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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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| 4. |
- Irestedt, Martin, et al.
(författare)
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The spatio-temporal colonization and diversification across the Indo-Pacific by a 'great speciator' (Aves, Erythropitta erythrogaster).
- 2013
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 280:1759, s. 20130309-
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Tidskriftsartikel (refereegranskat)abstract
- The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo, mode and magnitude of diversification across this region are scarce. We study the biogeographic history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic and population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping stone pathway, and that sea-level fluctuations during the Pleistocene may have promoted gene flow only locally. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized by diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a 'great speciator': it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species.
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| 7. |
- Sutton, Jill N., et al.
(författare)
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A review of the stable isotope bio-geochemistry of the global silicon cycle and its associated trace elements
- 2018
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Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 5
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Forskningsöversikt (refereegranskat)abstract
- Silicon (Si) is the second most abundant element in the Earth’s crust and is an important nutrient in the ocean. The global Si cycle plays a critical role in regulating primary productivity and carbon cycling on the continents and in the oceans. Development of the analytical tools used to study the sources, sinks, and fluxes of the global Si cycle (e.g., elemental and stable isotope ratio data for Ge, Si, Zn, etc.) have recently led to major advances in our understanding of the mechanisms and processes that constrain the cycling of Si in the modern environment and in the past. Here, we provide background on the geochemical tools that are available for studying the Si cycle and highlight our current understanding of the marine, freshwater and terrestrial systems. We place emphasis on the geochemistry (e.g., Al/Si, Ge/Si, Zn/Si, δ13 C, δ15 N, δ18 O, δ30 Si) of dissolved and biogenic Si, present case studies, such as the Silicic Acid Leakage Hypothesis, and discuss challenges associated with the development of these environmental proxies for the global Si cycle. We also discuss how each system within the global Si cycle might change over time (i.e., sources, sinks, and processes) and the potential technical and conceptual limitations that need to be considered for future studies.
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| 8. |
- Teece, Bronwyn L., et al.
(författare)
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Using laser micropyrolysis to assess potential relationships between Cambrian tommotiids and organophosphatic brachiopods
- 2021
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Ingår i: Journal of Analytical and Applied Pyrolysis. - : Elsevier BV. - 0165-2370 .- 1873-250X. ; 158, s. 105277-105277
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Tidskriftsartikel (refereegranskat)abstract
- Laser micropyrolysis gas chromatography-mass spectrometry enables researchers to selectively obtain chemical information about the organic matter in specific parts of a variety of specimens, such as coals and fossils, in order to elucidate chemical composition. This paper briefly reviews the history of this type of pyrolysis and examines whether the technique can be used to isolate and recover biogeochemical signatures directly from the mineralised organophosphatic sclerites of Cambrian tommotiids—a group of enigmatic lophotrochozoans—and potentially related organophosphatic brachiopods. We analysed specimens of two tommotiids (Micrina etheridgei and Dailyatia sp.) and the paterinate brachiopod Askepasma toddense from the lower Cambrian of South Australia. Pyrolysate hydrocarbons from the sclerites of these species were detected and compared. Results indicate that A. toddense is more chemically complex than either of the two tommotiid taxa, but that M. etheridgei is compositionally more similar to A. toddense. Importantly, this study has demonstrated that laser micropyrolysis gas chromatography-mass spectrometry of Cambrian organophosphatic small shelly fossils yields detectable pyrolysates that have geochemical significance. It will be analytically possible and useful in the future to apply this technique to a larger sample set to elucidate deep time biogeochemical homologies, and to test intra-shell heterogeneity.
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