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.
Highlights
Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography
Robust molecular dating depends on several factors, with the most critical being the use of suitable fossil calibration points, a broadly sampled and well-resolved phylogenetic topology, and adequate application of molecular clock methodologies [8]
The 75% complete matrix contained 3574 Ultraconserved element (UCE) loci that ranged from 216 to 1467 bp in length
Summary
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. Chen et al BMC Ecology and Evolution (2021) 21:209 resolved Both Neornithes birds and placental mammals are considered to have diversified prior to rather than after the Cretaceous to Paleogene (K-Pg) mass extinction [3,4,5,6], even when different datasets and molecular clock methods are used [7]. Robust molecular dating depends on several factors, with the most critical being the use of suitable fossil calibration points, a broadly sampled and well-resolved phylogenetic topology, and adequate application of molecular clock methodologies [8]. Use of fossils whose taxonomic placement is agreed upon [10], and assessment of whether certain fossils have an undue impact on date estimations [11], are improving our use of fossil calibrations
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