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Estimating migration of the cold-tolerant leaf beetle Gonioctena quinquepunctata inside a mountain range in a spatially explicit context

Citation

Kastally, Chedly et al. (2021), Estimating migration of the cold-tolerant leaf beetle Gonioctena quinquepunctata inside a mountain range in a spatially explicit context, Dryad, Dataset, https://doi.org/10.5061/dryad.cvdncjt4r

Abstract

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 (> 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.

Methods

Insect collection

Eight populations of Gonioctena quinquepunctata 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.

DNA extraction

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.

Data processing

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.

Funding

Université Libre de Bruxelles

Fonds De La Recherche Scientifique - FNRS, Award: J.0075.18

Fonds De La Recherche Scientifique - FNRS, Award: 2.5020.11