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- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)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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- Ruiz-Trillo, Iñaki, et al.
(author)
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A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians
- 2002
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In: Proc. Natl. Acad. Sci. USA. - : Proceedings of the National Academy of Sciences. ; 99, s. 11246-11251
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Journal article (peer-reviewed)abstract
- Bilateria are currently subdivided into three superclades: Deuterostomia, Ecdysozoa, and Lophotrochozoa. Within this new taxonomic frame, acoelomate Platyhelminthes, for a long time held to be basal bilaterians, are now considered spiralian lophotrochozoans. However, recent 18S rDNA [small subunit (SSU)] analyses have shown Platyhelminthes to be polyphyletic with two of its orders, the Acoela and the Nemertodermatida, as the earliest extant bilaterians. To corroborate such position and avoid the criticisms of saturation and long-branch effects thrown on the SSU molecule, we have searched for independent molecular data bearing good phylogenetic information at deep evolutionary nodes. Here we report a phylogenetic analysis of DNA sequences from the myosin heavy chain type II (myosin II) gene from a large set of metazoans, including acoels and nemertodermatids. Our study demonstrates, both for the myosin II data set alone and for a combined SSU + myosin II data set, that Platyhelminthes are polyphyletic and that acoels and nemertodermatids are the extant earliest bilaterians. Hence, the common bilaterian ancestor was not, as currently held, large and complex but small, simple, and likely with direct development. This scenario has far-reaching implications for understanding the evolution of major body plans and for perceptions of the Cambrian evolutionary explosion.
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