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| 2. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), 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. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Neves, Beatriz, et al.
(författare)
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Repeated evolution of pollination syndromes in a highly diverse bromeliad lineage is correlated with shifts in life form and habitat
- 2023
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Ingår i: Botanical Journal of the Linnean Society. - 0024-4074. ; 203:2, s. 111-22
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Tidskriftsartikel (refereegranskat)abstract
- Mutualistic plant-pollinator interactions play a critical role in the diversification of flowering plants. The spatiotemporal correlates of such interactions can be understood in a phylogenetic context. Here, we generate ddRAD-seq data for the highly diverse Vriesea-Stigmatodon lineage to test for correlated trait evolution among pollination syndromes and life form, habitat type, and altitude. Our results show that pollination syndromes are correlated with changes in life form and habitat type. The ancestor of the Vriesea-Stigmatodon lineage was likely bat pollinated, rock dwelling and inhabited open, mid-elevation forests. Transitions from bat to hummingbird pollination are correlated with transitions to the epiphytic life form in shaded habitats, whereas bat pollination is correlated with the rock-dwelling life form and open habitats. Our dated phylogenetic tree reveals independent origins of hummingbird pollination, occurring twice in Vriesea at c. 5.8 and 5.4 Mya. The timing for the shifts in pollination syndrome coincides with geological and environmental transformations across the Serra do Mar Mountain Chain, which increased habitat heterogeneity where Vriesea and their mutualists diversified. The phylogenetic tree reinforces the non-monophyly of taxonomic sections within the genus Vriesea previously defined by flower morphology, indicating that some lineages should be treated as species complexes. This study identifies synergetic drivers of speciation in a tropical biodiversity hotspot.
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- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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