DOI: 10.5061/dryad.9kd51c5v6
title: Data from: Spatial replication is important for developing landscape genetic inferences for a wetland salamander

description: Habitat fragmentation is one of the most pressing threats to wildlife
 populations. Maintenance of sustained dispersal and gene flow between
 populations is essential and often the end goal of conservation action.
 Use of resistance surfaces has emerged as an important strategy for
 developing conservation management strategies to mitigate the effects of
 habitat fragmentation (e.g., corridor design). However, recent studies
 have noted inconsistencies across study sites in the factors most strongly
 associated with genetic connectivity. Thus, replication of genetically
 based resistance surface optimization across landscapes may be necessary
 for making robust and generalizable conclusions about the influence of
 environmental variables on gene flow and for generating comprehensive
 predictions that can then be used by conservation practitioners in their
 focal landscape. In this study, we conducted replicated landscape genetic
 analyses across five sampling areas in Tennessee and Kentucky for a
 threatened wetland-obligate salamander, the four-toed salamander
 (Hemidactylium scutatum). We used genomic data to quantify fine-scale
 population structure in each of our study landscapes. We then tested
 multiple hypotheses of how different landscape features (e.g., canopy
 cover) influenced connectivity and gene flow. We found some concordance in
 the landscape features that were inferred to influence gene flow, but also
 some differences, potentially owing to the difference in variability of
 predictors at each site. Our work identifies landscape variables that may
 be important for H. scutatum conservation, and our
 replicated design allows us to identify important relationships that would
 have been missed if only using only one study site were used.
description: # Spatial replication is important for developing landscape genetic
 inferences for a wetland salamander
 [https://doi.org/10.5061/dryad.9kd51c5v6](https://doi.org/10.5061/dryad.9kd51c5v6) ## Description of the data and file structure To assess the influence of different landscape features on four-toed salamander gene flow, we generated genome-wide SNP data and used the R package radish. We assessed five different predictors at four different spatial resolutions using empirically generated FST matrices in a replicated landscape design, which included five study areas (Catoosa WMA [CWMA], the Great Smoky Mountains National Park [GSMNP], the Oak Ridge Reservation [ORR], Prentice Cooper State Forest [PCSF], and the Red River Gorge [RRG]). ### **Files and variables** #### SampleMetadata.csv: Data associated with each four-toed salamander sample used in landscape genetic analyses -Variables * ID: identification code for the sample * SiteCode: identification code from the sampling site * Landscape: study landscape that the sample came from #### coordinates.zip: A folder containing files (.csv) with obscured (centered on 0,0) coordinates for each sampling site/wetland-(Catoosa WMA [CWMA], the Great Smoky Mountains National Park [GSMNP], the Oak Ridge Reservation [ORR], Prentice Cooper State Forest [PCSF], and the Red River Gorge [RRG]). -Variables * Code: identification code from the sampling site * Latitude: obscured latitude of the sampling site * Longitude: obscured longitude of the sampling site #### tif_files.zip A folder containing a raster (.tif) for every predictor at each landscape at each spatial resolution (total 100). For example, ORRCAN30 would represent canopy cover on the ORR at 30m resolution. #### vcf_files.zip A folder containing VCF files for each landscape ((Catoosa WMA [CWMA], the Great Smoky Mountains National Park [GSMNP], the Oak Ridge Reservation [ORR], Prentice Cooper State Forest [PCSF], and the Red River Gorge [RRG])) in the study. VCF files named "landscape_full.vcf" are input directly from ipyrad assembly. VCF files named "landscapeoneperlocus.vcf" have been filtered to only include one SNP per locus.  #### fst.zip A folder containing Weir and Cockerham FST matrices for each study landscape (sites &gt; 2 samples)-(Catoosa WMA [CWMA], the Great Smoky Mountains National Park [GSMNP], the Oak Ridge Reservation [ORR], Prentice Cooper State Forest [PCSF], and the Red River Gorge [RRG]).  ## Code/software **Code_for_analyses**: We include a detailed pdf file that includes generalized code for ipyrad assembly, STRUCTURE, and R analyses.