DOI: 10.5061/dryad.4xgxd25nf
title: Data from: Brooding phylogenomics: Target-capture probe sets for the analysis of ultraconserved elements in the Peracarida

description: 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, an in vitro
 analysis targeting members of the amphipod families Crangonyctidae and
 Gammaridae was conducted. This analysis extracted up to 4,864 unique loci
 from the taxa sequenced, with an average of 1,897 loci among all taxa.
 Phylogenetic analysis of the data generated in vitro resulted in
 well-supported trees that were resolved at both shallow and deep taxonomic
 levels. Both analyses demonstrate the utility of these probe sets for
 phylogenomic research within the Peracarida. Additional attention to
 members of the superorder using target enrichment will doubtlessly assist
 in resolving poorly understood aspects of their evolutionary history and
 expand current knowledge of this group.
description: # 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 genome ####
 File: peracarida_probeset_plus_11_phaw5.fasta **Description:** UCE
 probeset using 11 exemplary taxa and *Parhyale hawaiensis* as a base
 genome #### File: peracarida_probeset_plus_10_phaw5.fasta
 **Description:** UCE probeset using 10 exemplary taxa and *Parhyale
 hawaiensis* as a base genome #### File:
 peracarida_probest_plus_2_phaw5.fasta **Description:** UCE probeset using
 2 exemplary taxa and *Parhyale hawaiensis* as a base genome