Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study

Abstract

Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.

The population bottleneck of the Iberian wolf impacted genetic diversity but not admixture with domestic dogs: A temporal genomic approach

“…Genotype calling was performed using GenomeStudio software (Illumina) following Illumina's recommendations. Additionally, we leveraged the availability of a comprehensive genome‐wide data set of 145 historical putative wolf samples genotyped for 100,000 genome‐wide SNPs targeted based on the Canine SNP chip, using an in‐solution target capture enrichment approach (Pacheco, Lobo, et al., 2022; Table S1). All individuals in our data set are not directly related to each other (identity‐by‐descent <0.5, following Galaverni et al.…”

“…Additionally, we leveraged the availability of a comprehensive genome-wide data set of 145 historical putative wolf samples genotyped for 100,000 genome-wide SNPs targeted based on the Canine SNP chip, using an in-solution target capture enrichment approach (Pacheco, Lobo, et al, 2022; Table S1). All individuals in our data set are not directly related to each other (identity-bydescent <0.5, following Galaverni et al (2017); IBD estimated in PLINK v.1.9 using the -genome function following PLINK's guidelines; Purcell et al, 2007).…”

Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens

“…Thus far, the majority of research investigating how to maximize the recovery of genetic data from non-ancient museum specimens has focused on the influence of DNA source or extraction method on DNA yield (Hahn et al, 2022; Hawkins, Flores, McGowen, & Hinckley, 2022; McDonough et al, 2018; Pacheco et al, 2022; Straube et al, 2021; Tsai et al, 2020; Zacho et al, 2021). However, DNA yield does not necessarily predict sequencing success or efficiency (McDonough et al, 2018; Straube et al, 2021; Zacho et al, 2021) because it is not possible to estimate the proportions of endogenous versus exogenous extracted DNA.…”

Library preparation method and DNA source influence endogenous DNA recovery from 100‐year‐old avian museum specimens

“…Thus far, the majority of research investigating how to maximize the recovery of genetic data from non‐ancient museum specimens has focused on the influence of DNA source or extraction method on DNA yield (Hahn et al, 2022 ; Hawkins et al, 2022 ; McDonough et al, 2018 ; Pacheco et al, 2022 ; Straube et al, 2021 ; Tsai et al, 2020 ; Zacho et al, 2021 ). However, DNA yield does not necessarily predict sequencing success or efficiency (McDonough et al, 2018 ; Straube et al, 2021 ; Zacho et al, 2021 ) because it is not possible to estimate the proportions of endogenous versus exogenous extracted DNA.…”