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- Title
Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens.
- Authors
Linck, Ethan B.; Hanna, Zachary R.; Sellas, Anna; Dumbacher, John P.
- 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 (hy RAD) is a recently developed method for population genomics with museum specimens. The hy RAD 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, hy RAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hy RAD 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 hy RAD 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.
- Subjects
BIRD hybridization; DNA probes; NUCLEOTIDE sequence; BIRD evolution; BIRDS; GENOMES
- Publication
Ecology & Evolution (20457758), 2017, Vol 7, Issue 13, p4755
- ISSN
2045-7758
- Publication type
Article
- DOI
10.1002/ece3.3065