DOI: 10.5061/dryad.5hqbzkh44
title: The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest

description: Biogeographic barriers such as rivers have been shown to shape spatial
 patterns of biodiversity in the Amazon basin, yet relatively little is
 known about the distribution of genetic variation across continuous
 rainforest. Here, we characterize the genetic structure of the
 brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long
 transect along the Purus-Madeira interfluve south of the Amazon river,
 based on 64 individuals genotyped at 7609 single-nucleotide polymorphism
 loci. A population tree and clustering analyses revealed 4 distinct
 genetic groups, one of which was strongly divergent. These genetic groups
 were concomitant with femoral spot coloration differences, which was
 intermediate within a zone of admixture between two of the groups. The
 location of these genetic groups did not consistently correspond to
 current ecological transitions between major forest types. A multimodel
 approach to quantify the relative influence of isolation-by-geographic
 distance (IBD) and isolation-by-environmental resistance (IBR)
 nevertheless revealed that, in addition to a strong signal of IBD, spatial
 genetic differentiation was explained by IBR primarily linked to dry
 season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show
 significant phylogenetic divergence in the absence of obvious
 biogeographical barriers and that finer-scaled measures of genetic
 structure show patterns that are associated with environmental variables
 also known to predict the density of A. femoralis.
description: Extraction of DNA and single-nucleotide polymorphism (SNP)
 discovery was carried out at Diversity Arrays Technology sequencing Pty.
 Ltd. (DArTseq) facility (Canberra, Australia; more detail, please see the
 Supplementary Information in the article). A modified double-digest
 restriction-site associated DNA sequencing protocol was performed on
 libraries prepared using a combination of Pstl-Hpall restriction enzymes.
 The Pstl enzyme adaptor also contained an Illumina adaptor sequence, a
 primer sequence and a variable-length barcode. The Hpall adaptor contained
 an Illumina flow cell attachment and overhang sequence. Following
 enzymatic digestion, fragments were amplified and sequenced on an Illumina
 HiSeq2500. DNA sequences were aligned via BLAST using the Nanorana parkeri
 reference genome. To check for contamination, sequences were also blasted
 to bacterial and fungal genomes (NCBI).
description: This data set was filtered for missing data using the filter_dart
 function of the R package RADIATOR v. 0.010. Only individuals and loci
 with ≥95% SNPs geno- typed were retained. SNPs were also screened for
 allele coverage, with any SNPs displaying a local and global minor allele
 frequency threshold of less than 1% removed from the dataset. In cases
 where multiple SNPs were found within the same read, only one locus was
 retained (chosen randomly per RAD tag) to avoid statistical bias from
 physical linkage. Two samples from M14 had &lt;95% of loci genotyped
 and were removed, which resulted in 64 individuals from 13 populations
 genotyped at 10 275 SNPs (please see the article Table S2 for summary of
 filtering steps).