DOI: 10.5061/dryad.cvdncjt4r
title: Estimating migration of the cold-tolerant leaf beetle Gonioctena quinquepunctata inside a mountain range in a spatially explicit context

description: The cold-tolerant leaf beetle Gonioctena quinquepunctata displays a large
 but fragmented European distribution and is restricted to mountain regions
 in the southern part of its range. Using a RAD-seq-generated large SNP
 data set (&gt; 10,000 loci), we investigated the geographic
 distribution of genetic variation within the Vosges mountains, where the
 species is common. To translate this pattern of variation in an estimate
 of its capacity to disperse, we simulated SNP data under a spatially
 explicit model of population evolution and compared the simulated and real
 data with an approximate Bayesian computation (ABC) approach. For this
 purpose, we propose a new SNP statistic summarizing genetic variation in a
 spatially explicit context. The estimated number of effective migrants
 inferred with this statistic was compared to that derived from a
 combination of standard population genetic statistics often used in
 population genetic analyses. We conducted this ABC analysis with a
 relatively low number of data points compared to traditional ABC analyses,
 because spatially explicit models require long simulation times. A test of
 our overall strategy was conducted with simulated data and showed that it
 could provide a good estimate of the level of dispersal of an organism
 over its continuous geographic range. We suggest that the lower number of
 explored data points were at least partially compensated by the much
 larger number of simulations per data point associated with a large SNP
 data set. The results of our analyses suggested that this insect disperses
 well within the Vosges mountains, much more than was initially expected
 given the current and probably past fragmentation of its habitat and given
 the results of previous studies on genetic variation in other mountain
 leaf beetles.
description: <em><strong>Insect
 collection</strong></em> Eight populations
 of <em>Gonioctena quinquepunctata</em> were sampled inside the
 Vosges. For each sampled population, 9 to 12 adults were collected, for a
 total of 93 individuals. Insects sampled from a single population were
 collected over a distance of up to 1 km, and pairwise geographic distances
 between populations ranged from 3.6 to 50.6 km.
 <em><strong>DNA
 extraction</strong></em> Genomic DNA was
 extracted using the Dneasy Tissue Kit from Qiagen (Hilden, Germany).
 RAD-seq libraries of DNA fragments from 300 to 600 bp were prepared by
 Floragenex (http://www.floragenex.com), generally following protocols
 described in Baird et al. (2008), Emerson et al. (2010) and Hohenlohe et
 al. (2010) and using the restriction enzyme sgrAI. Sequencing of the
 RAD-seq libraries was conducted on an Illumina sequencing platform
 Hiseq2500 by Eurofin Genomics (www.eurofinsgenomics.eu) and generated on
 average 3.4 million reads (125 bp) per sample.
 <em><strong>Data
 processing</strong></em> Reads were
 processed using Stacks v.1.40 (Catchen et al. 2011, 2013), using
 parameters  m = 10, M = 3 and n = 3, to produce SNP genotypes for all 93
 individuals. We retained a single SNP per rad-tag, and generated a total
 of 13,687 SNPs.