Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species.

We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250-km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA), similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3000 single nucleotide polymorphisms in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing. Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.

Environmental gradients of selection for an alpine-obligate bird, the white-tailed ptarmigan (Lagopus leucura).

The warming climate will expose alpine species adapted to a highly seasonal, harsh environment to novel environmental conditions. A species can shift their distribution, acclimate, or adapt in response to a new climate. Alpine species have little suitable habitat to shift their distribution, and the limits of acclimation will likely be tested by climate change in the long-term. Adaptive genetic variation may provide the raw material for species to adapt to this changing environment. Here, we use a genomic approach to describe adaptive divergence in an alpine-obligate species, the white-tailed ptarmigan (Lagopus leucura), a species distributed from Alaska to New Mexico, across an environmentally variable geographic range. Previous work has identified genetic structure and morphological, behavioral, and physiological differences across the species' range; however, those studies were unable to determine the degree to which adaptive divergence is correlated with local variation in environmental conditions. We used a genome-wide dataset generated from 95 white-tailed ptarmigan distributed throughout the species' range and genotype-environment association analyses to identify the genetic signature and environmental drivers of local adaptation. We detected associations between multiple environmental gradients and candidate adaptive loci, suggesting ptarmigan populations may be locally adapted to the plant community composition, elevation, local climate, and to the seasonality of the environment. Overall, our results suggest there may be groups within the species' range with genetic variation that could be essential for adapting to a changing climate and helpful in guiding conservation action.

Multiyear monitoring of survival following mitigation-driven translocation of a long-lived threatened reptile.

Translocation is used by managers to mitigate the negative impacts of development on species. Moving individuals to a new location is challenging, and many translocation attempts have failed. Robust, posttranslocation monitoring is therefore important for evaluating effects of translocation on target species. We evaluated the efficacy of a translocation designed to mitigate the effects of a utility-scale solar energy project on the U.S. federally listed Mojave desert tortoise (Gopherus agassizii). The species is a long-lived reptile threatened by a variety of factors, including habitat loss due to renewable energy development in the Mojave Desert and portions of the Colorado Desert in southern California (southwestern United States). We translocated 58 individual tortoises away from the project's construction site and intensively monitored them over 5 years (2012-2017). We monitored these individuals and tortoises located in the translocation release area (resident tortoises; n = 112) and control tortoises (n = 149) in a nearby location. We used our tortoise encounter data and known-fate survival models to estimate annual and cumulative survival. Translocated tortoises in each of 2 size classes (120-160 mm, >160 mm) did not survive at lower rates than resident and control tortoises over the study period. For models with different sets of biotic and abiotic covariates, annual and cumulative estimates of survival were always >0.87 and >0.56, respectively. Larger tortoises tended to have higher survival, but translocated tortoises were not differentially affected by the covariates used to model variation in survival. Based on these findings, our translocation design and study protocols could inform other translocation projects for desert species. Our case study highlights the benefits of combining rigorous scientific monitoring with well-designed, mitigation-driven management actions to reduce the negative effects of development on species of conservation concern.

Monitoreo Multianual de la Supervivencia de un Reptil Longevo en Peligro después de una Reubicación por Mitigación Resumen Los administradores utilizan la reubicación para mitigar los impactos negativos que el desarrollo tiene sobre las especies. El traslado de individuos hacia una nueva ubicación es todo un reto y muchos intentos de reubicación han fallado. Por esto el monitoreo robusto post-reubicación es importante para la evaluación de los efectos de la reubicación sobre las especies. Evaluamos la eficiencia de una reubicación diseñada para mitigar los efectos de un proyecto de energía solar fotovoltaica sobre la tortuga terrestre del desierto de Mojave (Gopherus agassizii), una especie en la lista federal estadunidense de especies en peligro. Los reptiles de esta especie son longevos y se encuentran en peligro por una variedad de factores, incluyendo la pérdida del hábitat por el desarrollo de energías renovables en el desierto de Mojave y en porciones del desierto del Colorado en el sur de California (suroeste de los Estados Unidos). Reubicamos a 58 individuos de esta especie para alejarlos del sitio de construcción del proyecto y los monitoreamos intensivamente durante cinco años (2012 - 2017). Monitoreamos a estos individuos y a las tortugas que ya se encontraban en el sitio de liberación (tortugas residentes; n = 112), así como a un grupo control de tortugas (n = 149) en una ubicación cercana. Usamos nuestros datos de encuentro con tortugas y modelos de supervivencia con destino conocido para estimar la supervivencia anual y acumulativa. Las tortugas reubicadas en cada una de las dos clases de tamaño (120-160 mm, >160 mm) no sobrevivieron a tasas más bajas que las residentes y las del grupo control durante el periodo de estudio. Para los modelos con conjuntos diferentes de co-variados bióticos y abióticos los estimados anuales y acumulativos de supervivencia fueron siempre >0.87 y >0.56, respectivamente. Las tortugas más grandes tendieron a tener una mayor supervivencia, aunque las tortugas reubicadas no se vieron afectadas diferencialmente por los co-variados que se usaron para modelar la variación de la supervivencia. Con base en estos hallazgos, nuestro diseño de reubicación y nuestros protocolos de estudio podrían informar a otros proyectos de reubicación para especies de desierto. Nuestro estudio de caso resalta los beneficios de la combinación del monitoreo científico riguroso con acciones de manejo bien diseñadas y llevadas por la mitigación para reducir los efectos negativos del desarrollo sobre las especies de importancia para la conservación.

Islands within an island: repeated adaptive divergence in a single population.

Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km(2) Santa Cruz Island, California, USA. Island scrub-jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species' mainland congener. Variation in both bill measurements was heritable, and island scrub-jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east-west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale--environmental heterogeneity and localized dispersal--are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds.

Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population.

Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong.

Non-breeding season events influence sexual selection in a long-distance migratory bird.

The study of sexual selection has traditionally focused on events and behaviours immediately surrounding copulation. In this study, we examine whether carry-over effects from the non-breeding season can influence the process of sexual selection in a long-distance migratory bird, the American redstart (Setophaga ruticilla). Previous work on American redstarts demonstrated that overwintering in a high-quality habitat influences spring departure dates from the wintering grounds, advances arrival dates on the breeding grounds and increases apparent reproductive success. We show that the mixed-mating strategy of American redstarts compounds the benefits of overwintering in high-quality winter habitats. Males arriving to breed in Canada from high-quality winter habitats arrive earlier than males from poor-quality habitats, resulting in a lower probability of paternity loss, a higher probability of achieving polygyny and ultimately higher realized reproductive success. Such results suggest that the process of sexual selection may be influenced by events interacting throughout the annual cycle.

Hydrogen isotopic variation in migratory bird tissues of known origin: implications for geographic assignment.

Continent-wide variation in hydrogen isotopic composition of precipitation is incorporated into animal diets, providing an intrinsic marker of geographic location at the time of tissue growth. Feathers from migratory birds are now frequently analyzed for stable-hydrogen isotopes (deltaD) to estimate the location of individuals during a preceding molt. Using known-origin birds, we tested several assumptions associated with this emerging technique. We examined hydrogen isotopic variation as a function of age, sex, feather type and the timing of molt in a marked population of American redstarts (Setophaga ruticilla) breeding in southeastern Ontario. We measured deltaD in feathers and blood from individuals that bred or hatched at our study site during the year in which those tissues were grown. Juvenile tissues from 5- to 10-day-old birds had more negative deltaD values than those from adults, which most likely reflected age-related differences in diet. Within adults, primary feathers had more negative deltaD values than contour feathers. The mean deltaD value in adult primary feathers was relatively consistent among years and with the value expected for our study population. However, among-individual variation in deltaD corresponded to an estimated latitudinal range of 6-8 degrees (650-900 km). We conclude that feathers sampled from recently hatched juveniles may not provide a reliable estimate of expected local isotopic signatures for comparison with adult feathers of unknown origin. Furthermore, we urge researchers to use caution when using deltaD values in feathers to infer geographic origin, and suggest that the best approach is to assign individuals to broad geographic zones within a species' potential molting range.