DOI: 10.5061/dryad.wstqjq2qd
title: Applying genomic approaches to identify historic population declines in European forest bats

description: Anthropogenically-driven environmental changes over the past two centuries
 have led to severe biodiversity loss, most prominently in the form of loss
 of populations and individuals. Better tools are needed to assess the
 magnitude of these wildlife population declines. Anecdotal evidence
 suggests European bat populations have suffered substantial declines in
 the past few centuries. However, there is little empirical evidence of
 these declines that can be used to put more recent population changes into
 historic context and set appropriate targets for species
 recovery.  This study is a collaboration between academics and
 conservation practitioners to develop molecular approaches capable of
 providing quantitative evidence of historic population changes and their
 drivers that can inform the assessment of conservation status and
 conservation management. We generated a genomic dataset for
 the Western barbastelle, Barbastella
 barbastellus, a globally Near Threatened and regionally
 Vulnerable bat species, including colonies from across the species’
 British and Iberian ranges. We used a combination of landscape genetics
 and approximate Bayesian computation model-based inference of demographic
 history to identify both evidence of population size changes and possible
 drivers of these changes.  We found that levels of genetic
 diversity and inbreeding were related to broadleaf woodland cover around
 the colony location. Genetic connectivity was impeded by artificial lights
 and facilitated by the combination of rivers and broadleaf woodland
 cover.  The demographic history analysis showed that both the
 northern and southern British barbastelle populations have declined by 99%
 over the past 330–548 years. These declines may have been triggered by
 loss of large oak trees and native woodlands due to shipbuilding during
 the early colonial period. Synthesis and applications. Genomic
 approaches can be applied to provide a better understanding of the
 conservation status of threatened species, within historic and
 contemporary context, and inform their conservation
 management. This study shows how we can bridge the implementation
 gap and promote the application of genomics in conservation management
 through co-designing studies with conservation practitioners and
 co-developing applied management targets and recommendations.
description: SNP datasets were generated from ddRADseq data for the western
 barbastelle bat, <em>Barbastella barbastellus,</em> from
 Britain, Spain and Portugal. SNPs called with Stacks and filtered in Plink
 to remove SNPs with &gt;10% missing data. SNP datasets in vcf
 format.
description: Most population genomics R packages can open vcf format
 files.
description: # Applying genomic approaches to identify historic population declines in
 European forest bats The Dryad submission includes SNP datasets generated
 from a ddRADseq genomic dataset for the western barbastelle bat,
 Barbastella barbastellus, from Britain, Spain and Portugal. ## Description
 of the Data and file structure The Dryad submission includes 3 SNP files
 in vcf format generated from a ddRADseq genomic dataset for the western
 barbastelle bat, Barbastella barbastellus, from Britain, Spain and
 Portugal. SNPs were called with Stacks and filtered in Plink to remove
 SNPs with &gt;5% missing data. The following files are included in the
 submission: 1. SD1 - full neutral SNP dataset used in the manuscript. This
 dataset includes all individual bats (95 individuals) and 46,872 SNPs. 2.
 SD2 - smaller neutral SNP dataset used only in the demographic history
 analysis. This dataset only includes individuals from Spain and Britain
 (85 individuals) and SNPs with &gt;99% coverage (25,844 SNPs). 3. SD3
 - revised full neutral SNP dataset using to compare population structure
 results with a dataset where relatives were removed and SNPs out of
 Hardy-Weinberg equilibrium retained (90 individuals and 46,968 SNPs). 4.
 Table 1 - a table listing sample location records (with GWS1984
 coordinates) and population codes (CSV format). NA refers to a location
 with individual samples that were not grouped into colonies for the
 colony-based analysis. Other locations within 30 km of each other were
 grouped together into a single colony, as they represent the breeding
 range of the species. ## Sharing/access Information The data is linked to
 the publication: Razgour et al. Applying genomic approaches to identify
 historic population declines in European forest bats. Journal of Applied
 Ecology.