Effects of aging on gene expression in blood of captive Tibetan macaques (Macaca thibetana) and comparisons with expression in humans

DEAR EDITOR,Changes in gene expression occur as animals,including primates,age.Macaques have long been used as a model species for primate evolution and biomedical studies.Here,to study gene expression in Tibetan macaques (Macaca thibetana,TMs) and its differences to humans,we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs.

Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques(genus Macaca)

The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification(about five million years ago)and rapid radiation of constituent species.To understand evolutionary gene flow in macaques,we sequenced four whole genomes(two M.arctoides and two M.thibetana)and combined them with publicly available macaque genome data for genome-wide analyses.We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals,with the strongest signals between the fascicularis and silenus species groups.Notably,we detected bidirectional gene flow between M.fascicularis and M.nemestrina.The estimated proportion of the genome inherited via gene flow between the two species was 6.19%.However,the introgression signals found among studied island species,such as Sulawesi macaques and M.fuscata,and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression.Furthermore,gene flow signals varied in individuals of the same species(M.arctoides,M.fascicularis,M.mulatta,M.nemestrina and M.thibetana),suggesting very recent gene flow after the populations split.Pairwise sequentially Markovian coalescence(PSMC)analysis showed all macaques experienced a bottleneck five million years ago,after which different species exhibited different fluctuations in demographic history trajectories,implying they have experienced complicated environmental variation and climate change.These results should help improve our understanding of the complicated evolutionary history of macaques,particularly introgressive gene flow.

Genomics and morphometrics reveal the adaptive evolution of pikas

Pikas(Lagomorpha: Ochotonidae) are small mouselike lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet) Plateau(QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81specimens, representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera, i.e., Alienauroa, Conothoa,Lagotona, Ochotona, and Pika, consistent with morphometric data. Morphologically, Alienauroa and Ochotona had similar traits, including smaller size and earlier divergence time compared to other pikas.Consistently, the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera. Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics, including several visual and hearingrelated genes. Analysis of shared amino acid substitutions and positively selected genes(PSGs) in Alienauroa and Ochotona identified two genes, i.e.,mitochondrial function-related TSFM(p.Q155E) and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas, and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake. Alienauroa and Ochotona individuals mostly inhabit different environments(e.g., subtropical forests) than other pikas, suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments. This study increases our understanding of the evolutionary history of pikas.

First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge(Arborophila ardens)

Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.