A genomic perspective on the evolutionary diversification of turtles

To examine phylogenetic heterogeneity in turtle evolution, we collected
thousands of high-confidence single-copy orthologs from 19 genome
assemblies representative of extant turtle diversity and estimated a
phylogeny with multispecies coalescent and concatenated partitioned
methods. We also collected next-generation sequences from 26 turtle
species and assembled millions of biallelic markers to reconstruct
phylogenies based on annotated regions from the western painted turtle
(Chrysemys picta bellii) genome (coding regions, introns, untranslated
regions, intergenic, and others). We then measured gene tree-species tree
discordance, as well as gene and site heterogeneity at each node in the
inferred trees, and tested for temporal patterns in phylogenomic conflict
across turtle evolution. We found strong and consistent support for all
bifurcations in the inferred turtle species phylogenies. However, a number
of genes, sites, and genomic features supported alternate relationships
between turtle taxa. Our results suggest that gene tree-species tree
discordance in these datasets is likely driven by population-level
processes such as incomplete lineage sorting. We found very little effect
of substitutional saturation on species tree topologies, and no clear
phylogenetic patterns in codon usage bias and compositional heterogeneity.
There was no correlation between gene and site concordance, node age, and
DNA substitution rate across most annotated genomic regions. Our study
demonstrates that heterogeneity is to be expected even in well resolved
clades such as turtles, and that future phylogenomic studies should aim to
sample as much of the genome as possible in order to obtain accurate
phylogenies for assessing conservation priorities in turtles.