DOI: 10.5061/dryad.m94f4
title: Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA

description: Over the last decade, protocols aimed at reproducibly sequencing
 reduced-genome subsets in non-model organisms have been widely developed.
 Their use is however limited to DNA of relatively high molecular weight.
 During the last year, several methods exploiting hybridization capture
 using probes based on RAD-sequencing loci have circumvented this
 limitation and opened avenues to the study of samples characterized by
 degraded DNA, such as historical specimens. Here, we present a major
 update to those methods, namely Hybridization capture from RAD-derived
 probes obtained from a reduced eXome template (hyRAD-X), a technique
 applying RAD-sequencing to messenger RNA from one or few fresh specimens
 to elaborate bench-top produced probes, i.e., a reduced representation of
 the exome, further used to capture homologous DNA from a samples set. In
 contrast to previous hybridization-capture methods, the reference catalog
 on which reads are aligned does not rely on de novo assembly of anonymous
 RAD-sequencing loci, but on an assembled transcriptome obtained from
 RNAseq data, thus increasing the accuracy of loci definition and
 Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically,
 expressed genes. Finally, the capture step of hyRAD-X relies on RNA
 probes, increasing stringency of hybridization, making it well suited for
 low-content DNA samples. As a proof of concept, we applied hyRAD-X to
 subfossil needles from the coniferous tree Abies alba, collected in lake
 sediments (Origlio, Switzerland) and dating back from 7200-5800 years
 before present (BP). More specifically we investigated genetic variation
 before, during, and after an anthropogenic perturbation that caused an
 abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X
 produced a matrix encompassing 524 exome-derived SNPs. Despite a lower
 observed heterozygosity was observed during the 6.500-6.200 years BP time
 slice, genetic composition was nearly identical before and after the
 perturbation, indicating that re-expansion of the population after the
 decline was driven by autochthonous specimens. To the best of our
 knowledge, this is the first time a population genomic study incorporating
 ancient DNA samples of tree subfossils is conducted at a moderate cost
 using reproducible exome-reduced complexity.
description: HyRAD alignment against
 de novo generated catalog with Rainbow from sequenced probes (with
 Paleomix, which uses BWA)Alignment_hyRAD_denovo.tar.gzHyRAD alignment against Abies alba transcriptome (with Paleomix, which uses BWA)Alignment_hyRAD_Transcriptome.tar.gzHyRAD-X alignment against Abies alba transcriptome (with Paleomix, which uses BWA)Alignment_hyRADX_Transcriptome.tar.gzDemultiplexed hyRAD reads, trimmed and filtered according to qualityhyRAD_Demultipexed_Filtered_Reads.tar.gzDemultiplexed hyRAD-X reads, trimmed and filtered according to qualityhyRADX_Demultipexed_Filtered_Reads.tar.gzSNPs generated with hyRAD aligned against de novo catalog using VCFtoolsSNPs_hyRAD_denovo_Filtered.vcfSNPs generated with hyRAD aligned against Abies alba transcriptome using VCFtoolsSNPs_hyRAD_Transcriptome_Filtered.vcfSNPs generated with hyRAD-X aligned against Abies alba transcriptome using VCFtoolsSNPs_hyRADX_Transcriptome_Filtered.vcf