DOI: 10.5061/dryad.zkh1893b9
title: Microsatellite data for Bull Trout

description: Freshwater ecosystems are negatively impacted by a variety of
 anthropogenic stressors, with concomitant elevated rates of population
 decline for freshwater aquatic vertebrates. Because reductions in
 population size and extent can negatively impact genetic diversity and
 gene flow, which are vital for sustained local adaptation, it is important
 to measure these characteristics in threatened species that may yet be
 rescued from extinction. Across its native range, Bull Trout (Salvelinus
 confluentus) extent and abundance are in decline due to historic
 overharvest, invasive nonnative species, and habitat loss. In Alberta’s
 Eastern Slope region, populations at the range margin have progressively
 been lost, motivating us to better understand the amount and distribution
 of genetic variation in headwater habitats and some downstream sites where
 they continue to persist. Across this region, we sampled 431 Bull Trout
 from 20 sites in the Athabasca and Saskatchewan River basins and assayed
 10 microsatellite loci to characterize within- and among-population
 genetic variation. The Saskatchewan and Athabasca River basins contained
 similar levels of heterozygosity but were differentiated from one another.
 Within the Athabasca River basin, five genetically differentiated clusters
 were found. Despite the evidence for genetic differentiation, we did not
 observe significant isolation-by-distance patterns among these sites. Our
 findings of ample genetic diversity and no evidence for hybridization with
 non-native Brook Trout in headwater habitats provide motivation to
 ameliorate downstream habitats and remove anthropogenic barriers to
 connectivity towards the goal of long-term persistence of this species.
description: Sample collection: Adipose fin tissue samples were non-lethally
 obtained by clipping and immediately transferred into 95% EtOH at
 4°C. Samples obtained from W. Hughson, S. Herman, M. Sullivan, and W.
 Warnock were collected using similar methods, although the latter three
 collectors preserved the sample by drying the adipose fin tissue and
 storing them in separate envelopes in a cool, dry location. All samples
 were collected within eight years; a time span comparable to a single Bull
 Trout generation within the region. Processing: Nuclear
 DNA was extracted from EtOH-preserved adipose fin tissue using a standard
 proteinase-K phenol-chloroform protocol and stored in ddH2O at 4°C. DNA
 quantity was determined using a Nanodrop 1000 Spectrophotometer V3.7and
 sample concentrations were subsequently adjusted to 50 ng/μl. During PCR,
 DNA regions, excised by forward fluorescently labeled oligonucleotide
 primers for 10 microsatellite loci (Omm1128, Sco102, Sco105, Sco106,
 Sco109, Sco215, Sco216, Sco220, Sfo18, and Smm22), were multiplexed in
 four optimized groups. These loci were chosen based on the degree of
 polymorphism, ability to detect Bull Trout × Brook Trout hybrids, and
 resolution to detect population structure of the samples. Desired
 fragments were amplified using a C1000 Touch Thermal Cycler. PCR products
 were run on a 1.5% w/v agarose gel using a standard gel electrophoresis
 protocol and visualized using DigiDOC IT electrophoresis gel imager.
 Samples showing clearly defined bands representing the DNA fragment PCR
 products of the specified microsatellite loci were then analyzed. Fragment
 lengths were determined using a standard protocol for microsatellite
 fragment analysis with an ABI 3500XL Capillary Electrophoresis Genetic
 Analyzer and scaled against GeneScan-500LIZ size standard. For each
 sample, electropherograms were produced, which were scored using
 GENEMAPPER v.4.1. Raw genotype scores were assessed by MICROCHECKER
 v.2.2.3 to uncover genotyping errors and presence of null alleles that did
 not amplify during PCR. Because null alleles were present in no more than
 four of the 10 loci, all samples were used for further analyses.
description: Spreadsheet: The first sheet of the spreadsheet contains notes on
 (1) the formatting of the entries and (2) how we coded missing
 values. Table 1: Microsatellites loci targeted to
 determine levels of genetic differentiation and population structure of
 Bull Trout in the Athabasca River basin. Table 2:
 Expected heterozygosity, allelic richness and total private alleles at
 each sampling site.