Phylogeny And Adaptive Evolution Of The Trachypithecus Spp.

Trachypithecus belongs to the Primates,the family Cercopithecidae,and the subfamily Colobinae.Based on morphology and habitat distribution,the 15 species of langurs were divided into four species groups.They radiated into two groups(forest and limestone langur)dwelling various type of habitats(forests and limestone hills).It is considered as the ideal system to explore adaptive radiation due to its wide distribution.Rapid advances in genome sequencing and assembling technologies have promoted the study about the biology and evolution of humans and non-human primates(NHPs)and expanding our understanding of how populations adapt to extreme environments.Here,phylogenetic and comparative genomes were analyzed with a highly quality-improved genome assembly(Tfra?3.0)of a limestone langur(T.francoisi),and the genome resequencing data of 44 langurs from 15 species.The quality assessment of genomic showed that the contiguity and accurate of 3.0 version of the langur genome have highly improved compared with the 2.0 version(Tfra?2.0).Phylogenetic genomic analysis found that the two groups about limestone and forest langurs diverge at about 3.5 million years ago(Mya).T.pileatus group diverged from all other Trachypithecus spp.firstly and formed the ancestral lineage of langurs.Subsequently,T.francoisi group diverged from the ancestor of T.obscurus and T.cristatus groups.Nuclear genomic data suggested T.crepusculus clustered with the T.obscurus group,whereas in mt-genomes tree,T.crepusculus was shown as a sister taxon to the T.francoisi group.Comparative genomic analysis showed that the 94 th position of the melanocortin 1-receptor(MC1R)of limestone langurs has a mutation from glutamate(E)to aspartate(D),compared with forest langurs and other primates.We suspect that this mutation is the primary cause of darker fur color in the limestone langurs than the forest langur.Our findings provided a potential explanation for limestone langurs morphological adaptive to karst habitats.By calculating the nonsynonymous/synonymous substitution rates(dN/dS)of genes related to calcium metabolism limestone langurs comparing to forest langurs,we identified the rapidly evolving genes,the positive selection genes and the mutant site specific to the langur.We therefore hypothesize that these changes may be important components in facilitating the adaptation to the karst environment with high calcium and water shortage.This thesis suggest that genomic assembly of quality improvement combined with,gene annotation,and large-scale phylogenetic comparative studies provide a new perspective and understanding phylogenetic and adaptive radiation evolution of langurs.