DOI: 10.5061/dryad.cnp5hqcfm
title: Genlight table of ddRADseq-DArTseq Baikal sculpins adaptive radiation

description: Lake Baikal ranks among the most species-rich freshwater environments on
 the planet; however, the evolutionary histories of endemic taxa remain
 poorly understood. The unique abiotic environments of Lake Baikal include
 the only bathybenthic, bathypelagic, and deep hydrothermal vent
 communities in freshwater, each of which supports species with derived
 morphological and physiological traits. As the only vertebrate radiation
 endemic to a non-tropical ancient lake, the Baikal sculpins represent an
 underappreciated resource for investigating evolutionary processes that
 underlie adaptive radiation. We examined morphological and ecological
 diversity among Baikal sculpins and present the first interspecific
 phylogeny inferred from unlinked nuclear genomic markers. The new
 phylogeny supports a holarctic lotic common ancestor to a limnetic
 radiation, and reveals convergent adaptations to bathyal and pelagic
 habitats. Ecomorphological shifts involved dramatic modification of
 skeletal elements, sensory systems, and reproductive mode. We apply the
 new phylogeny to revise a recent taxonomic update to Baikal sculpins, and
 we resurrect the monotypic genus Uranidea as the sister group to the
 Baikal sculpin radiation. According to previous research, our data support
 the independent evolution of pelagic and bathypelagic ecomorphs and
 multiple invasions of bathybenthic habitats. Analysis of morphological
 diversification and speciation rates in Lake Baikal sculpins supports this
 group as an understudied yet iconic adaptive radiation of freshwater
 fishes.
description: # Genlight table of ddRADseq-DArTseq Baikal sculpins adaptive radiation
 [https://doi.org/10.5061/dryad.cnp5hqcfm](https://doi.org/10.5061/dryad.cnp5hqcfm) ## Description of the data and file structure Folder: Report-DCot20-5454.zip contains a reduced-representation nuclear genotype data set generated for 347 BCR specimens and multiple outgroups using a double digest restriction-site associated DNA sequencing (ddRADseq) protocol developed by Diversity Arrays Technology (DArT). The DArTseq approach uses the methylation-sensitive *Pst*I paired with *Sph*I, a combination designed to enrich the assay with genes that are actively transcribed. Library preparation and DNA fragment enrichment steps were performed by DArT starting from 1 μg of genomic DNA in 50 μL aliquots. Sequencing-by-synthesis technology and proprietary DArTseq algorithms were used to generate fragment consensus sequences (sequence tags) containing binary single-nucleotide polymorphisms (SNPs). Per convention, non-binary SNPs were omitted from the data set *a priori*. The reproducibility of nucleotide base calls was assessed during technical replicate assays and reported for each SNP in the output metadata. Approximately 12% (n=43) of ingroup samples were resubmitted as technical replicates to evaluate reproducibility among individuals. The ind.metafile is a metadata table with 730 entries (rows) and 24 columns. Links each sample ID to its species identity, geographic origin, and lab storage location. Includes quality control flags for filtering which samples should be kept in analyses. Provides higher-level groupings (Baikal group, top6) for analysis subsets.