Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

Abstract

Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics‐based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin‐fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol‐preserved museum specimens. Alongside sequencing of “fresh” specimens preserved in >95% ethanol and stored at −80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%–80% ethanol and stored at room temperature, the standard for such ethanol‐preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol‐preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off‐target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol‐preserved museum specimens held in collections worldwide.

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

“…In addition, the effects of sample age on NGS data quality are generally understudied in a quantitative framework. Though some studies have noted negative relationships between sample age and parameters such as read length and number of reads [3,[26][27][28][29][30][31], focused analyses of the ways in which sample age, alongside approaches employed during library preparation, may affect estimators of sequencing quality are rare. Such information is particularly pertinent to population-scale museum studies, where users would benefit from further understanding of the quantitative effects of sample age on sequencing quality and the adjustments to library preparation protocol that could improve sequence quality.…”

Optimized and affordable high‐throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens

“…Despite these numerous research opportunities, samples of small-bodied individuals or museum samples are strongly underutilized (Cruaud et al, 2019;Derkarabetian, Benavides, & Giribet, 2019) for approaches using high-throughput sequencing techniques due to difficulties in extracting sufficient amounts of high-quality DNA (Grealy et al, 2019;Staats et al, 2013). (Cruaud et al, 2019;Lack et al, 2017), cultures in the laboratory (Cornetti et al, 2019;Lynch et al, 2017), pooling of multiple individuals for extraction (Cornetti et al, 2019;Lynch et al, 2017), or using complete specimens for extractions (Scherz et al, 2019).…”

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

“…The technological innovations underlying next generation sequencing (NGS) have resulted in an unprecedented ability to obtain DNA sequence data from specimens encompassing the vast diversity of biological life [1][2][3]. In recent times, NGS has opened up possibilities not just for recovering DNA data from extant species, but also from historical samples and even extinct species.…”

“…In addition, the effects of sample age on NGS data quality are generally understudied in a quantitative framework. Though some studies have noted negative relationships between sample age and parameters such as read length and number of reads [3,[26][27][28][29][30][31], focused analyses of the ways in which sample age, alongside approaches employed during library preparation, may affect estimators of sequencing quality are rare. Such information is particularly pertinent to population-scale museum studies, where users would benefit from further understanding of the quantitative effects of sample age on sequencing quality and the adjustments to library preparation protocol that could improve sequence quality.…”