Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
The positive relationship between range size and abundance is one of the best‐documented patterns in macroecology, but a growing number of studies from isolated tropical areas have reported negative or neutral relationships. It has been hypothesized that the combination of geographic isolation and environmental stability create selection pressures that favor narrowly specialized species, which could drive these non‐positive relationships. To test this idea, we measured the range size–abundance relationships of eleven bird communities in mature and degraded forest on four islands in the Indo‐Pacific, namely Flores in the Lesser Sundas, Seram in the Moluccas, and the New Caledonian islands of Grande Terre and Lifou. Local abundance data was gathered through extensive and methodologically consistent surveying, and regressed against global range size using linear mixed effect models. The relationship between range size and abundance was significantly negative across all combined mature and degraded forest communities. As negative relationships were found in degraded forest with little environmental stability, we conclude that the abundance of small‐ranged species on the study islands cannot be ascribed to narrow specialization. Rather, cross‐habitat community comparisons indicate that locally abundant endemic and near‐endemic species adapted to a broad spectrum of local environmental conditions cause the observed negative relationships. We suspect that geographic isolation facilitates the evolution of species that are simultaneously broad‐niched, small‐ranged, and abundant, as water barriers limit the range expansions that would typically accompany species’ attainment of high local population densities. The consistently negative relationships found across Indo‐Pacific islands represent a striking deviation from the positive range size–abundance relationship ‘rule’, and future studies should seek to determine whether the patterns detected here extend to geographically isolated mainland environments.
Background Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. Conclusions We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.
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