DOI: 10.5061/dryad.kkwh70s51
title: Data from: Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks

description: River otters (Lontra canadensis) were extirpated from New Mexico by the
 1950s. A limited reintroduction occurred during 2008–2010 in which 33
 otters sourced from Washington (WA) were translocated to the Upper Rio
 Grande Basin (URG) of New Mexico. We conducted a noninvasive genetic
 capture-recapture survey during the winter of 2018 by collecting fecal DNA
 samples from river otter scats found at latrines in the URG dendritic
 network of perennial waterways. Our objectives were to: 1) estimate
 genetic diversity and effective population size; 2) genetic divergence
 from the WA source population and potential connectivity with regionally
 proximal populations; 3) spatially explicit population density and size;
 and 4) population growth rate since the founder event. Between February
 and April 2018, we collected 1,184 fecal DNA samples from 622 individual
 scats at 20 latrines; genotyping was attempted at 10 otter-specific
 microsatellite loci for a subsample of 543 samples. A bottlenecking
 founder effect was strongly supported, which, combined with genetic drift,
 reduced genetic diversity and effective population size by 20–26% and
 106–170%, respectively, compared with the WA source population. Estimated
 population density from spatial capture-recapture models was 0.23–0.28
 otter/km of waterway, or 1 otter/3.57–4.35 km of waterway, corresponding
 to a total population size of 83–100 otters across 359 km of the perennial
 dendritic network from La Mesilla, New Mexico to Alamosa National Wildlife
 Refuge, Colorado. Estimated average annual population growth rate since
 the founder event was 1.12–1.15/year. Despite successful population
 establishment, the URG river otter population remains small, is
 genetically degraded, and does not yet meet the criteria for long-term
 reintroduction success. Projections suggested that the population could
 reach the recommended minimum viable population size of ≥400 otters by the
 years 2030–2033, though sufficient habitat may not exist in the URG Basin
 to support that many otters. 
description: Scat samples were collected from a reintroduced population of
 North American river otters (<em>Lontra canadensis</em>) via a
 capture-recapture survey design in the Upper Rio Grande River Basin of the
 southwestern, USA. Otter latrine sites were surveyed for 8 consecutive
 occasions, each of which were 7-10 days in duration, during
 February-April, 2018. Additional tissue samples were obtained from the
 reintroduction source population in Washington, USA, to investigate
 genetic changes since the founder event. All collected
 samples were processed at the Laboratory for Ecological, Evolutionary and
 Conservation Genetics at University of Idaho (Moscow, USA) for DNA
 extraction, PCR amplification, and microsatellite genotyping. DNA was
 extracted from tissue and fecal samples using DNeasy Blood and Tissue Kits
 and QIAmp Fast DNA Stool Mini Kits (Qiagen, Inc.), respectively. Fecal
 samples were extracted in a separate laboratory dedicated to low quality,
 low quantity DNA sources, and one negative control was included in each
 extraction to monitor reagent contamination. Twelve candidate
 otter-specific microsatellite loci were evaluated (Dallas &
 Piertney, 1998; Beheler<i> et al.</i>, 2004, 2005;
 Mowry<i> et al.</i>, 2011); however, locus RIO03 was
 monomorphic in the tissue samples and locus RIO11 failed to amplify.
 Therefore, we used a 10-locus multiplex to obtain genotypes: RIO01, RIO02,
 RIO04, RIO06, RIO07, RIO08, RIO12, RIO13, RIO16, and Lut453, as well as
 the SRY2 sex marker (Dallas <i>et al</i>., 2000). Four to six
 replicate PCRs were performed for the fecal samples that consistently
 amplified after an initial screening step of two amplifications; the
 tissue samples were amplified in duplicate. PCR products were visualized
 using a 3130xl DNA Sequencer and allele sizes were scored using Genemapper
 5.0 (Applied Biosystems, Foster City, USA). Sample quality assessment and
 genotype screening methods followed those described by Stenglein et al.
 (2010). In short, we developed consensus genotypes for each sample by
 requiring an allele be detected in two independent PCRs to confirm a
 heterozygote and an allele be detected in three independent PCRs to
 confirm a homozygote. The SRY2 sex marker amplifies a fragment in males
 but not females (Dallas <i>et al</i>., 2000); we required 3–6
 replicates for sex determination using this marker. If ≥2 replicates
 detected the Y chromosome, the sample was classified as a confirmed male,
 whereas if one replicate amplified the Y chromosome, we classified the
 sample as unconfirmed male because the Y chromosome amplification result
 was not confirmed. If no replicates amplified the Y chromosome, we
 classified the sample as female because 8–10 loci worked, thereby
 indicating sufficient DNA in the sample to avoid allelic dropout of the Y
 chromosome across 3–6 replicates. Probability of
 identity for siblings (<i>PI</i><sub>sibs</sub>)
 was calculated separately for tissue and scat genotypes using GenAlEx v6.5
 (Peakall & Smouse, 2012).
 <i>PI</i><sub>sibs</sub> ≤ 0.01 was used as a
 cutoff for the number of loci required to distinguish among unique
 genotypes; to determine the number of unique genotypes, matching analysis
 was conducted using GenAlEx (Stenglein<i> et al.</i>, 2010).
 Two fecal samples were conservatively considered as originating from the
 same individual if their locus-specific alleles matched across ≥8 loci,
 and also if two fecal samples matched at only eight loci but the
 mismatches at locus nine or 10 were likely due to allelic dropout. If the
 8–10 locus consensus genotype matched another sample, but the sex results
 differed, we conservatively retained the samples as a match and the sex of
 the individual as male. We calculated genotyping error rates from the
 first two PCR replicates of fecal samples that had consensus genotypes at
 8–10 loci, following the methods of Broquet & Petit
 (2004).
description: This dataset contains the genotypes, genotyping error rates,
 spatial capture-recapture detection histories, and latrine site locations
 (geographical coordinates) for the study by Murphy et al.,
 "Evaluating otter reintroduction outcomes using genetic spatial
 capture-recapture modified for dendritic networks."