DOI: 10.6078/d1n141
title: Variant call file for mountain yellow-legged frog (MYLF) selection analysis

description: Vast alteration of the biosphere by humans is causing a sixth mass
 extinction. Adaptation to modified environments often is the only means
 for species to persist, but the extent to which such "evolutionary
 rescue" can prevent or reverse biodiversity loss is largely unknown.
 Using results from genomic analyses, a 15-year reintroduction effort, and
 population modeling, we provide a compelling example of evolution
 reversing the declines of an imperiled amphibian and allowing the
 reestablishment of extirpated populations. The once-common mountain
 yellow-legged (MYL) frog is threatened with extinction by the
 human-facilitated emergence of a lethal fungal pathogen (Batrachochytrium
 dendrobatidis; "Bd"). Although most MYL frog populations are
 extirpated following disease outbreaks, some persist and eventually begin
 to recover. Using an exome capture approach, we show that MYL frogs have
 undergone substantial evolutionary change following disease outbreaks.
 Moreover, in naturally recovering populations observed changes in immune
 function loci are associated with increased resistance/tolerance to Bd
 infection. Large-scale reintroduction of frogs from rescued populations
 resulted in the establishment of reproducing populations despite ongoing
 disease. In addition, results from viability modeling suggest that
 established populations have a low probability of extinction over 50
 years. Collectively, these results provide a rare example of how
 evolutionary rescue and the reintroduction of resistant/tolerant
 individuals can allow the landscape-scale recovery of disease-impacted
 species. This example has potentially broad implications for the many taxa
 worldwide that are threatened with extinction by anthropogenic stressors.
description: Raw reads were filtered for
 adapters and contaminants using fastp and aligned to the <em>Rana
 muscosa</em> genome (NCBI SRA: SRS6533475), with repetitive elements
 masked using bwa (“mem” mode). Exact PCR duplicates were marked using
 Picard. Variants were then called following GATK best practices
 (v.4.2.0.0). Briefly, raw variants were called for each sample using
 HaplotypeCaller and combined using CombineGVCFs. Next, genotypes were
 jointly called using GenotypeGVCFs. Variants were then hard filtered using
 gatk VariantFiltration using the following parameters to remove
 low-quality sites: QD &lt; 2.0, FS &gt; 40.0, SOR &gt; 3.0, MQ
 &lt; 50.0, MQRankSum &gt; 3.0, MQRankSum &lt; -3.0,
 ReadPosRankSum &gt; 3.0, ReadPosRankSum &lt; -3.0. This initial
 filter resulted in 1,595,206 variant sites across 53 individuals. We then
 further filtered our dataset at the individual and variant level. First,
 we trimmed our variants to only include those with minor allele frequency
 &gt; 0.03, a maximum depth of 250 and minimum depth of 5, a minimum
 genotype quality of 20, and a maximum missing proportion of 0.5. This
 filter resulted in 427,038 sites, of which 353,172 were SNPs and 73,866
 were INDELS. Finally, we trimmed samples with an average depth across
 filtered sites &lt; 7x. Our final dataset included 50 samples, 23 from
 naive and 27 from recovering populations, with an average depth of 16.7x
 (range = 7.4x – 26.1x).