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The origin, peopling and evolution of human beings have all contributed greatly to shaping the genetic diversity of present human populations, and are the research focus of multiple disciplines. Molecular genetics has tried to deduce the human history through genetic analysis of modern human populations. It proposed the well-recognized out of Africa human origin model with Homo sapiens replaced all the other human species. As modern humans migrated out of Africa, they encountered multiple environmental conditions which could exert selection pressure upon them, as exemplified by the evolutionary elucidation of human phenotypes like skin pigmentation and height as well as physiological traits like lactase tolerance, starch digestion, immune response and hypoxia adaptation. However, this indirect approach could be largely influenced by undetected population structure and model parameter settings, still cannot fully reveal the genuine human history, and sometimes could even produce misleading results based on Occam’s razor theory. Recently, whole genome resequencing is used to directly analyse ancient DNA samples collected from different time periods to investigate a specific history event. In addition, the genetic data from both ancient and modern human populations are systematically compared to obtain a more straightforward elucidation of human history. To be more specific, analyses from archaic human populations have demonstrated strong evidence of gene flow between Homo sapiens and other extinct human species, e.g. Neanderthals and the Danisova hominin, which gave rise to a leaky replacement model. That is, other ancient human species also have contributed to modern human populations. Together with the remaining Homo sapien s genome, the introgression from ancient human species went through genetic drift and natural selection. For example, the EPAS1 gene encoding endothelial Per-Arnt-Sim (PAS) domain protein 1 has been indicated to play an important role in hypoxia adaptation among Tibetan individuals. 31 SNPs of this gene are significantly associated with haemoglobin (Hb) levels, and the Tibetan dominant alleles are significantly associated with low Hb levels, a trait featured in Tibetan hypoxia adaptation. Interestingly, the dominant Tibetan haplotype can only be observed in Tibetans and Danisova hominin with high frequency, and further genetic analysis revealed this gene was from Danisova hominin. Similar stories could also be observed for other human phenotypes and physiological traits. Therefore, as demonstrated by the illustrious example of EPAS1 gene, ancient DNA research is revealing a human history far more complex than what we have inferred from parsimonious models based on modern DNA. In this review, we will briefly overview some key events in human environmental adaptation in the light of ancient DNA findings, and discuss new evidence how natural selection has shaped human populations, which might provide clues for future studies.

Prion plays a central role in the pathogenesis of transmissible spongiform encephalopathies, also known as prion diseases. However, the biology of the protein and the pathophysiology of these diseases remain largely unknown. It has been speculated that additional factor or factors may be involved in the pathogenesis of prion diseases. Recently, a PrP-like protein, recognized as shadow of prion protein (Shadoo, Sho), is thought to be an interesting candidate factor because both the prion protein and Sho have been shown to have overlapping expression patterns and shared functions. Therefore, extensive study of Sho may advance our understanding of the enigmatical biology of prion and prion diseases. In this review, recent studies on Sho associated with prion diseases and functions are summarized. These studies have demonstrated the functional importance of Sho, and they further need to investigate its biological roles in prion diseases.

Extant genes can be modified, or ‘tinkered with’, to provide new roles or new characteristics of these genes. At the genetic level, this often involves gene duplication and specialization of the resulting genes into particular functions. We investigate how ligand-receptor partnerships evolve after gene duplication. While significant work has been conducted in this area, the examination of additional models should help us better understand the proposed models and potentially reveal novel evolutionary patterns and dynamics. We use bioinformatics, comparative genomics and phylogenetic analyses to show that preproghrelin and prepromotilin descended from a common ancestor and that a gene duplication generated these two genes shortly after the divergence of amphibians and amniotes. The evolutionary history of the receptor family differs from that of their cognate ligands. GPR39 diverges first, and an ancestral receptor gives rise to receptors classified as fish-specific clade A, GHSR and MLNR by successive gene duplications occurring before the divergence of tetrapods and ray-finned fish. The ghrelin/GHSR system is maintained and functionally conserved from fish to mammals. Motilin-MLNR specificity must have arisen by ligand-receptor coevolution after the MLN hormone gene diverged from the GHRL gene in the amniote lineage. Conserved molecular machinery can give rise to new neuroendocrine response mechanisms by the co-option of duplicated genes. Gene duplication is both parsimonious and creative in producing elements for evolutionary tinkering and plays a major role in gene co-option, thus aiding the evolution of greater biological complexity.

Orogenesis of the Qinghai-Tibetan Plateau, which occurred in a stepwise manner, contributed to the extreme aridity of the Tarim Basin, resulting in vulnerable and unstable ecosystems. Quaternary climatic oscillations may have affected the ecosystems and, consequently, the distributions and genetic structuring of the Tarim Basin’s biota. We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin’s endemic Yarkand hare (Lepus yarkandensis). Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network. Populations from the northern and eastern Tarim Basin shared a similar history, as did those from the western and southern regions. Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations. The distribution of the Yarkand hare, especially in the northern and eastern parts, probably represented 3 postglacial colonization events, dated to 0.21, 0.090 and 0.054 MYA, which corresponded to known interglacial periods. Given the relatively complete geographic isolation between the eastern and southern populations, the Yarkand hare likely dispersed during postglacial periods from the southwest to the north, and then onward to the east. The absence of water likely forced the species into refugia, and this differed from other Pleistocene biogeographical drivers. The demographical and historical patterns have important implications for conservation.

The occurrence of polyploidy, or whole genome duplication, can result in instantaneous speciation. Because new polyploids are immediately reproductively isolated from their non-polyploid congeners, polyploidization has played an important role in the diversification of flowering plants and some vertebrates. Newly formed polyploids must respond to this instantaneous genomic change, which resembles “genome shock” syndrome to survive and reproduce successfully. Epigenetic changes, which do not cause changes to the sequence of DNA, can significantly contribute to the survival of and ultimately to the evolutionary success of new polyploids. Epigenetic regulation, both transcriptional and post-transcriptional, entails changes in DNA methylation, gene status and/or nucleolus dominance. These changes provide effective and flexible ways for a new polyploid to respond quickly to the enormous change in genetic material, to survive and potentially reproduce. We examine and assess certain epigenetic phenomena and possible pathways that may facilitate the evolutionary success of polyploid organisms.

Natural selection has a critical role in the diversity of morphological traits. However, the genetic basis underlying the evolution and diversity of morphological characteristics, particularly in the context an organism’s behavior, lifestyle, and environment, is not well understood. The discovery of nasal chemoreceptors in mammals provided an opportunity to address this question. Here, we identify 4 nasal chemoreceptor gene families (V1R, V2R, OR, and TAAR) from horse, guinea pig, marmoset and orangutan genome sequences, respectively. Together with previously described mammalian nasal chemoreceptor gene repertoires, we found a significant positive correlation between functional gene number and morphological complexity, both in the main olfactory system and the vomeronasal system. The combined analysis of morphological data, behavioral data, and gene repertoires suggests that nocturnal mammals tend to possess more species-specific chemoreceptor genes and more complicated olfactory organs than diurnal mammals. Moreover, analysis of evolutionary forces revealed the existence of positive selection on the species-specific genes, likely reflecting the species-specific detection of odors and pheromones. Taken together, these results reflect a rare case of adaptation to circadian rhythm activity at the genome scale, and strongly suggest that the complexity of morphological olfactory organs and the diversification of nasal chemoreceptors in nocturnal mammals are under selection for the ability to perceive the variety of odors that nocturnal mammals may encounter in their particular dark environments.

Chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They represent an interesting model organism of adaptation to the extreme environmental stresses. However, no study at the molecular level has yet been reported for the high-altitude adaptation in Chinese snub-nosed monkeys. Leptin, as an adipocyte-derived hormone, is believed to play an important role in energy homeostasis in adaptation to high altitude environments. In the present study, we sequenced and compared leptin sequences of the Chinese snub-nosed monkeys (R. bieti and R. roxellana) with their lowland close relative R. avunculus and other Colobines. Unexpectedly, no amino acid changes were observed in the 7 Colobinae species examined, including the 2 Chinese snub-nosed monkeys, indicating no difference in the evolutionary pattern of the Leptin gene between high-altitude monkeys and their lowland counterparts. In contrast to a previous finding of adaptive evolution of Leptin gene in plateau pikas, our study suggests that this gene may not have an important role in high-altitude adaptation of Chinese snub-nosed monkeys. Other nuclear genes associated with energy metabolism, or mitochondrial genes, are most likely to be involved the molecular mechanism underlying adaptation of these monkeys to cold and hypoxia associated with the highland environment.

The recognition and perception of chemical signals from environments are very important for the survival of organisms. In mammals, general chemical signals are mainly detected by the main olfactory system (MOS), while pheromones are primarily perceived by the vomeronasal system (VNS). Pheromones are chemicals released and recognized by individuals within the same species, which then induce physiological and behavioral changes in social and sexual activities. In this review, we focus on the recent advances on research in mammalian vomeronasal pheromone perception and those genetic components unique to vomeronasal signal transduction pathway, including vomeronasal receptor V1R and V2R gene families as well as transient receptor potential channel 2 gene (TRPC2), trying to shed light on further study of the molecular mechanisms of mammalian pheromone perception.

Adaptation is one of the most fundamental issues in the studies of organismal evolution. Pancreatic ribonuclease is a very important digestive enzyme and secreted by the pancreas. Numerous studies have suggested that RNASE1 gene duplication is closely related to the functional adaptation of the digestive system in the intestinal fermentation herbivores. RNASE1 gene thus becomes one of the most important candidate genetic markers to study the molecular mechanism of adaptation of organisms to the feeding habit. Interestingly, RNASE1 gene duplication has also been found in some non-intestinal fermentation mammals, suggesting that RNASE1 gene may have produced novel tissue specificity or functions in these species. In this review, RNASE1 gene and its implications in adaptive evolution, especially in association with the feeding habit of organisms, are summarized.

The Yunnan box turtle (Cuora yunnanensis, Boulenger, 1906), which has drawn much attention in conservation biology, was regarded as extinct since it was previously known only from 12 specimens collected in Yunnan, China, before 1908. Recently, live specimens have been discovered which are suggested to be C. yunnanensis. To determine whether the newly discovered specimens are really C. yunnanensis, we have established a molecular phylogeny, with a 1725-bp fragment of mitochondrial DNA, using samples from three live individuals of C. yunnanensis, together with sequence data from a museum specimen of C. yunnanensis (MNHN 1907.10) and other members of the genus Cuora. We found that the three newly discovered individuals and the old museum specimen of C. yunnanensis are very similar both in morphology and in mitochondrial DNA sequence, suggesting that the three new individuals are the very C. yunnanensis, and thus the species is not extinct. Our phylogenetic analysis also demonstrates that C. yunnanensis is not of recent hybrid origin, but rather represents a distinct evolutionary lineage.

To investigate the genetic diversity of Tricholoma matsutake, we studied ITS and IGS1 sequences and PCR polymorphism of a retrotransposon in 56 fruit bodies collected from 13 counties of 9 regions in Yunnan Province. We found one and three haplotypes based on ITS and IGS1 sequences, respectively. Moreover, there was no significant difference in PCR polymorphism of the retrotransposon among different populations. Compared with Jilin Province (China) and Japanese populations, although Yunnan was highly homogenous to Japanese populations, low genetic diversity of T. matsutake in Yunnan did not support the view that this species originated from Yunnan.

Two multigene superfamilies, named V1R and V2R, encoding seven-transmembrane-domain G-protein coupled receptors (GPCRs) have been identified as pheromone receptors in mammals. Three V2R gene families have been described in mouse and rat. Here we screened the updated mouse genome sequence database and finally retrieved 63 putative functional V2R genes including three newly identified genes which formed a new additional family. We described the genomic organization of these genes and also characterized the conservation of mouse V2R protein sequences. These genomic and sequence information we described are useful as part of the evidence to speculate the functional domain of V2Rs and should give aid to the functionality study in the future.

Congenital microphthalmia is a developmental ocular disorder and might be caused by the mutations in the genes involved in eye development. To uncover the genetic cause in a six-generation Chinese pedigree with autosomal dominant congenital microphthalmia, we performed genescan and linkage analysis in this family. Fourteen microsatellite markers on chromosomes 3, 11, 14 and 15 were selected as genetic markers according to the five previously reported loci associated with microphthalmia (MITF, SOX2, PAX6, MCOP and NNO2). The genomic DNA of each member in the pedigree was amplified with 14 pairs of fluorescence labeled primers. Genome screening and genotyping were conducted on ABI377 DNA sequencer and linkage analysis was performed with Linkage software package. All two-point LOD scores of linkage analysis between the suggested disease genes and microsatellite markers were

Previous study using protein electrophoresis shows no polymorphism in 44 nuclear loci of Sichuan golden monkey (Rhinopithecus roxellana), which limits our understandings of its population genetic patterns in the nuclear genome. In order to obtain sufficient information, we scanned 14 microsatellite loci in a sample of 32 individuals from its three major habitats (Minshan, Qinling and Shennongjia). A considerable amount of polymorphisms were detected. The average heterozygosities in the local populations were all above 0.5. The differentiations among local populations were significant. There was evidence of geneflow among subpopulations, but geneflow between Qinling and Shennongjia local populations was the weakest. Minshan and Qinling populations might have gone through recent bottlenecks. The estimation of the ratio of the effective population sizes among local populations was close to that from census sizes. Comparisons to available mitochondria data suggested thatR. roxellana’s social structures played an important role in shaping its population genetic patterns. Our study showed that the polymorphism level ofR. roxellana was no higher than other endangered species; therefore, measures should be taken to preserve genetic diversity of this species.

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

Mitochondrial cytochrome b genes of about 450 bp fragments from 3 proturan species, 5 collembolan species and 2 dipluran species have been sequenced. The number of nucleotide substitutions and Kimura 2-parameter distances have also been calculated, and a series of molecular phylogenetic trees reconstructed by using parsimony and distance methods. The proturan, collembolan and dipluran species have evolved monophyletic groups. The results suggest that Protura and Collembola are sister groups, while Diplura is more or less demonstrating a closer phylogenetic relationship to the pterygotan insects. The phylogeny and their systematic position of protura and other groups are also discussed.

A method for DNA isolation from early development of blastocyst and further analysis of nuclear and mitochondrial DNA was developed in present study. Total DNA was prepared from interspecies reconstructed blastocyst and a giant panda specific microsatellite locus g010 was successfully amplified. DNA sequencing of the PCR product showed that two sequences of reconstructed blastocysts are the same as that of positive control giant panda. Our results prove that the nucleus of interspecies reconstructed blastocyst comes from somatic nucleus of donor giant panda.

In the present study, we obtained exon 2-5 of prolactin (PRL) gene from four primate species by PCR and sequencing. Adding other genes available in GenBank, we calculate amino acid substitution rates for prolactin gene in primate. Comparison of nonsynonymous substitution rate to synonymous substitution rate ratios shows no evidence of positive selection for any lineage of primate prolactin gene. According to this and the facts that (i) no sites under positive selection are inferred by using maximum-likelihood method; (ii) among 32 amino acid replacement that occurred along the rapid evolutionary phase, only two are included in the 40 functionally important residues, indicating that amino acid replacement tends to occur in those functionally unimportant residues; (iii) partial of prolactin function is replaced by placental lactogen in primate at the rapid evolutionary phase of prolactin gene, we thus deem that it is relaxation of purifying selection to some extent rather than positive selection that enforces the rapid evolution of primate prolactin gene.

Both the rhino mouse and hairless mouse resulted from hairless gene mutation, but they show different phenotypes of skin physiology. The rhino mouse has more similar histological characters to human papular alopecia. Therefore rhino mouse is a good experimental animal model for human papular alopecia. This study reports a hairless mouse named rhino KIZ, arose from KM colony in Kunming Institue of Zoology, by systematic studies on morphology, skin histopathology, gene sequence, pedigree and protein domain analysis. The results demonstrate that a C-to-T transition in exon 11 of hr gene (The mutant gene has been applied for a Chinese patent (patent No. 03135280)) results in the rhino KIZ. The rhino KIZ with clear genetic mechanism will be a useful animal model.

Many studies have been reported the origin and evolution of domesticated animals, particularly dogs, however, few have systematically examined the Tibetan Mastiff (TM), a dog that lives primarily in the Qing-Tibet Plateau. Here, we study the origin and evolution of TM based on the population comparison of mtDNA D-loop sequences from TM and other dogs across the world. Intriguingly, non-simultaneous arrivals of Tibetan Mastiffs ancestors to Tibet occurred, which may result from continuous Tibetans’ settlement on Qing-Tibet Plateau supported by archaeological and genetic evidence. High genetic and haplotype diversity and robust haplotypes sharing with other dogs unique to East Asia are observed in Tibetan Mastiff, supporting that it is a very archaic breed derived probably from East Asia.

The phylogeny of the colobine monkeys has a complex evolutionary history, evolving several distinct radiations and owned a wide range of forest and woodland habits in tropical Africa and in southern and eastern Asia. Understanding the true evolutionary history of the colobine monkeys becomes an important field and has received special attention. In this article, we review phylogeny of Colobinae based on previous fossil, cytological, morphological and molecular evidence and indicate the phylogenetic controversies. This review is expected to guide the future research of Colobinae phylogeny, and also provide theoretic evidence for the conservation of these highly endangered and unique primates.

The phylogenetic relationships of European and African Barbus and their West Asian relatives in Cyprininae remain largely unresolved. Consequently, little is known about the drivers of their evolution, including the possible association of uplifting of the Qinghai-Tibetan Plateau (QTP) with the early divergence of the subfamily. We use complete sequence data of the mitochondrial DNA gene encoding the protein cytochrome b (Cytb) to hypothesize the phylogeny of 85 species belonging to 47 genera in the Cyprininae plus 6 species from the Leuciscinae. We employ 6 other species from Cypriniformes as outgroup taxa and estimate divergence times. Our results indicate that European Barbus sensu stricto lineage including Aulopyge shares a common ancestor with specialized and highly specialized schizothoracins and the genera Cyprinion and Scaphiodonichtys. The common ancestor appears to have originated in the Qinghai-Tibetan Plateau (QTP) region about 19.4–17.8 Ma. Barbus sensu stricto lineage appears to have originated about 16.6–15.5 Ma. Small to medium sized African Barbus sensu lato appear to have had an Oriental origin about 19.1–15.3 Ma and are closely related to Asian Puntius. West Asian Carasobarbus lineage including large African Barbus sensu lato might have originated about 9.94 Ma, also in Oriental Realm and has a close relationship to Asian Neolissochilus and Tor. The large-sized Barbus sensu lato appear to have diverged from Carasobarbus about 7.7 Ma. Finally, the Cyprininae appear to have radiated rapidly into nine lineages and many sublineages from about 27.8 to 17.8 Ma, close to the time of the second-stage tectonic movements of the QTP. Our analyses provide evidence that the uplifting of the QTP drove early diversification of the Cyprininae. Our extensive sampling of species involving all of the important areas results in clear evolutionary scenario for the Cyprininae.

Leptin is an adiposity-secreted hormone that is pivotal in regulating feeding behavior, energy metabolism and body mass. The study of leptin has been of crucial importance for public health and pharmaceutical intervention given its role in obesity. Generally, leptin is highly conserved due to its functional importance. However, episodes of rapid sequence evolution and positive selection have been observed in some mammalian species, indicating that the leptin functions in these animals may have undergone adaptive modification to their environments. In this article, we review the adaptive evolution of leptin and its potential functional consequences. This review is expected to guide future research of molecular evolution and functional assays of this gene, and also to provide a theoretical foundation for the use of leptin in therapeutic applications.