Individual identification in acoustic recordings.

Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.

Local and regional-scale effects of hedgerows on grassland- and forest-associated bird populations within agroecosystems.

Linear woody features (LWFs), like hedgerows along field edges, provide wildlife habitat and support biodiversity in agroecosystems. Assessments of LWFs usually focus on community-level indices, such as species richness. However, effective conservation actions need to balance the contrasting habitat preferences of different wildlife species, necessitating a focus on population-level effects in working landscapes. We assessed associations between LWFs and abundance for 45 bird species within an intensive agroecosystem in eastern Ontario, Canada. We used distance- and removal-sampling methods across 4 years (2016-2019) to estimate local bird abundance in habitats representing a range of LWF densities. We also predicted abundance across a subset of the study region with and without LWFs to understand their contribution to regional population density. Associations between local bird abundance and LWFs were variable among species, but overall community effects were clearly positive, particularly for forest and shrubland species. At the site level, 20/45 species (44%) had higher densities associated with greater LWF presence on average, compared to 5/45 (11%) with negative associations. At the regional scale, LWFs had predicted benefits on total abundance for 31 species (69%), contributing to an estimated 20% increase on average. Positive effects were most pronounced in areas with greater agricultural land use (primarily field crops), suggesting LWFs may provide crucial habitat in heavily modified landscapes but have little to no additional benefit for the avian community in areas with greater existing heterogeneity and habitat retention. Species that responded negatively tended to be at risk with strong habitat preferences for intact forests or large, open grasslands and, thus, greater sensitivity to potential edge effects. With rapidly declining songbird populations and a global need for food security, conservation strategies that amplify biodiversity and enhance agricultural productivity through ecosystem services such as pest control, pollination, and water regulation are vital. We demonstrate the benefits of habitat heterogeneity in agroecosystems on songbird densities and highlight the need to integrate local and landscape-level assessments in conservation planning. An effective, balanced strategy includes concentrating LWFs in areas of extensive arable crops, with habitat retention patches where possible, while maintaining heterogeneity through mixtures of natural habitats and pastoral farming in less intensive regions.

Les caractéristiques d'emboisement linéaires (CEL), tels que les haies en bordure de champs, fournissent un habitat à la faune et à la flore et favorisent la biodiversité dans les agroécosystèmes. Les évaluations des caractéristiques d'emboisement linéaires se concentrent généralement sur des indices au niveau de la communauté, tels que la richesse des espèces. Cependant, pour être efficaces, les actions de conservation doivent équilibrer les préférences variables des différentes espèces sauvages en matière d'habitat, ce qui nécessite de se concentrer sur les effets au niveau de la population dans les paysages exploités. Nous avons évalué les associations entre les CEL et l'abondance de 45 espèces d'oiseaux dans un agroécosystème intensif de l'est de l'Ontario, au Canada. Nous avons utilisé des méthodes d'échantillonnage par distance et par enlèvement sur quatre ans (2016­2019) pour estimer l'abondance locale des oiseaux dans des habitats représentant une gamme de densités de CEL. Nous avons également prédit l'abondance dans un sous­ensemble de la région étudiée avec et sans CEL pour comprendre leur contribution à la densité de la population régionale. Les associations entre l'abondance des oiseaux locaux et les CEL étaient variables d'une espèce à l'autre, mais les effets globaux sur les communautés étaient clairement positifs, en particulier pour les espèces des forêts et des zones arbustives. Au niveau du site, 20/45 espèces (44%) avaient des densités plus élevées associées à une plus grande présence de CEL en moyenne, contre 5/45 (11%) avec des associations négatives. À l'échelle régionale, les CEL ont eu des effets bénéfiques sur l'abondance totale de 31 espèces (69%), contribuant à une augmentation estimée à 20% en moyenne. Les effets positifs étaient plus prononcés dans les zones où l'utilisation des terres agricoles était plus importante (principalement les grandes cultures), ce qui suggère que les CEL peuvent fournir un habitat crucial dans les paysages fortement modifiés, mais qu'elles ont peu ou pas d'avantages supplémentaires pour la communauté aviaire dans les zones où l'hétérogénéité existante et la conservation de l'habitat sont plus importantes. Les espèces qui ont répondu négativement avaient tendance à être en danger, avec de fortes préférences d'habitat pour les forêts intactes ou les grandes prairies ouvertes, et donc une plus grande sensibilité aux effets de lisière potentiels. Avec le déclin rapide des populations d'oiseaux chanteurs et le besoin mondial de sécurité alimentaire, les stratégies de conservation qui amplifient la biodiversité et améliorent la productivité agricole grâce aux services écosystémiques tels que la lutte contre les ravageurs, la pollinisation et la régulation de l'eau sont vitales. Nous démontrons les avantages de l'hétérogénéité de l'habitat dans les agroécosystèmes sur les densités de passereaux et soulignons la nécessité d'intégrer les évaluations locales et au niveau du paysage dans la planification de la conservation. Une stratégie efficace et équilibrée consiste à concentrer les CEL dans les zones de cultures arables extensives, avec des parcelles de conservation de l'habitat là où c'est possible, tout en maintenant l'hétérogénéité grâce à des mélanges d'habitats naturels et à l'agriculture pastorale dans les régions moins intensives.

Occupancy trends of overwintering coastal waterbird communities reveal guild-specific patterns of redistribution and shifting reliance on existing protected areas.

Climate change and anthropogenic stressors are redistributing species and altering community composition globally. Protected areas (PAs) may not sufficiently protect populations of species undergoing distributional shifts, necessitating that we evaluate existing PAs and identify areas for future protection to conserve biodiversity across regional and temporal scales. Coastal waterbirds are important indicators of marine ecosystem health, representing mobile, long-lived, higher trophic-level consumers. Using a 20-year citizen science dataset (1999-2019) with a before-after control-intervention sampling framework for habitat protection, we applied dynamic occupancy models to assess winter occupancy trends along the Pacific coast of Canada. Specifically, we sought to understand potential drivers of regional declines, spatial commonalities among guilds, and changes in habitat use before and after PA designation, as well as between PAs and non-PAs. Occupancy trends varied regionally, with greater declines in the south compared to the north. Regional differences underlined potential range shifts, particularly for species with traits linked to temperature tolerance, movement, and high productivity foraging, as cold-tolerant, migratory benthivores and piscivores wintered farther north relative to 20 years ago or retreated to cold-water fjords. While 21 of 57 (36.8%) species responded positively to PA designation (before-after), greater occupancy declines tended to occur in PAs established pre-1999 relative to non-PAs (control-intervention). Since PAs are currently concentrated in the south, negative associations were most apparent for species retreating northward, but existing PAs may have a stabilizing or transitory effect on southern wintering species shifting into the region from farther south. We emphasize that conservation strategies must balance persistence of current communities with preserving the climate-adapted biodiversity of tomorrow by accounting for community-level effects of species moving into and out of existing PAs. Incorporating range shifts into PA planning by predicting distributional changes will allow conservation practitioners to identify priority habitats, such as cold-water refugia, for persistent wildlife communities.

Le changement climatique et les facteurs de stress anthropiques redistribuent les espèces et modifient la composition des communautés à l'échelle mondiale. Les zones protégées (ZP) ne protègent peut-être pas suffisamment les populations d'espèces qui subissent des changements de répartition, ce qui nous oblige à évaluer les ZP existantes et à identifier les zones à protéger à l'avenir pour conserver la biodiversité à l'échelle régionale et temporelle. Les oiseaux côtiers sont des indicateurs importants de la santé des écosystèmes marins, car ils représentent des consommateurs mobiles, ont une longue durée de vie et représente le niveau trophique supérieur. En utilisant un ensemble de données de science participative sur 20 ans (1999-2019) avec un échantillonnage avant-après contrôle-intervention (AACI) pour la protection de l'habitat, nous avons appliqué des modèles d'occupation dynamiques pour évaluer les tendances de l'occupation hivernale le long de la côte pacifique du Canada. Plus précisément, nous avons cherché à comprendre les moteurs potentiels des déclins régionaux, les points communs spatiaux entre les guildes et les changements dans l'utilisation de l'habitat avant et après la désignation de le ZP, ainsi qu'entre les ZP et les non-ZP. Les tendances en matière d'occupation varient d'une région à l'autre, avec des déclins plus importants dans le sud que dans le nord. Les différences régionales soulignent les déplacements potentiels de l'aire de répartition, en particulier pour les espèces dont les caractéristiques sont liées à la tolérance à la température, aux déplacements et à la recherche de nourriture à rendement élevé, car les benthivores et les piscivores migrateurs tolérants au froid ont hiverné plus au nord qu'il y a 20 ans ou se sont retirés dans les fjords aux eaux froides. Alors que 21 des 57 (36,8 %) espèces ont réagi positivement à la désignation des aires protégées (avant-après), les baisses d'occupation ont eu tendance à être plus importantes dans les aires protégées créées avant 1999 que dans les aires non protégées (contrôle-intervention). Comme les aires protégées sont actuellement concentrées dans le sud, les associations négatives étaient plus évidentes pour les espèces qui se retirent vers le nord, mais les aires protégées existantes peuvent avoir un effet stabilisateur ou transitoire sur les espèces hivernant dans le sud qui se déplacent dans la région à partir d'une région plus au sud. Nous soulignons que les stratégies de conservation doivent trouver un équilibre entre la persistance des communautés actuelles et la préservation de la biodiversité adaptée au climat de demain, en tenant compte des effets au niveau des communautés des espèces qui entrent dans les aires protégées existantes ou qui en sortent. L'intégration des changements d'aire de répartition dans la planification des aires protégées en prédisant les changements de distribution permettra aux praticiens de la conservation d'identifier les habitats prioritaires, tels que les refuges d'eau froide, pour les communautés d'espèces sauvages persistantes.

GABB: A global dataset of alpine breeding birds and their ecological traits.

Alpine ecosystems represent varied climates and vegetation structures globally, with the potential to support rich and functionally diverse avian communities. High mountain habitats and species are under significant threat from climate change and other anthropogenic factors. Yet, no global database of alpine birds exists, with most mountain systems lacking basic information on species breeding in alpine habitats, their status and trends, or potential cryptic diversity (i.e., sub-species distributions). To address these critical knowledge gaps, we combined published literature, regional monitoring schemes, and expert knowledge from often inaccessible, data-deficient mountain ranges to develop a global list of alpine breeding bird species with their associated distributions and select ecological traits. This dataset compiles alpine breeding records for 1,310 birds, representing 12.0% of extant species and covering all major mountain regions across each continent, excluding Antarctica. The Global Alpine Breeding Bird dataset (GABB) is an essential resource for research on the ecological and evolutionary factors shaping alpine communities, as well as documenting the value of these high elevation, climate-sensitive habitats for conserving biodiversity.

The relative influence of cross-seasonal and local weather effects on the breeding success of a migratory songbird.

In seasonal environments, fluctuating early-season weather conditions and short breeding windows limit reproductive opportunities such that breeding earlier or later than the optimum may be particularly costly. Given the risk of early-season energy limitations, time- and energy-based carry-over effects stemming from environmental conditions across the annual cycle may have pronounced consequences for breeding phenology and fitness. Generally, when and where environmental conditions are most influential are poorly understood, limiting our ability to predict the future of climate-sensitive populations. For an alpine-breeding, migratory population of horned lark Eremophila alpestris in northern British Columbia, Canada (54.8°N), we assessed how weather conditions across the annual cycle influenced clutch initiation date and offspring development. We also addressed how cross-seasonal effects on breeding parameters combine to influence reproductive fitness. With 12 years of breeding data and 3 years of migration data, we used a sliding window approach to identify points during the annual cycle when weather events most influenced breeding phenology and offspring development. Consequences for breeding success were assessed using nest survival simulations. Average clutch initiation date varied up to 11 days among years but did not advance from 2003 to 2019. Warmer temperatures at stopover and breeding sites advanced clutch initiation, but winter conditions had no effect. Sub-zero stopover temperatures carried over to prolong offspring development independent of clutch initiation date, potentially indicating energy-based carry-over effects acting on parental investment. Nest survival decreased with both later clutch initiation and prolonged offspring development such that females nesting earlier and fledging offspring at a younger age were up to 45% more likely to reproduce successfully. We demonstrate that stronger carry-over effects originated from environmental conditions closer to the breeding site in time and space, as well as the potential for energy-based mechanisms to link pre-breeding conditions to reproductive fitness. We also highlight the importance of extended stopovers for songbirds breeding in seasonal environments, particularly given that climatic conditions are becoming increasingly decoupled across stages of the annual cycle. Understanding the cross-seasonal mechanisms shaping breeding decisions in stochastic environments allows for more accurate predictions of population-level responses to climate change.

Les variations saisonnières de l'environnement, notamment due aux conditions climatiques changeantes en début de saison ainsi que la réduction de la période propice à l'accouplement contraint fortement les possibilités de reproduction. Dans ces conditions, s'accoupler avant ou après le moment optimal peut s'avérer particulièrement coûteux. Les effets de report (temporels et énergétiques) causés par ces variations environnementales peuvent avoir des conséquences notables sur la phénologie de la reproduction, et ultimement sur la valeur sélective des individus. Où et quand les effets des conditions environnementales sont le plus critiques reste encore méconnu, limitant notre capacité à prédire le futur des populations sensibles aux variations climatiques. Ici, nous avons évalué comment des conditions climatiques au cours de l'année influencent la date de ponte et le développement des oisillons dans une population migratrice d'Alouette hausse-col Eremophila alpestris se reproduisant en milieux alpin. Nous tirons profit de données issues de 12 ans de suivit de la reproduction et de 3 ans de suivit migratoire, et utilisons une approche dite de 'sliding window' pour identifier les moments du cycle annuel pour lequel le climat a eu le plus d'influence sur la phénologie de la reproduction et le développement des oisillons. La date moyenne de ponte s'avère variable d'une année à l'autre (certaine différence allant jusqu'à 11 jours), mais ne se décale pas sur la période de 2003 à 2019. Nos résultats montrent que des conditions climatiques plus chaudes lors des haltes migratoires ainsi que sur les sites de reproductions rendent la date de ponte plus précoces. Des températures négatives lors des haltes migratoires aussi ont pour conséquences un temps de développement des oisillons plus long, et ceci indépendamment de la date de ponte. Cela suggère des effets de report, notamment énergétique, affectant l'investissement des parents. Nos résultats montrent que la survie au nid diminue lorsque la date de ponte est plus tardive ou que le temps de développement des oisillons est rallongé. De cette manière, les femelles commençants la nidification plus tôt et pour qui les oisillons quittent le nid plus tôt ont 45% plus de chance de se reproduire avec succès. Nous démontrons que des conditions environnementales proche du site de reproduction (que ce soit dans le temps ou dans l'espace) cause un fort effet de report, et suggérons un possible mécanisme reliant les conditions climatiques pré-reproductives au succès reproducteur. De plus, nous mettons en lumière l'importance des haltes migratoires prolongées pour la reproduction des passereaux en environnement saisonnier, particulièrement du fait que les conditions climatiques sont de plus en plus découplées au cours des les étapes du cycle annuel. Une meilleure compréhension des mécanismes inter-saisonniers influençant les décisions de reproduction en environnement stochastique permettrait de mieux prédire les réponses des populations aux changements climatiques.

Pleiotropic opposing dominance within a color gene block contributes to a nascent species boundary via its influence on hybrid male territorial behavior.

The divergence of plumage color genes contributes to songbird radiation. However, the mechanisms by which color gene divergence counteracts gene flow to maintain reproductive isolation during the formation of new species boundaries remain elusive. The hybrid zone between Setophaga occidentalis (SOCC) and S. townsendi (STOW) in the Cascade Range provides a natural observatory to investigate potential behavioral mechanisms underlying divergent selection on color genes. Recently, we found that selection within a single gene block associated with plumage color variation has maintained a stable and narrow hybrid zone. Here, we investigated the potential role of plumage signals in moderating a behavioral mechanism of selection. Specifically, we assessed whether two plumage traits are associated with body size among breeding males and if trait mismatch predicted aggressive behavior within hybrid and parental individuals in response to simulated territorial intrusion. The two plumage signals, cheek and flank coloration, though associated with the same gene block, reflect opposing dominance of SOCC and STOW alleles. We found that both plumage traits significantly predict the body size in the territorial sex (i.e. males). The opposing dominance of the single color gene block resulted in plumage signal discordance in heterozygotes, which in turn was associated with reduced hybrid territorial performance, an important proxy of fitness in this system. Taken together, these observations point to a single-locus-two-alleles mechanism of incompatibility in shaping a natural species boundary in the early stage of speciation.

Combining point counts and autonomous recording units improves avian survey efficacy across elevational gradients on two continents.

Accurate biodiversity and population monitoring is a requirement for effective conservation decision making. Survey method bias is therefore a concern, particularly when research programs face logistical and cost limitations.We employed point counts (PCs) and autonomous recording units (ARUs) to survey avian biodiversity within comparable, high elevation, temperate mountain habitats at opposite ends of the Americas: nine mountains in British Columbia (BC), Canada, and 10 in southern Chile. We compared detected species richness against multiyear species inventories and examined method-specific detection probability by family. By incorporating time costs, we assessed the performance and efficiency of single versus combined methods.Species accumulation curves indicate ARUs can capture ~93% of species present in BC but only ~58% in Chile, despite Chilean mountain communities being less diverse. The avian community, rather than landscape composition, appears to drive this dramatic difference. Chilean communities contain less-vocal species, which ARUs missed. Further, 6/13 families in BC were better detected by ARUs, while 11/11 families in Chile were better detected by PCs. Where survey conditions differentially impacted method performance, PCs mostly varied over the morning and with canopy cover in BC, while ARUs mostly varied seasonally in Chile. Within a single year of monitoring, neither method alone was predicted to capture the full avian community, with the exception of ARUs in the alpine and subalpine of BC. PCs contributed little to detected diversity in BC, but including this method resulted in negligible increases in total time costs. Combining PCs with ARUs in Chile significantly increased species detections, again, for little cost.Combined methods were among the most efficient and accurate approaches to capturing diversity. We recommend conducting point counts, while ARUs are being deployed and retrieved in order to capture additional diversity with minimal additional effort and to flag methodological biases using a comparative framework.

Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species.

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.

Treeline ecotones shape the distribution of avian species richness and functional diversity in south temperate mountains.

Mountains produce distinct environmental gradients that may constrain or facilitate both the presence of avian species and/or specific combinations of functional traits. We addressed species richness and functional diversity to understand the relative importance of habitat structure and elevation in shaping avian diversity patterns in the south temperate Andes, Chile. During 2010-2018, we conducted 2202 point-counts in four mountain habitats (successional montane forest, old-growth montane forest, subalpine, and alpine) from 211 to 1,768 m in elevation and assembled trait data associated with resource use for each species to estimate species richness and functional diversity and turnover. We detected 74 species. Alpine specialists included 16 species (22%) occurring only above treeline with a mean elevational range of 298 m, while bird communities below treeline (78%) occupied a mean elevational range of 1,081 m. Treeline was an inflection line, above which species composition changed by 91% and there was a greater turnover in functional traits (2-3 times greater than communities below treeline). Alpine birds were almost exclusively migratory, inhabiting a restricted elevational range, and breeding in rock cavities. We conclude that elevation and habitat heterogeneity structure avian trait distributions and community composition, with a diverse ecotonal sub-alpine and a distinct alpine community.