Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla).

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Community modeling reveals the importance of elevation and land cover in shaping migratory bird abundance in the Andes.

The tropical Andes are characterized by extreme topographic and climatic complexity, which has likely contributed to their outstanding current species diversity, composed of many range-restricted species. However, little is known about how the distribution and abundance of highly mobile organisms, like long-distance migratory birds, varies across different land covers, elevations, and climatic conditions within the Andes. We conducted 1,606 distance-sampling point counts across the Colombian Andes, spanning elevations from 253 to 3,708 m, a range of precipitation regimes and representative land covers. We then employed a novel application of a multispecies hierarchical modeling approach to evaluate how elevation, local land cover, aboveground woody biomass, cloud cover, precipitation, and seasonality in precipitation shape the abundance of the migratory land bird community in the Andes. We detected 1,824 individuals of 29 species of migratory land birds, six of which were considered incidental in our study region. We modeled the abundance of the remaining 23 species, while considering observer and time of day effects on detectability. We found that both elevation and land cover had an overriding influence on the abundance of migratory species across the Andes, with strong evidence for a mid-elevation peak in abundance, and species-specific responses to both variables. As a community, migratory birds had the highest mean abundance in shade coffee plantations, secondary forest, and mature forest. Aboveground woody biomass did not affect the abundance of all species as a group, but a few showed strong responses to this variable. Contrary to predictions of a positive correlation between abundance and precipitation, we found no evidence for community-level responses to precipitation, aside for a weak tendency for birds to select areas with intermediate levels of precipitation. This novel use of a multispecies model sheds new light on the mechanisms shaping the winter distribution of migratory birds and highlights the importance of elevation and land cover types over climatic variables in the context of the Colombian Andes.

Migratory connectivity then and now: a northward shift in breeding origins of a long-distance migratory bird wintering in the tropics.

Temporal variation in the connectivity of populations of migratory animals has not been widely documented, despite having important repercussions for population ecology and conservation. Because the long-distance movements of migratory animals link ecologically distinct and geographically distant areas of the world, changes in the abundance and migratory patterns of species may reflect differential drivers of demographic trends acting over various spatial scales. Using stable hydrogen isotope analyses (δ2H) of feathers from historical museum specimens and contemporary samples obtained in the field, we provide evidence for an approximately 600 km northward shift over 45 years in the breeding origin of a species of songbird of major conservation concern (blackpoll warbler, Setophaga striata) wintering in the foothills of the eastern Andes of Colombia. Our finding mirrors predictions of range shifts for boreal-breeding species under warming climate scenarios and habitat loss in the temperate zone, and underscores likely drivers of widespread declines in populations of migratory birds. Our work also highlights the value of natural history collections to document the effects of global change on biodiversity.

Earlier and slower or later and faster: Spring migration pace linked to departure time in a Neotropical migrant songbird.

Migratory birds travel vast distances and the timing of migratory flights can affect survival and the ability to reproduce. For Neotropical migrant songbirds, early spring departure from wintering sites, early arrival to the breeding grounds and higher reproductive success have been related to the use of suitable habitats and environmental conditions during the non-breeding season. However, how migratory strategies are shaped by winter habitat choice is largely unknown due to the general inability to track birds from specific wintering habitats to stopovers or breeding destinations. We assessed how winter habitat (native forest vs. shade-grown coffee plantations) relates to spring departure date and migration pace in Swainson's Thrush Catharus ustulatus. We also determined the effect of departure date and total migration duration on the arrival date of birds detected near or within their breeding range. We used a novel application of Motus radiotelemetry arrays to track individuals from their wintering grounds in the Andes of South America along their migratory journey to North America. We found variation in migratory strategies between habitats, with birds wintering in native forest departing later than birds in coffee. We present isotopic evidence for native forest being of higher quality than shade-coffee for Swainson's Thrush and hypothesize that moister conditions in forest, as shown by stable isotope (δ13 C) analysis of thrush whole blood, provides favourable pre-migratory conditions allowing birds to delay departure from wintering grounds. Habitat, between-site and -year variation in departure date, suggests that birds made facultative adjustments to winter habitat quality and environmental conditions. Independent of habitat, birds that departed later migrated faster and this pattern was maintained along the migration route (n = 44). Migrating earlier and slower or later and faster was unlikely to result in significant differences in arrival time to breeding destinations. Our findings reveal underappreciated complexity in migratory decisions by long-distance migrants that contrast with the current paradigm of earlier departures and arrival from optimal habitats. The next step is to understand the relative fitness benefits of early versus late schedules or whether each strategy is an equally good response to experienced conditions.

Las aves migratorias viajan largas distancias y la fecha de sus vuelos migratorios puede afectar su supervivencia y habilidad para reproducirse. Para las aves migratorias Neotropicales canoras, salir más temprano de los sitios de invernada, llegar más temprano a los sitios de reproducción y tener mayor éxito reproductivo, está relacionado con el uso de hábitats y condiciones medioambientales adecuadas durante la época no reproductiva. Sin embargo, la forma en que las estrategias migratorias son moldeadas por la selección del hábitat invernal es en gran parte desconocida debido a la inhabilidad general de rastrear las aves desde hábitats de invernada específicos hasta los sitios de descanso o de reproducción. Determinamos la relación entre el hábitat de invierno (bosque nativo vs. plantaciones de café con sombra), la fecha de salida durante la migración de primavera y el número de días usados durante la migración por la mirla buchipecosa Catharus ustulatus. También determinamos el efecto de la fecha de salida y la duración total de la migración en la fecha de llegada de las aves detectadas cerca o dentro de su rango de reproducción. Usamos la novedosa red de radio telemetría Motus para rastrear individuos desde sus sitios de invernada en las montañas de los Andes en Sudamérica a lo largo de su viaje migratorio hasta Norte América. Encontramos variación en las estrategias migratorias entre hábitats, las aves invernando en bosque nativo salieron más tarde que las aves invernando en cafetales. Presentamos evidencia isotópica, que sugiere que el bosque nativo es de mejor calidad que las plantaciones de café con sombra. Hipotetizamos que condiciones más húmedas en el bosque, indicadas por análisis de isotopos estables (δ13 C) de la sangre de las mirlas, proveen condiciones favorables antes de la migración permitiendo a las aves retrasar su salida de los territorios de invernada. La variación en la fecha de salida entre hábitats, años y sitios, sugiere que las aves hicieron ajustes facultativos a la calidad del hábitat de invierno y a las condiciones medio ambientales. Independientemente del hábitat, las aves que salieron más tarde migraron más rápido, y este patrón fue mantenido a lo largo de la ruta migratoria (n = 44). Fue poco probable que migrar más temprano y más lento o más tarde y más rápido resultara en diferencias significativas en la fecha de llegada a los sitios de reproducción. Nuestros resultados revelan una subestimada complejidad en las decisiones migratorias de las aves y contrastan con el paradigma actual de salida y llegada más temprana en aves que usan hábitats óptimos. El siguiente paso es entender los beneficios relativos de migrar temprano versus tarde en el desempeño o si cada estrategia es una respuesta igualmente buena a las condiciones experimentadas.

Opportunities for the conservation of migratory birds to benefit threatened resident vertebrates in the Neotropics.

Neotropical countries receive financing and effort from temperate nations to aid the conservation of migratory species that move between temperate and tropical regions. If allocated strategically, these resources could simultaneously contribute to other conservation initiatives. In this study, we use novel distribution maps to show how those resources could aid planning for the recovery of threatened resident vertebrates.Using eBird-based relative abundance estimates, we first identified areas with high richness of Neotropical migrant landbirds of conservation concern (23 species) during the stationary non-breeding period. Within these areas, we then identified threatened species richness, projected forest loss and conducted a prioritization for 1,261 red-listed vertebrates using Terrestrial Area-of-Habitat maps.Richness for migrants was greatest along a corridor from the Yucatan peninsula south to the northern Andes but also included south-west Mexico and Hispaniola. Protected areas account for 22% of this region while 21% is at risk of forest loss. Within this focal region for migrants, all four vertebrate groups showed hotspots of threatened species richness along the west and east Andean slopes. Taxa-specific hotspots included montane areas of southern Mexico and central Guatemala (amphibians/reptiles) and the entire east slope of the Colombian East Andes (mammals).Our prioritization highlighted several areas of importance for conservation due to high threatened species richness and projected forest loss including (a) the Pacific dry forests of south-west Mexico, (b) montane regions of northern Central America and (c) the west Andean slope of Colombia and Ecuador. At a landscape scale in southern Colombia, we show how conservation efforts for six Neotropical migrants could benefit 56 threatened residents that share a similar elevational range. Synthesis and applications. Funding and effort for migratory bird conservation also has potential to benefit threatened resident vertebrates in the Neotropics. Our study highlights how novel, high-resolution information on species distributions and risk of forest loss can be integrated to identify priority areas for the two groups at regional and landscape scales. The approach and data can be further modified for more specific goals, such as within-country initiatives.

Los países neotropicales reciben financiamiento y recursos esfuerzos de países templados para ayudar a la conservación de las aves migratorias que se mueven entre estas dos regiones. Si se asignan estratégicamente, estos recursos podrían beneficiar simultáneamente a otras iniciativas de conservación. En esta investigación, usamos novedosos mapas de distribución para mostrar cómo esos recursos podrían ayudar a planificar la conservación de especies residentes amenazadas.Utilizando estimaciones de abundancia de eBird, delineamos la Región Focal con la mayor riqueza de aves migratorias neotropicales de interés para la conservación durante el periodo invernal (23 especies). Dentro de esta región, determinamos la riqueza de especies residentes amenazadas, la proyección de pérdida de bosque, y realizamos una priorización para 1261 especies de vertebrados incluidos en la lista roja de la IUCN utilizando mapas del área de hábitat terrestre.En la Región Focal, la riqueza de aves migratorias fue mayor a lo largo de un corredor desde el sur de la península de Yucatán hasta el norte de los Andes, y en el suroeste de México y la isla La Española. Las áreas protegidas representan 22% de esta región mientras que el 21% está en riesgo de pérdida de bosque. Dentro de la Región Focal para las aves migratorias, todos los vertebrados residentes mostraron puntos de mayor riqueza de especies amenazadas en los Andes occidentales y orientales. Las regiones con mayor riqueza para taxones específicos incluyeron las montañas del sur de México y del centro de Guatemala (anfibios y reptiles) y la vertiente oriental de la cordillera oriental de Colombia (mamíferos).La priorización destacó varias áreas de importancia para la conservación debido a la alta riqueza de especies amenazadas y a la pérdida de bosque proyectada incluyendo 1) los bosques secos del Pacífico del suroeste de México, 2) las regiones montañosas del norte de Centroamérica y 3) la vertiente occidental de los Andes Occidental de Colombia y Ecuador. A escala del paisaje en el sur de Colombia, mostramos cómo los esfuerzos para la conservación de 6 aves migratorias podrían beneficiar a 56 especies residentes amenazadas que comparten un rango altitudinal similar. Síntesis y aplicaciones. La financiación y esfuerzos para la conservación de las aves migratorias tienen el potencial a beneficiar a los vertebrados residentes amenazados en el Neotrópico. Nuestro estudio resalta como se puede integrar información novedosa y de alta resolución acerca de la distribución de especies y el riesgo de pérdida de bosques para identificar áreas prioritarias para los dos grupos a escala regional y paisajística. El enfoque y los datos se pueden modificar para objetivos más específicos, como por ejemplo iniciativas dentro de cada país.

Body mass data set for 1,317 bird and 270 mammal species from Colombia.

Body mass is one of the most important phenotypic attributes in animal ecology and life history. This trait is widely used in the fields of ecology and macroevolution, since it influences physiology, morphological functions, and a myriad of ecological and social interactions. In this data set, our aim was to gather a comprehensive bird and mammal body mass data set from northern South America. We report body mass, discriminated by sex, for 42,022 individual birds and 7,441 mammals representing 1,317 bird species (69% of Colombia's avifauna) and 270 mammal species (51% of Colombian mammals) from the Neotropics. The data were sourced from vouchers collected between 1942 and 2020 and from individuals captured and released at banding stations over the last two decades for birds (2000-2020) and the last decade for mammals (2010-2020), by 10 research groups and institutions in Colombia. This data set fills gaps identified in other similar databases, as it focuses on northern South America, a highly diverse Neotropical region often underrepresented in morphological data sets. We provide wide taxonomic coverage for studies interested in information both at regional and local scales. There are no copyright restrictions; the present data paper should be appropriately cited when data are used for publication. The authors would appreciate learning about research projects, teaching exercises, and other uses given to this data set and are open to contribute in further collaborations using these data.

Fuel loads acquired at a stopover site influence the pace of intercontinental migration in a boreal songbird.

Long-distance migratory organisms are under strong selection to migrate quickly. Stopovers demand more time than flying and are used by individuals to refuel during migration, but the effect of fuel loads (fat) acquired at stopover sites on the subsequent pace of migration has not been quantified. We studied stopover behaviour of Grey-cheeked Thrush (Catharus minimus) at a site in northern Colombia and then tracked their migration using an intercontinental radio-telemetry array. Tracking confirmed long-distance flights of more than 3000 km, highlighting the key importance of a single stopover site to the migration strategy of this species. Our results suggest that these songbirds behave as time-minimizers as predicted by optimal migration theory, and that fuel loads acquired at this South American stopover site, together with departure date, carry-over to influence the pace of migration, contributing to differences in travel time of up to 30 days in birds subsequently detected in the U. S. and Canada. Such variation in the pace of migration arising from a single stopover site, likely has important fitness consequences and suggests that identifying important fuelling sites will be essential to effectively conserve migratory species.