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

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  • De Chen
  • Hosner, Peter Andrew
  • Donna L. Dittmann
  • John P. O’Neill
  • Sharon M. Birks
  • Edward L. Braun
  • Rebecca T. Kimball

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.

OriginalsprogEngelsk
Artikelnummer209
TidsskriftBMC Ecology and Evolution
Vol/bind21
Antal sider15
ISSN1472-6785
DOI
StatusUdgivet - 2021

Bibliografisk note

Funding Information:
This research was funded by grants from the US National Science Foundation grants to RTK and ELB (DEB- 1118823 and DEB-1655683). PAH acknowledges the support of the Villum Fonden for the Center for Global Mountain Biodiversity (grant no 25925). DC was supported by the National Natural Science Foundation of China (31601839).

Funding Information:
We would like to thank museums and their staff who provided tissue samples sequenced in this project: Australian National Wildlife Collection (ANWC: Leo Joseph), Field Museum of Natural History (FMNH: Ben Marks, John Bates, Shannon Hackett), Florida Museum of Natural History (FLMNH: Andrew Kratter, David Steadman), American Museum of Natural History (AMNH: Paul Sweet, Joel Cracraft, Brian Smith, George Barrowclough), Sam Noble Oklahoma Museum of Natural History (OMNH; Tamaki Yuri), University of Kansas Biodiversity (KU: Mark Robbins, Rob Moyle, Town Peterson). The Kimball-Braun lab provided helpful comments on an earlier version that improved this manuscript. We also thank editors and two anonymous reviewers whose feedback helped to improve the manuscript substantially.

Publisher Copyright:
© 2021, The Author(s).

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