ArticleBMC ecology and evolution2021
Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements.
Article in BMC ecology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
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- Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge.Scientific reports · 2024Article
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- Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses.Microorganisms · 2023Article
- The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications.BMC genomics · 2023Article
- A new haplotype-resolved turkey genome to enable turkey genetics and genomics research.GigaScience · 2022Article
- A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl.GigaScience · 2022Article
- Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere.Nature communications · 2022Article
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7 authors.
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Abstract
backgroundDivergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results.
resultsIn this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different "gene shopping" schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree.
conclusionsWe provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.
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