Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples

DNA studies of endangered or extinct species often rely on ancient or degraded remains.The majority of ancient DNA(aDNA)extraction protocols focus on skeletal elements,with skin and hair samples rarely explored.Similar to that found in bones and teeth,DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes.Thus,the development of effective DNA extraction methods is required for these materials.Here,we compared the performance of two DNA extraction protocols(commercial and custom laboratory aDNA methods)on hair and skin samples from decades-old museum specimens to Iron Age archaeological material.We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation,skin yielded more endogenous DNA than hair of the samples and protocols tested.While both methods recovered DNA from ancient soft tissue,the laboratory method performed better overall in terms of DNA yield and quality,which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.

Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei(Blyth, 1847) and description of a new species

Trachypithecus,which currently contains 20 species divided into four groups,is the most speciose and geographically dispersed genus among Asian colobines.Despite several morphological and molecular studies,however,its evolutionary history and phylogeography remain poorly understood.Phayre’s langur(Trachypithecus phayrei) is one of the most widespread members of the genus,but details on its actual distribution and intraspecific taxonomy are limited and controversial.Thus,to elucidate the evolutionary history of Trachypithecus and to clarify the intraspecific taxonomy and distribution of T.phayrei,we sequenced 41 mitochondrial genomes from georeferenced fecal samples and museum specimens,including two holotypes.Phylogenetic analyses revealed a robustly supported phylogeny of Trachypithecus,suggesting that the T.pileatus group branched first,followed by the T.francoisi group,and the T.cristatus and T.obscurus groups most recently.The four species groups diverged from each other 4.5-3.1 million years ago(Ma),while speciation events within these groups occurred much more recently(1.6-0.3 Ma).Within T.phayrei,we found three clades that diverged 1.0-0.9 Ma,indicating the existence of three rather than two taxa.Following the phylogenetic species concept and based on genetic,morphological,and ecological differences,we elevate the T.phayrei subspecies to species level,describe a new species from central Myanmar,and refine the distribution of the three taxa.Overall,our study highlights the importance of museum specimens and provides new insights not only into the evolutionary history of T.phayrei but the entire Trachypithecus genus as well.

Importance of genetic data from type specimens:The questionable type locality of southern white-cheeked gibbon,Nomascus siki(Delacour,1951)

DEAR EDITOR,Many historical descriptions of new species have included vague or inaccurate information about the type locality.This can lead to confusion in the study of the species and their geographic distributions,thereby hindering conservation efforts.One such example is the southern white-cheeked gibbon(Nomascus siki(Delacour,1951)).The type locality is given as Thua Luu in central Vietnam,which is located within the range of another crested gibbon species(N.annamensis)and more than 200 km south of the known range of N.siki.To investigate the problematic type locality of N.siki,we sequenced the mitochondrial genome of the holotype and compared its cytochrome b gene sequence to those of other georeferenced crested gibbon samples.