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- 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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- Schodde, R., et al.
(författare)
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Why neotypification of Lophorina superba (Pennant, 1781) (Aves: Paradisaeidae) is justified—and necessary
- 2021
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Ingår i: Zootaxa. - : Magnolia Press. - 1175-5326 .- 1175-5334.
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Tidskriftsartikel (refereegranskat)abstract
- We review Irestedt et al.'s (2017) neotypification of the senior species name superba Pennant, 1781 in the bird-of-paradise genus Lophorina in response to Elliott et al.(2020) who challenged the resultant shift in name from the small isolate in New Guinea's Vogelkop to the widespread species in the island's central cordillera. In nine male plumage traits which differentiate the two species, six of which had been identified as novel by Irestedt et al., we show that the only two figures of the perished male holotype of superba match the central cordillera species more closely than the Vogelkop. We find as well that not only was the trading of bird-of-paradise skins from the central cordillera to coastal ports in the Vogelkop feasible before European contact, but application of superba to the central cordillera species also promotes nomenclatural stability: the name has been used overwhelmingly at species rank for that widespread form throughout post-19th century media. Re-assessment of Irestedt et al.'s point-by-point justification of neotypification under Article 75.3 of the ICZN (1999) Code establishes, furthermore, that their case meets the requirements of every condition specified in the article; the neotypification is thus valid. Elliott et al.'s alternative to fix superba to the Vogelkop isolate by type locality restriction is not Code-compliant, nor is their evidence for interpreting JR Forster as the author of the name. In conclusion, we lay out the correct nomenclature for the taxa of Lophorina under the Code.
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