DOI: 10.5061/dryad.41ns1rnhx
title: Genetic data from: Cryptic persistence and loss of local endemism in Lake Constance charr subject to anthropogenic disturbance

description: 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 gill raker number over time and distinctly
 different body shapes and growth patterns. RAD-based population genomic
 analyses of the contemporary samples support these results, revealing the
 two extant forms to be highly divergent, albeit with a few putative
 hybrids. SNPs-based population assignment tests of historical and
 contemporary samples strongly suggest that deep-water charr persisted
 unaltered in Lake Constance during the eutrophic phase. Meanwhile, none of
 the historical genomic samples could be assigned to the extant normal
 S. cf. umbla population. Functional analyses of gill
 raker number and stocking intensity pointed to stocking with non-endemic
 charr as the most likely reason for the disappearance of the endemic
 normal form. These results show that interplay between different
 anthropogenic impacts, i.e. eutrophication and stocking can lead to
 irreversible but hard-to-detect impacts on endemic biodiversity.
 Understanding these impacts is a prerequisite for effective conservation
 of endangered populations of cryptic fish.
description: <strong>Dataset_1: RAD sequencing data</strong>.
 <em>Salvelinus</em> DNA-extractions were sent to Floragenex
 (Portland, Oregon, USA) for <em>SbfI</em>-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
 <em>process</em> <em>radtags</em> 2.4 script of
 the <em>stacks</em> 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 <em>cutadapt</em> v.1.12 (Martin 2011) was used to trim the
 first 6 bp cutting sites of each read.  
 <strong>Dataset_2</strong>: Based on the
 locus-specific F-statistics we initially selected 182 RAD locus sequences
 featuring comparatively high F<sub>st</sub>-Values between
 deep-water charr and normal charr phenotypes and containing only a single
 “diagnostic” SNP. Those 182 loci were clustered at 86% similarity in order
 to remove candidate bait loci with too high similarity; further, these
 loci were checked with the same script for low complexity due to
 microsatellites or other short repeats. 164 candidate bait loci were
 retained and sent together with DNA extracts from historical scale samples
 to the Arbor Biosciences lab (Ann Arbor, Michigan, USA), which
 BLAST-filtered 99 out of 164 loci for bait design that would not target
 overrepresented regions in the charr genome. Based on this selection 497
 baits were designed, each 60 bp in length and spaced every 15 bp along RAD
 loci and representing these 99 loci. Subsequent laboratory steps performed
 by Arbor BioSciences comprised hybridization of baits to the 99 target
 loci in the double-stranded DNA libraries constructed from DNA extracts,
 amplification of captured libraries and sequencing on an Illumina
 HiSeq2500 platform (paired end, 2x150 bp). Sequencing reads of
 library-prepped individuals were downloaded and corresponding reads of
 identical individuals merged using a custom script. After visual quality
 check in FASTQC 0.11.3 (Andrews
 2010), we used <em>cutadapt</em> v.1.12 (Martin 2011) to remove the first
 15 bp of all reads (including the 13bp adaptors), to filter out only reads
 with a minimum length of 25 bp long reads. We further trimmed all reads to
 a maximum length of 100bp.
 <strong>Dataset_3</strong>: 99 SbfI-RAD derived
 target loci selected based on locus-specific F-statistics (for details,
 see MS)
description: Dataset 1: 89 demultiplexed, quality filtered and trimmed 85bp
 .fastq-files derived from SbfI_RAD libraries run on two Illumina HiSeq
 (1x100 bp) lanes. Individuals are labeled according to phenotypic
 assignment of samples to either "Tiefseesaibling"  (N=46) or
 "Normal" (N= 43) in combination with sample-ID numbers of the
 Fisheries Research Station Baden-Württemberg. Dataset
 2: 14 demultiplexed, quality filtered trimmed to 100bp .fastq-files mapped
 to the <em>Salvelinus sp.</em> GCF_002910315.2 reference
 genome derived from Illumina HiSeq2500 runs of hybridisation capture
 libraries targeting 99 RAD loci differentiating between
 "Tiefseesaibling" and "Normal"-Saibling, i.e. the
 extant <em>Salvelinus</em> forms in Lake Constance.
 Dataset 3: 99 SbfI-RAD derived target loci selected based on
 locus-specific F-statistics.