence during speciation is essential to our broader understanding of the generation of biological diversity. Genetic changes accumulate at variable rates across the genome as populations diverge, leading to heterogenous landscapes of genetic differentiation. The ‘islands of differentiation’ that characterise these landscapes harbour genetic signatures of the evolutionary processes that led to their formation, providing insight into the roles of these processes in adaptation and speciation. Here, we study swallows in the genusHirundoto investigate genomic landscapes of differentiation between species spanning a continuum of evolutionary divergence. Genomic differentiation spans a wide range of values (F_ST= 0.01–0.8) between species, with substantial heterogeneity in genome‐wide patterns. Genomic landscapes are strongly correlated among species (ρ= 0.46–0.99), both at shallow and deep evolutionary timescales, with broad evidence for the role of linked selection together with recombination rate in shaping genomic differentiation. Further dissection of genomic islands reveals patterns consistent with a model of ‘recurrent selection’, wherein differentiation increases due to selection in the same genomic regions in ancestral and descendant populations. Finally, we use measures of the site frequency spectrum to differentiate between alternative forms of selection, providing evidence that genetic hitchhiking due to positive selection has contributed substantially to genomic divergence. Our results demonstrate the pervasive role of recurrent linked selection in shaping genomic divergence despite a history of gene flow and underscore the importance of non‐neutral evolutionary processes in predictive frameworks for genomic divergence in speciation genomics studies. 

Abstract BackgroundThe increasing number of chromosome-level genome assemblies has advanced our knowledge and understanding of macroevolutionary processes. Here, we introduce the genome of the desert horned lizard, Phrynosoma platyrhinos, an iguanid lizard occupying extreme desert conditions of the American southwest. We conduct analysis of the chromosomal structure and composition of this species and compare these features across genomes of 12 other reptiles (5 species of lizards, 3 snakes, 3 turtles, and 1 bird). FindingsThe desert horned lizard genome was sequenced using Illumina paired-end reads and assembled and scaffolded using Dovetail Genomics Hi-C and Chicago long-range contact data. The resulting genome assembly has a total length of 1,901.85 Mb, scaffold N50 length of 273.213 Mb, and includes 5,294 scaffolds. The chromosome-level assembly is composed of 6 macrochromosomes and 11 microchromosomes. A total of 20,764 genes were annotated in the assembly. GC content and gene density are higher for microchromosomes than macrochromosomes, while repeat element distributions show the opposite trend. Pathway analyses provide preliminary evidence that microchromosome and macrochromosome gene content are functionally distinct. Synteny analysis indicates that large microchromosome blocks are conserved among closely related species, whereas macrochromosomes show evidence of frequent fusion and fission events among reptiles, even between closely related species. ConclusionsOur results demonstrate dynamic karyotypic evolution across Reptilia, with frequent inferred splits, fusions, and rearrangements that have resulted in shuffling of chromosomal blocks between macrochromosomes and microchromosomes. Our analyses also provide new evidence for distinct gene content and chromosomal structure between microchromosomes and macrochromosomes within reptiles.