Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation.

When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome-for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA-show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z. leucophrys subspecies show moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species Z. leucophrys and Z. atricapilla show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between Z. atricapilla and Z. leucophrys appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria are highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing a lack of gene flow between populations many hundreds of thousands of years before other genomic regions.

Mercury in Neotropical birds: a synthesis and prospectus on 13 years of exposure data.

Environmental mercury (Hg) contamination of the global tropics outpaces our understanding of its consequences for biodiversity. Knowledge gaps of pollution exposure could obscure conservation threats in the Neotropics: a region that supports over half of the world's species, but faces ongoing land-use change and Hg emission via artisanal and small-scale gold mining (ASGM). Due to their global distribution and sensitivity to pollution, birds provide a valuable opportunity as bioindicators to assess how accelerating Hg emissions impact an ecosystem's ability to support biodiversity, and ultimately, global health. We present the largest database on Neotropical bird Hg concentrations (n = 2316) and establish exposure baselines for 322 bird species spanning nine countries across Central America, South America, and the West Indies. Patterns of avian Hg exposure in the Neotropics broadly align with those in temperate regions: consistent bioaccumulation across functional groups and high spatiotemporal variation. Bird species occupying higher trophic positions and aquatic habitats exhibited elevated Hg concentrations that have been previously associated with reductions in reproductive success. Notably, bird Hg concentrations were over four times higher at sites impacted by ASGM activities and differed by season for certain trophic niches. We developed this synthesis via a collaborative research network, the Tropical Research for Avian Conservation and Ecotoxicology (TRACE) Initiative, which exemplifies inclusive, equitable, and international data-sharing. While our findings signal an urgent need to assess sampling biases, mechanisms, and consequences of Hg exposure to tropical avian communities, the TRACE Initiative provides a meaningful framework to achieve such goals. Ultimately, our collective efforts support and inform local, scientific, and government entities, including Parties of the United Nations Minamata Convention on Mercury, as we continue working together to understand how Hg pollution impacts biodiversity conservation, ecosystem function, and public health in the tropics.

RESúMEN: La contaminación ambiental por mercurio (Hg) en los trópicos supera nuestra comprensión de sus consecuencias para la biodiversidad. Los vacíos de conocimiento que existen sobre la exposición a la contaminación podrían ocultar las amenazas para la conservación en el Neotrópico: una región que alberga a más de la mitad de las especies del mundo, pero que enfrenta una continua intensificación de las emisiones de Hg y del cambio de uso del suelo por el avance de la minería de oro artesanal y de pequeña escala (MAPE). Debido a su distribución global y su sensibilidad a la contaminación, las aves brindan una oportunidad valiosa como bioindicadores para evaluar cómo las emisiones de Hg afectan la capacidad de un ecosistema para sustentar la biodiversidad y, en última instancia, la salud global. Presentamos la más grande base de datos sobre concentraciones de Hg en aves Neotropicales (n = 2,316) para establecer una línea base para los niveles de exposición a Hg en 322 especies de aves de nueve países de América Central, América del Sur, y el Caribe. Encontramos patrones de las concentraciones de Hg en aves de los trópicos que se asemejan a los de las regiones templadas: mostrando una bioacumulación consistente a través de grupos funcionales y una alta variación espaciotemporal. Las especies de aves que ocupan posiciones más altas en la cadena trófica y en hábitats acuáticos registraron concentraciones elevadas de Hg que podrían tener efectos negativos en su éxito reproductivo. Es importante resaltar que las concentraciones de Hg en las aves de los sitios afectados por la MAPE fueron cuatro veces más altas que las de los sitios control y además difirió por temporada para ciertos nichos tróficos. Desarrollamos esta síntesis a través de una red de investigación colaborativa, la Iniciativa de Investigación Tropical para la Conservación y Ecotoxicología Aviar (TRACE), que ejemplifica un intercambio de datos inclusivo, equitativo e internacional. Si bien nuestros hallazgos sugieren una necesidad urgente de evaluar los sesgos en el muestreo, los mecanismos, y las consecuencias de la exposición al Hg en las comunidades de aves tropicales, la Iniciativa TRACE proporciona un marco para abordar estos objetivos. Nuestro esfuerzo colectivo tiene como propósito respaldar y brindar información a las entidades locales, científicas, y gubernamentales, incluyendo las Partes de la Convención de Minamata de las Naciones Unidas sobre el Mercurio, mientras continuamos trabajando juntos para comprender cómo la contaminación por Hg en los trópicos puede afectar la salud pública, el funcionamiento de los ecosistemas, y la conservación de la biodiversidad. Total mercury (THg) concentrations (µg/g) and sample sizes of birds across Central America, South America, and the West Indies from 2007­2023. Point size and color are arranged in order of increasing THg concentration and hexagonal grid cells are colored in terms of increasing sample size.