Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

Abstract

Laboratory techniques for high‐throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site‐associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site‐associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.

Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

“…In this study, we took advantage of the availability of museum specimens from different locations and time points to provide an insight into the genetic dynamics of O. decorus at both spatial and temporal scales. By successfully applying hyRAD to 119 specimens, we retrieved more than a thousand of SNPs, a major improvement compared to previous studies using museum specimens (e.g., Kindler et al., ; Spurgin et al., ), confirming the recent findings of Linck, Hanna, Sellas, and Dumbacher (), who successfully tested hyRAD on bird samples.…”

“…By successfully applying hyRAD to 119 specimens, we retrieved more than a thousand of SNPs, a major improvement compared to previous studies using museum specimens (e.g., Kindler et al, 2012;Spurgin et al, 2014), confirming the recent findings of Linck, Hanna, Sellas, and Dumbacher (2017), who successfully tested hyRAD on bird samples.…”

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

“…There are several methods for accounting for post-mortem damage in specimens. Generally these techniques fall into two categories: (a) Presequencing repair and high-fidelity polymerase enzymes that increase amplification efficiency (Bi et al, 2013;Binladen et al, 2006;Burrell et al, 2015;Rowe et al, 2011;Willerslev & Cooper, 2005), and (b) post-sequencing filtering and weighting of damaged regions (Bi et al, 2013;Jónsson, Ginolhac, Schubert, Johnson, & Orlando, 2013;Linck, Hanna, Sellas, & Dumbacher, 2017;Zhou et al, 2017).…”

“…There has been increasing effort to develop reduced-representation sequencing methods that maximize the data generated from historical samples (e.g., Besnard et al, 2016;Bi et al, 2013;Burrell et al, 2015;Lim & Braun, 2016;Linck et al, 2017;McCormack et al, 2016;Suchan et al, 2016). Generally, these reduced-representation sequencing approaches are best suited to hDNA because they sequence smaller fragments of DNA (Bi et al, 2013;Hung et al, 2013;McCormack et al, 2016;Suchan et al, 2016).…”

Avian introgression in the genomic era

“…For example, by comparing historical (2000)(2001)(2002) and recent (2010-2012) genetic data, Taylor et al (2014) showed that the hybrid zone between Black-capped Chickadee (Poecile atricapillus) and Carolina Chickadee (P. carolensis) in Pennsylvania has moved north due to changing winter temperatures. However, a temporal comparison is only possible when historical data is available or can be obtained from museum specimens (Spurgin et al 2014;Linck et al 2017). An alternative strategy is to compare different hybrid zones between the same species (Schaefer et al 2016;Kingston et al 2017;Lackey and Boughman 2017).…”