Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

• DOI: 10.1101/gr.120196.111
• Publication Date: 2011-09-01T11:10:48Z
• Authors: Victor C. Mason; Gang Li; Kristofer M. Helgen; William J. Murphy
• Keywords: 0301 basic medicine; Likelihood Functions; Lemur; Museums; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; DNA, Mitochondrial; Specimen Handling; Evolution, Molecular; 03 medical and health sciences; Genome, Mitochondrial; Animals; Phylogeny; DNA Damage

The ability to uncover the phylogenetic history of recently extinct species and other known only from archived museum material has rapidly improved due reduced cost increased sequence capacity next-generation sequencing technologies. One limitation these approaches is difficulty isolating large, orthologous DNA regions across multiple divergent species, which exacerbated for specimens, where quality varies greatly between samples contamination levels are often high. Here we describe use cross-species capture hybridization techniques selectively isolate partial full-length mitochondrial genomes degraded using probes generated a single extant species. We demonstrate our approach on specimens an enigmatic gliding mammal, Sunda colugo, widely distributed throughout Southeast Asia. isolated 13 colugo collected 47–170 years ago, successfully captured sequenced every specimen, frequently recovering fragments with 10%–13% divergence probe sequence. Phylogenetic results reveal deep genetic among colugos, both within islands Borneo Java, as well Malay Peninsula different Sundaic islands. Our method based noninvasive sampling minute amounts soft tissue leaving original specimen essentially undamaged. This represents paradigm shift away standard PCR-based accessing population phylogenomic information poorly difficult-to-study