Brooding phylogenomics: Target-capture probe sets for the analysis of ultraconserved elements in the Peracarida

Sequencing via target capture is becoming an important phylogenetic tool that has been used to great effect with organisms such as insects, arachnids, and various vertebrate taxa. However, other taxa, such as the Crustacea, have received limited genomic attention despite the amount of diversity present within the taxon and the intensity of research on this group. Here we describe generalized probe sets targeting ultraconserved elements (UCEs) for members of the crustacean orders Amphipoda and Isopoda in the superorder Peracarida. These probe sets employ 50-100,000 probes targeting up to 10,000 UCE loci. In-silico analysis of these probe sets recovered an average of 5,087 UCE loci; an average of 4,633 unique loci were retained post-filtering. Phylogenetic analysis of this dataset resulted in well-supported trees that align with previously reconstructed relationships among the taxa selected, while also providing resolution of previously uncertain nodes. Following the in-silico analysis, a..., , # Data from: Brooding phylogenomics: Target-capture probe sets for the analysis of ultraconserved elements in the Peracarida

Dataset DOI: [10.5061/dryad.4xgxd25nf](10.5061/dryad.4xgxd25nf)

## Description of the data and file structure

Included here are the alignment of filtered UCEs for all individuals in a phylip format (along with the associated partition file), and the three probe sets generated as a part of this project.

### Files and variables

#### File: Cannizzaro_and_Berg_UCEs_concatenated_alignment_partitions.charsets

**Description:** \".charsets\" file associated with \"Cannizzaro_and_Berg_UCEs_concatenated_alignment.phylip\" used in RaxML / IQTREE reconstruction

#### File: Cannizzaro_and_Berg_UCEs_concatenated_alignment.phylip

**Description:** Concatenated alignment of all UCES extracted from data sequenced here, in phylip forma

#### File: peracarida_probeset_plus_12_phaw5.fasta

**Description:** UCE probeset using 12 exemplary taxa and *Parhyale hawaiensis* as a base gen...,