Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
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Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements. / Chen, De; Hosner, Peter A.; Dittmann, Donna L.; O’Neill, John P.; Birks, Sharon M.; Braun, Edward L.; Kimball, Rebecca T.
In: BMC Ecology and Evolution, Vol. 21, 209, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
AU - Chen, De
AU - Hosner, Peter A.
AU - Dittmann, Donna L.
AU - O’Neill, John P.
AU - Birks, Sharon M.
AU - Braun, Edward L.
AU - Kimball, Rebecca T.
N1 - Publisher Copyright: © 2021, The Author(s).
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - Data heterogeneity
KW - Fossil calibration
KW - Galliformes
KW - Molecular dating
KW - PartitionFinder
KW - Phylogenomics
KW - Ultraconserved elements
U2 - 10.1186/s12862-021-01935-1
DO - 10.1186/s12862-021-01935-1
M3 - Journal article
C2 - 34809586
AN - SCOPUS:85119893536
VL - 21
JO - BMC Ecology
JF - BMC Ecology
SN - 1472-6785
M1 - 209
ER -
ID: 286494437