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Abstract The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists. 

Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family‐based genome‐wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p < 0.05 andp < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance‐related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci.F_SToutlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.

 

Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identifySNPmarkers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein‐coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis ariesv. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR‐basedSNPchip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositanandbayescan), we detected 28SNPloci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease‐regulating functions (e.g. Ovar‐DRA,APC,BATF2,MAGEB18), cell regulation signalling pathways (e.g.KRIT1,PI3K,ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene‐targetedSNPdiscovery and subsequentSNPchip genotyping using low‐quality samples in a nonmodel species.