Speciation is one of the most important processes in biology, yet the study of the genomic changes underlying this process is in its infancy. North American warbler species Setophaga townsendi and Setophaga occidentalis hybridize in a stable hybrid zone, following a period of geographic separation. Genomic differentiation accumulated during geographic isolation can be homogenized by introgression at secondary contact, whereas genetic regions that cause low hybrid fitness can be shielded from such introgression. Here, we examined the genomic underpinning of speciation by investigating (1) the genetic basis of divergent pigmentation traits between species, (2) variation in differentiation across the genome, and (3) the evidence for selection maintaining differentiation in the pigmentation genes. Using tens of thousands of single nucleotide polymorphisms (SNPs) genotyped in hundreds of individuals within and near the hybrid zone, genome-wide association mapping revealed a single SNP associated with cheek, crown, breast coloration, and flank streaking, reflecting pleiotropy (one gene affecting multiple traits) or close physical linkage of different genes affecting different traits. This SNP is within an intron of the RALY gene, hence we refer to it as the RALY SNP. We then examined between-species genomic differentiation, using both genotyping-by-sequencing and whole genome sequencing. We found that the RALY SNP is within one of the highest peaks of differentiation, which contains three genes known to influence pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). Heterozygotes at this gene block are likely of reduced fitness, as the geographic cline of the RALY SNP has been narrow over two decades. Together, these results reflect at least one barrier to gene flow within this narrow (∼200 kb) genomic region that modulates plumage difference between species. Despite extensive gene flow between species across the genome, this study provides evidence that selection on a phenotype-associated genomic region maintains a stable species boundary.

Pregnancy associated plasma protein A2 (PAPP-A2) is a protease of insulin-like growth factor binding protein 5 and is receiving increasing attention for its roles in pregnancy and postnatal growth. The goals of the present study were to characterize the effects of PAPP-A2 deletion on bone size and shape in mice at 10 weeks of age, and to determine whether Pappa2 is the gene responsible for a previously-identified quantitative trait locus (QTL) contributing to natural variation in postnatal growth in mice. Mice homozygous for constitutive PAPP-A2 deletion were lighter than wild-type littermates, and had smaller mandible dimensions and shorter skull, humerus, femur, tibia, pelvic girdle, and tail bone. Furthermore, PAPP-A2 deletion reduced mandible dimensions and the lengths of the skull, femur, pelvic girdle, and tail bone more than would be expected due to the effect on body mass. In addition to its effects on bone size, PAPP-A2 deficiency also altered the shape of the mandible and pelvic girdle, as assessed by geometric morphometrics. Mice homozygous for the PAPP-A2 deletion had less deep mandibles, and pelvic girdles with a more feminine shape. Using a quantitative complementation test, we confirmed that Pappa2 is responsible for the effects of the previously-identified QTL, demonstrating that natural variation in the Pappa2 gene contributes to variation in postnatal growth in mice. If similar functional variation in the Pappa2 gene exists in other species, effects of this variation on the shape of the pelvic girdle might explain the previously-reported associations between Pappa2 SNPs and developmental dysplasia of the hip in humans, and birthing in cattle.

For migratory animals, events at one stage of the annual cycle can produce constraints or benefits that carry over to subsequent stages. Differing life-history strategies among individuals can influence the expression of these carry-over effects, leading to pronounced within-population variation in migration. For example, reproductive roles can drive spatiotemporal segregation during the non-breeding season and promote sex-specific carry-over effects, such as reproductive effort affecting autumn migration behavior. For an alpine breeding population of horned larks Eremophila alpestris in northern British Columbia, Canada, we addressed sex-specific variation in migration behavior and carry-over effects during both autumn and spring migration using light-level geolocators. Males spent more time farther north and arrived an average of 6 days earlier at the breeding site in spring. Females delayed autumn departure following greater reproductive effort, in turn demonstrating flexible migration behavior by increasing migration speed and decreasing stopover use. Males maintained autumn migration behavior regardless of reproductive effort or departure date. Finally, both sexes used staging areas in spring (average stopover = 41 days), with consequences for breeding success. Individuals that used staging areas during spring migration exhibited greater nest success and produced 1.8 more fledglings on average than those that migrated directly from their winter site. Consistent use of staging areas may allow individuals to monitor environmental conditions and optimize their breeding arrival date to acquire high-quality territories while avoiding the cost of arriving too early in a harsh alpine habitat. Overall, our results indicate: (1) sex-specific flexibility in migration strategies that carry-over to and from the reproductive period, and (2) spring staging areas may be a critical component of the annual life-cycle for alpine breeding larks. These behaviors may be particularly important for alpine and arctic birds because the stochastic nature of their breeding habitat likely selects for flexible responses to prevailing conditions.

Variation in offspring development is expected to be driven by constraints on resource allocation between growth and maintenance (e.g. thermoregulation). Rapid post‐natal development decreases predation risk to offspring, while inclement weather likely prolongs development. For taxa with parental care, parental behaviour may partially buffer offspring against extrinsic drivers like predation risk and severe weather. Using a 7‐year dataset from an alpine population of horned lark Eremophila alpestris, a ground‐nesting songbird in northern British Columbia, Canada, we investigated multiple potential drivers of variation in the duration of incubation and nestling development. Using path analysis, we evaluated the direct effects of weather, predation risk and parental care on offspring development, as well as indirect developmental “carry‐over” effects of conditions during incubation on the nestling period. Nestling period duration varied by nearly 100% (7–13 days) and incubation duration by 40% (10–14 days). Cold ambient temperatures late in the nestling period prolonged development by 1 day for every 2 days below 10°C, particularly when combined with heavy precipitation. Rapid nestling development was associated with high predation risk, and prolonging development incurred a nest survival cost (–2.3% per day). Females in good condition created nest environments that promoted rapid nestling development periods (average = 8–9 days) compared to poor condition females during harsh, early‐season conditions (10–11 days), indicating parental buffering capabilities against environmental constraints. Fledging age was weakly correlated with incubation duration (r = –0.21) suggesting minimal developmental carry‐over effects. Given high nest predation risk, immediate fitness benefits can be derived by overcoming environmental constraints and reducing development time. While predation risk was influential, inclement weather and maternal condition had stronger effects on variation in offspring development. Addressing multiple drivers of variation in key life‐history traits can provide important context for understanding life‐history theory under changing environmental conditions. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13273/suppinfo is available for this article.

Songbird nests are an important life‐history component with multiple functions, including the creation of a suitable microclimate for offspring development. Thus, functional nest characteristics may influence fitness correlates, such as nestling size traits, and may co‐vary with prevailing environmental conditions. We investigated among‐ and within‐female variation in nest substrate, lining and decoration structures with associated fitness consequences (hatching success, nestling size traits, nest survival) across two breeding seasons for an alpine population of Horned Lark Eremophila alpestris. We combined these observations with explicit measures of nest temperature to address the influence of nest characteristics on microclimate. Nests in heather substrate had the coldest microclimates compared with grass and bare‐ground substrate, but also the greatest nest survival rates (68% versus 37–44% in other substrates), indicating the potential for substrate use decisions to reflect a trade‐off between microclimate and nest survival in response to prevailing weather and predation risk conditions. Furthermore, nest lining and nest decoration patterns indicated some support for a thermoregulatory function. Nests that were lined with willow (Salix sp.) seed‐down were associated with larger, heavier nestlings and the use of down lining decreased in frequency as the season warmed up. Nest decoration placed in front of the nest (e.g. stones or dirt clumps varying in mass from 5.3 to 186.6 g) was positively associated with warmer nest microclimates. Females demonstrated high phenotypic flexibility, as 61–94% of the observed variance in nest characteristics was explained by within‐female rather than among‐female differences. Such flexible nesting behaviour suggests the capacity to adjust to changing environmental conditions to maintain vital fitness correlates such as nest survival and nestling size development.