Browsing by Author "Bi X"

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    Genomic insights into the secondary aquatic transition of penguins
    (Springer Nature Limited, 2022-07-19) Cole TL; Zhou C; Fang M; Pan H; Ksepka DT; Fiddaman SR; Emerling CA; Thomas DB; Bi X; Fang Q; Ellegaard MR; Feng S; Smith AL; Heath TA; Tennyson AJD; Borboroglu PG; Wood JR; Hadden PW; Grosser S; Bost C-A; Cherel Y; Mattern T; Hart T; Sinding M-HS; Shepherd LD; Phillips RA; Quillfeldt P; Masello JF; Bouzat JL; Ryan PG; Thompson DR; Ellenberg U; Dann P; Miller G; Dee Boersma P; Zhao R; Gilbert MTP; Yang H; Zhang D-X; Zhang G
    Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.
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    High-coverage genomes to elucidate the evolution of penguins
    (Oxford University Press and BGI, 2019-09-18) Pan H; Cole TL; Bi X; Fang M; Zhou C; Yang Z; Ksepka DT; Hart T; Bouzat JL; Argilla LS; Bertelsen MF; Boersma PD; Bost C-A; Cherel Y; Dann P; Fiddaman SR; Howard P; Labuschagne K; Mattern T; Miller G; Parker P; Phillips RA; Quillfeldt P; Ryan PG; Taylor H; Thompson DR; Young MJ; Ellegaard MR; Gilbert MTP; Sinding M-HS; Pacheco G; Shepherd LD; Tennyson AJD; Grosser S; Kay E; Nupen LJ; Ellenberg U; Houston DM; Reeve AH; Johnson K; Masello JF; Stracke T; McKinlay B; Borboroglu PG; Zhang D-X; Zhang G
    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.