Abstract
BackgroundPrevious phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.MethodsWe generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus (a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus.ResultsAll of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.ConclusionsOverall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets (both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.
Highlights
Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement
Two of the samples were from males (G. lafayettii and G. varius), while the other was from a female (G. sonneratii)
We tested whether there was a difference among the spectra of gene tree topologies for trees generated using introns, exons, and ultra-conserved element (UCE). We did this because some previous analyses have shown that different data types can yield distinct topologies (Jarvis et al 2014; Chen et al 2017; Reddy et al 2017). For the latter test we examined whether exons, introns, and UCEs were significantly different from expectation given homogeneity rather than testing for deviation from the multispecies coalescent
Summary
Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Genomes of many of the hundreds of different breeds of Gallus gallus have been sequenced (e.g., Imsland et al 2012; Yi et al 2014; Wang et al 2015; Lawal et al 2018; Li et al 2019; Yang et al 2019), resulting in a large number of available chicken genomes. In addition to G. gallus, the genus Gallus has three additional species (Gill and Donsker 2019): Gallus lafayettii (Sri Lanka Junglefowl), G. sonneratii (Grey Junglefowl), and G. varius (Green Junglefowl). These species are relatively closely related, with the earliest divergence approximately 4‒5 million years ago (Mya; Hosner et al. Tiley et al Avian Res (2020) 11:7
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