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