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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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| 2. |
- Sandell, Maria, et al.
(författare)
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Pre-breeding diet affects the allocation of yolk hormones in zebra finches Taeniopygia guttata
- 2007
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Ingår i: Journal of Avian Biology. - 0908-8857. ; 38:3, s. 284-290
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Tidskriftsartikel (refereegranskat)abstract
- The ability of mothers to modify offspring phenotype to match prevailing environmental conditions is an important component of reproductive success, especially in variable environments. Pre-breeding conditions, such as food abundance, may have significant consequences for both the number and quality of offspring a female produces as well as her ability to rear the offspring. In an experiment where pre-breeding diet was manipulated, we investigated if allocation of yolk androgens (testosterone and 5 alpha-dihydrotestosterone) was related to the quality of diet experienced prior to breeding. Female zebra finches Taeniopygia guttata produced larger clutches on high quality diet than on low quality diet but with no differences in egg mass. Yolk androgen levels were repeatable within subsequent clutches of the same female and females did not change mean androgen content in eggs in relation to diet quality. However, within-in Clutch pattern of yolk testosterone and DHT changed with diet treatment. Testosterone and DHT decreased with laying order on the low quality diet but remained constant on the high quality diet. Differential yolk androgen allocation within the clutch may alter the competitive differences between chicks and provide females the possibility to adjust reproductive investment and offspring phenotype already at the egg stage.
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