Genetic data from: Cryptic persistence and loss of local endemism in Lake Constance charr subject to anthropogenic disturbance ...

• Main Authors: Schliewen, Ulrich, Baer, Jan, Schedel, Frederic, Straube, Nicolas, Roch, Samuel, Brinker, Alexander
• Format: Dataset
• Language: English
• Published: Dryad 2022
• Subjects: FOS Biological sciences; Arctic charr; deep-water form; RAD-based genomics; Salvelinus profundus; Stocking; Arctic; Lanes
• Online Access: https://dx.doi.org/10.5061/dryad.41ns1rnhx; https://datadryad.org/stash/dataset/doi:10.5061/dryad.41ns1rnhx

Habitat restoration can help to protect and support endangered species. Following the restoration of Lake Constance to oligotrophic conditions, deep-water charr (originally described as Salvelinus profundus Schillinger, 1901) were rediscovered after more than 40 years of presumed extinction caused by eutrophication. Subsequent targeted surveys lead to the capture of a further 127 deep-water charr and 233 sympatric normal charr, Salvelinus cf. umbla. Given a history of intensive stocking in the lake and the possibility of introgressive hybridization, a discussion arose about the genetic status and future conservation strategies of both forms. The current study gathered life history traits and morphological and population genomic data for both extant forms, for comparison with 60–120 years' worth of historical data and museum specimens. The extant deep-water charr resembled historical specimens in terms of body shape, but significant differences between historical and extant normal charr included a decline in ... : Dataset_1: RAD sequencing data. Salvelinus DNA-extractions were sent to Floragenex (Portland, Oregon, USA) for SbfI-RAD-Seq library preparation. One 95-plex library containing all recently collected charr individuals from Lake Constance was sequenced twice on two Illumina HiSeq (1x100bp) lanes. Returning fastq-files were demultiplexed on the basis of 10bp individual barcodes, which were removed after demultiplexing. They were quality filtered (phred score -33) using the process radtags 2.4 script of the stacks 2.4 program package (Catchen et al. 2013). All reads of the same individual of both lanes were merged using a custom script. The program cutadapt v.1.12 (Martin 2011) was used to trim the first 6 bp cutting sites of each read. Dataset_2: Based on the locus-specific F-statistics we initially selected 182 RAD locus sequences featuring comparatively high Fst-Values between deep-water charr and normal charr phenotypes and containing only a single “diagnostic” SNP. Those 182 loci were clustered at 86% ...