Fine-scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic

BMC Research Notes Lai et al. BMC Res Notes (2017) 10:663 DOI 10.1186/s13104-017-3002-1 Open Access RESEARCH NOTE Fine‑scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic Sandra Lai1* , Adrien Quiles2, Josie Lambourdière3, Dominique Berteaux1 and Aude Lalis2 Abstract Objective: The arctic fox (Vulpes lagopus) is a circumpolar species inhabiting all accessible Arctic tundra habitats. The species forms a panmictic population over areas connected by sea ice, but recently, kin clustering and population differentiation were detected even in regions where sea ice was present. The purpose of this study was to examine the genetic structure of a population in the High Arctic using a robust panel of highly polymorphic microsatellites. Results: We analyzed the genotypes of 210 individuals from Bylot Island, Nunavut, Canada, using 15 microsatellite loci. No pattern of isolation-by-distance was detected, but a spatial principal component analysis (sPCA) revealed the presence of genetic subdivisions. Overall, the sPCA revealed two spatially distinct genetic clusters corresponding to the northern and southern parts of the study area, plus another subdivision within each of these two clusters. The north–south genetic differentiation partly matched the distribution of a snow goose colony, which could reflect a preference for settling into familiar ecological environments. Secondary clusters may result from higher-order social structures (neighbourhoods) that use landscape features to delimit their borders. The cryptic genetic subdivisions found in our population may highlight ecological processes deserving further investigations in arctic foxes at larger, regional spatial scales. Keywords: Vulpes lagopus, Microsatellite multiplex PCR, Population genetics, Fine-scale genetic structure, Bylot Island Introduction The arctic fox Vulpes lagopus has a circumpolar distribution and inhabits all accessible Arctic tundra habitats [1]. The species is relatively common across its range, except in Fennoscandia and on islands in the Bering Sea where populations are at critically low levels [1]. At the circumpolar scale, panmixia was reported in arctic foxes, due to the combination of connectivity offered by the sea ice and high mobility of this species [2–5]. Recently, however, kin clustering linked to female philopatry and fine-scale population genetic differentiation were found in Svalbard and Alaska despite the presence of sea ice in these regions [6, 7]. Currently, most studies using microsatellites in wild arctic fox populations typically used 10 markers or less [reviewed in 8]. Genetic homogeneity of populations was *Correspondence: 1 Canada Research Chair on Northern Biodiversity, Centre for Northern Studies and Quebec Center for Biodiversity Science, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC G5L 3A1, Canada Full list of author information is available at the end of the article found at continental or circumpolar scales, but the use of a higher genetic resolution may allow detection of finescale genetic structure at more regional scales [9, 10]. Building on a previous study of arctic fox extra-pair mating in the same study area [11], we developed a panel of 15 microsatellite markers combined and amplified in two multiplex and one singleplex PCR assays. We used this set of highly polymorphic microsatellite markers to assess the genetic structure of a High Arctic population in a heterogeneous landscape. Main text Methods Tissue samples were collected from individuals captured on Bylot Island (73°N, 80°W), Nunavut, Canada, from 2003 to 2015, as detailed in Ref. [11]. The 600-km2 study area comprises approximately 60 km of coastline extending 5–15 km inland. The southern part of the study area hosts a Greater snow goose Chen caerulescens atlantica nesting colony during summer (Fig. 1). Total genomic DNA was extracted from ethanol-fixed ear © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Lai et al. BMC Res Notes (2017) 10:663 Fig. 1 Map of spatial PCA global scores for arctic foxes in the south plain of Bylot Island (Nunavut, Canada) displaying a the first and b the second principal components. Each square represents the score of an individual positioned by its spatial coordinates. White squares show negative scores and black squares show positive scores. Larger squares reflect greater absolute values. Squares of different colors are strongly differentiated, while squares of the same color but of different sizes are weakly differentiated. The study area is delimited by a black line. Blue lines indicate rivers. The extent of a snow goose nesting colony is shown in red. Base map source from Google Maps: Imagery ©2017 Google, TerraMetrics Page 2 of 6 samples stored at − 20 °C using the Qiagen DNeasy Kit. We randomly selected 15 samples from the tissue collection and 15 polymorphic primer pairs (Ref. [12–15]; Table 1) for microsatellite genotyping. These primers were used to determine optimal amplification conditions. PCRs were performed in a volume of 10 µl reaction containing 1.00 mM M gCl2, 1.00 µl DMSO, 1.00 µl BSA, 0.06 µl QBioTaq (all from Qiagen, Hilden, Germany), 0.40 µM dNTP (MP Biomedicals Europe, Illkirch, France), 0.25 µM each of forward and reverse primers (Eurofins Genomics, Ebersberg, Germany), 4.03 µl H 2O and 2 ng DNA. Amplification conditions were as follows: 95 °C for 5 min, 30 cycles at 95 °C for 30 s, locus-specific annealing temperature ( Ta) for 1.3 min, 72 °C for 30 s and a final extension at 60 °C for 10 min. T a of every primer pair was determined with a Mastercycler gradient 107 thermocycler (Eppendorf ) PCR machine set according to the melting temperature (Tm) values of primer pairs. The PCR products were electrophoresed on 6% denaturing polyacrylamide gels. These 15 primer pairs were selected to synthesize fluorescently-labeled primers for multiplex PCR. A Qiagen multiplex PCR Kit was used and reaction mixtures contained 1 µl DNA, 6.25 µl Master Mix (Qiagen, Hilden, Germany) with 1.25 µl primer mix (100 pM/ µl) and 3.5 µl RNAse-free water to a final volume of 12 µl. The reaction comprised an activation step at 95 °C for 5 min, followed by 35 cycles of initial denaturation at 95 °C for 30 s, Ta for 30 s (Table 1) and 72 °C for 30 s, ending with a final extension step at 60 °C for 30 min, and followed by a holding step at 20 °C. Fluorescently-labeled PCR (...truncated)