Data from: Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

Background: High-throughput sequencing using targeted enrichment and
transcriptomic methods enables rapid construction of phylogenomic data
sets incorporating hundreds to thousands of loci. These advances have
enabled access to an unprecedented amount of nucleotide sequence data, but
they also pose new questions. Given that the loci targeted for enrichment
are often highly conserved, how informative are they at different
taxonomic scales, especially at the intraspecific / phylogeographic scale?
We investigate this question using Australian scincid lizards in the
Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid
enriched loci for 43 individuals and mined 1650 exons (1648 loci) from
transcriptomes (transcriptome mining) from 11 individuals, including
multiple phylogeographic lineages within several species of Carlia,
Lampropholis, and Saproscincus skinks. We assessed the phylogenetic
information content of these loci at the intergeneric, interspecific, and
phylogeographic scales. As a further test of the utility at the
phylogeographic scale, we used the anchor hybrid enriched loci to infer
lineage divergence parameters using coalescent models of isolation with
migration. Results Phylogenetic analyses of both data sets inferred very
strongly supported trees at all taxonomic levels. Further, AHE loci
yielded estimates of divergence times between closely related lineages
that were broadly consistent with previous population-level analyses.
Conclusions Anchored-enriched loci are useful at the deep phylogeny and
phylogeographic scales. Although overall phylogenetic support was high
throughout the Australian Eugongylus group phylogeny, there were
nonetheless some conflicting or unresolved relationships, especially
regarding the placement of Pseudemoia, Cryptoblepharus, and the
relationships amongst closely-related species of Tasmanian Niveoscincus
skinks.