Data from: Sequence capture versus restriction site associated DNA sequencing for shallow systematics

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture datasets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq datasets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of datasets and inferences with those of prior work. In RAD-Seq datasets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a dataset to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among datasets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas. We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography.UCE and Exon Alignments from 40 Neotropical BirdsAlignments of 2,416 loci from 40 species of Neotropical birds. For each species at each alignment, a single sample was selected from a population-level dataset.one_align_for_overlap_count.zipSupplemental Methods, Figures, and TablesAdditional information on methods and results of analyses of sequence capture and RAD-Seq datasets from Xenops minutus.Supplemental_Information.docxRaw reads from sequence capture with 8 *Xenops minutus* samplesIllumina reads from sequence capture of 1,358 ultraconserved element (UCE) loci in 4 *X. minutus* samples from either side of the Andes. Tissue numbers corresponding to those used in the Table S1 and barcodes are provided in the filename for each sample.Xenops_SeqCap_reads.zipRaw reads from RAD-Seq with 8 *Xenops minutus* samplesIllumina reads from genotyping by sequencing (a RAD-Seq method) using the enzyme PstI in 4 *X. minutus* samples from either side of the Andes. Tissue numbers corresponding to those used in the Table S1 and barcodes are provided in the filename for each sample.Xenops_RADseq_reads.zi