Initiation of the Primate Genome Project

A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea(Spix,1823)resolves a taxonomic conundrum

The pygmy marmoset,the smallest of the anthropoid primates,has a broad distribution in Western Amazonia.Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimoes-Amazonas rivers.However,reconciling this new biological evidence with current taxonomy,i.e.,two subspecies,Cebuella pygmaea pygmaea(Spix,1823)and Cebuella pygmaea niveiventris(Lönnberg,1940),was problematic given the uncertainty as to whether Spix’s pygmy marmoset(Cebuella pygmaea pygmaea)was collected north or south of the Napo and Solimoes-Amazonas rivers,making it unclear to which of the two newly revealed species the name pygmaea would apply.Here,we present the first molecular data from Spix’s type specimen of Cebuella pygmaea,as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality(Tabatinga)on both sides of the river.With these data,we can confirm the correct names of the two species identified,i.e.,C.pygmaea for animals north of the Napo and Solimoes-Amazonas rivers and C.niveiventris for animals south of these two rivers.Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to reevaluate the geographical distribution for the two Cebuella species.We dated the split of these two species to 2.54 million years ago.We discuss additional,more recent,subdivisions within each lineage,as well as potential contact zones between the two species in the headwaters of these rivers.

Mitogenomes of historical type specimens unravel the taxonomy of sportive lemurs(Lepilemur spp.)in Northwest Madagascar

Accurate information on name-bearing types,including corresponding type localities,is essential for proper taxonomy.However,such geographic information is often missing or unreliable.The localities of type specimens collected 100–200 years ago can be difficult to trace due to changes in local names or simple inaccuracies.Such a case can be found for the gray-backed sportive lemur(Lepilemur dorsalis),with its type locality imprecisely fixed as Northwest Madagascar.In recent years,eight species have been newly described for the Inter-River-Systems(IRSs)of this region,however the designation of L.dorsalis remains controversial due to a lack of a precise type locality.Here,we sequenced the complete mitochondrial genomes(mitogenomes)of type specimens of L.dorsalis and L.grandidieri,which is currently recognized as a synonym of L.dorsalis and compared their sequences with those of samples of known provenance from different IRSs.Results showed that the two type specimens of L.dorsalis and L.grandidieri had identical mitogenome sequences and clustered closely with samples collected in IRS V,indicating that the type locality could be fixed to IRS V.Consequently,L.dorsalis occurs in IRS V,and L.grandidieri and L.mittermeieri are junior synonyms of L.dorsalis.This finding demonstrates the value of type specimens for clarifying phylogeographic and taxonomic questions and clarifies the taxonomy of sportive lemurs in Northwest Madagascar.

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.

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.

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.

Reconstructing the phytogeny of new world monkeys(platyrrhini):evidence from multiple non-coding loci

Among mammalian phylogenies,those characterized by rapid radiations are particularly problematic.The New World monkeys(NWMs,Platyrrhini)comprise 3 families and 7 subfamilies,which radiated within a relatively short time period.Accordingly,their phylogenetic relationships are still largely disputed.In the present study,56 nuclear non-coding loci,including 33 introns(INs)and 23 intergenic regions(IGs),from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies.Of the 56 loci,43 have not been used in previous NWM phylogenetics.We applied concatenation and coalescence tree-inference methods,and a recently proposed question-specific approach to address NWM phylogeny.Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets.However,a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods,albeit with varying degrees of statistical support.In detail,our results indicated the sister-group relationships between the families Atelidae and Pitheciidae,and between the subfamilies Aotinae and Callithrichinae among Cebidae.Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches.However,the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling.Overall,our work has important implications for phylogenetic studies dealing with rapid radiations.