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Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

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Chen, De, Hosner, Peter A., Dittmann, Donna L., O’Neill, John P., Birks, Sharon M., Braun, Edward L., Kimball, Rebecca T.·2021·BMC Ecology and Evolution
DOI 10.1186/s12862-021-01935-1PMC PMC8609756
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Abstract

Background: Divergence 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. Results: In 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. Conclusions: We 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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Authors
Chen, D., Hosner, P. A., Dittmann, D. L., O’Neill, J. P., Birks, S. M., Braun, E. L., & Kimball, R. T.
Affiliations
  • Beijing Normal University (CN)
  • University of Copenhagen (DK)
  • Louisiana State University (US)
  • University of Washington (US)
  • University of Florida (US)
Corresponding author
Kimball, Rebecca T.
ORCID
Venue
BMC Ecology and Evolution
Publisher
Springer Science and Business Media LLC
Published
2021-11-22
Volume
21
Issue
1
Pages
209-209
ISSN
2730-7182 (ISSN-L)
DOI
10.1186/s12862-021-01935-1
PMC
PMC8609756
OpenAlex
W3217113965
Cited by
52
References
6
Citations by year
2026: 8 · 2025: 8 · 2024: 20 · 2023: 10 · 2022: 6
FWCI
6.76
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Ecology and Evolution (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Natural Science Foundation of China (31601839)
  • Villum Fonden for the Center for Global Mountain Biodiversity (25925)
  • National Science Foundation (DEB- 1118823)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords
Galliformes, divergence time estimation, ultraconserved elements, fossil calibration, molecular clock, phylogenomics, partition selection
MeSH terms
Animals, Fossils, Phylogeny, Time, Galliformes

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