Biomedical subjects

Ya-ping Zhang

Publications and source records attributed to Ya-ping Zhang.

At least 19 recordsLinked to original sources

PubMed2006

The unusual adaptive expansion of pancreatic ribonuclease gene in carnivora.

Pancreatic ribonuclease (RNASE1) is a digestive enzyme that has been recognized to be one of the most attractive model systems for molecular evolutionary studies. The contribution of RNASE1 gene duplication to the functional adaptation of digestive physiology in foregut-fermenting herbivores, mostly in ruminants, has been well documented. However, no one has ever done a comprehensive study on the carnivores, which are sister to the artiodactyls. Here, we sequenced this gene from 15 species of the superfamily Caniformia in order Carnivora, which all have a relatively simple digestive system and lack the microbial digestion in rumen or cecum typical of most herbivores. In contrast to our initial expectation that only a single RNASE1 gene is present in these carnivores, we observed a "birth (gene duplication)-and-death (gene deactivation)" process for the evolution of RNASE1 genes in all 3 species of Mustelidae family examined here, adding the growing diversity of RNASE1 gene family evolution. In addition, bursts of positive selection have been shown to contribute the enigmatic diversification of these RNASE1 genes in Mustelidae. The finding of the adaptive expansion of RNASE1 in animals without foregut fermentation provides another opportunity for further studies of the structure, function, and evolution of this gene, raising the possibility that new tissue specificity or other functions of RNASE1 genes might have developed in these species.

Adaptation, Biological↗

PubMed2006

Genetic differentiation and cryptic speciation in natural populations of Drosophila lacertosa.

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two genetically significantly diverged lineages with 2.1% DNA sequence divergence. These two lineages are largely allopatric: one is mainly found in southwest China (lineage A), whereas the other ranges central and east of China to northeast Asia (lineage B). The geographic distributions of these two clades narrowly overlap near the provincial boundaries of Yunnan and Guizhou or Guangxi, probably as a consequence of population expansion and secondary contact. These two lineages were estimated to have diverged about 0.56 Mya, and the estimated time of expansion was approximately 70,000 years ago for lineage A population, and 110,000 years ago for lineage B population. The present molecular analysis, together with nearly complete reproductive isolation between those two lineages, strongly suggests that the two lineages might be incipient species.

Animals↗

PubMed2006

Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences.

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.

Animals↗

PubMed2006

Phylogeny of the caniform carnivora: evidence from multiple genes.

The monophyletic group Caniformia in the order Carnivora currently comprises seven families whose relationships remain contentious. The phylogenetic positions of the two panda species within the Caniformia have also been evolutionary puzzles over the past decades, especially for Ailurus fulgens (the red panda). Here, new nuclear sequences from two introns of the beta-fibrinogen gene (beta-fibrinogen introns 4 and 7) and a complete mitochondrial (mt) gene (ND2) from 17 caniform representatives were explored for their utilities in resolving higher-level relationships in the Caniformia. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Combined analyses of four nuclear and one mt genes (4417 bp) recover a branching order in which almost all nodes were strongly supported. The present analyses provide evidence in favor of Ailurus fulgens as the closest taxon to the procyonid-mustelid (i.e., Musteloidea sensu stricto) clade, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae (including Ailuropoda melanoleuca), and Canidae, the most basal lineage in the Caniformia. The potential utilities of different genes in the context of caniform phylogeny were also evaluated, with special attention to the previously unexplored beta-fibrinogen intron 4 and 7 genes.

Algorithms↗

PubMed2006

Evolutionary implications of Avian Infectious Bronchitis Virus (AIBV) analysis.

For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus (AIBV) antigenic domain of a vaccine serotype (DE072) and a virulent viral strain (GA98) to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus (SARS-CoV) was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.

Amino Acid Substitution↗

PubMed2006

Taxonomic problems in the Drosophila melanica species group (Diptera: Drosophilidae) from Southern China, with special reference to karyotypes and reproductive isolation.

Karyotypes and reproductive isolation were studied in two allopatric populations of Drosophila tsigana, one from Guizhou Province in southern China and the other from Hokkaido in northern Japan, and in one population of a closely related species, D. longiserrata, from Guizhou. In metaphase plates of larval brain cells, both geographic strains of Drosophila tsigana showed 2n=10 chromosomes, with 2 pairs of metacentric (V-shape), 2 pairs of acrocentric (R-shape), and 1 pair of dot-liked (D-shape) chromosomes. Drosophila longiserrata showed the same number, 10 chromosomes, comprising 2V, 1J (sub-metacentric chromosome), 1R, and 1D. X chromosomes of both species were acrocentric, the presumed ancestral form. Premating isolation was complete between D. tsigana and D. longiserrata, and successful mating was also limited in crosses between the two geographic populations of D. tsigana, especially in crosses between Japanese (JP) females and Guizhou (GZ) males. F1 hybrids were obtained only from crosses between GZ females and JP males, and fertilities of both F1 females and males were quite incomplete. The results of morphological observations, karyotypic analyses, and crossing experiments clearly showed that the GZ and JP populations of "D. tsigana" were highly divergent from each other and that each population should be recognized as a biologically valid species. The present morphological observations and chromosomal analyses, together with the original descriptions, strongly suggest that "Guizhou D. tsigana" might be conspecific with D. bisetata Toda, 1988 from Myanmar, and that D. longiserrata might be conspecific with D. afer Tan, Hsu, and Sheng, 1949 from Meitan, Guizhou.

Animals↗

PubMed2005

Molecular evolution of growth hormone gene family in old world monkeys and hominoids.

Growth hormone is a classic molecule in the study of the molecular clock hypothesis as it exhibits a relatively constant rate of evolution in most mammalian orders except primates and artiodactyls, where dramatically enhanced rate of evolution (25-50-fold) has been reported. The rapid evolution of primate growth hormone occurred after the divergence of tarsiers and simians, but before the separation of old world monkeys (OWM) from new world monkeys (NWM). Interestingly, this event of rapid sequence evolution coincided with multiple duplications of the growth hormone gene, suggesting gene duplication as a possible cause of the accelerated sequence evolution. Here we determined 21 different GH-like sequences from four species of OWM and hominoids. Combining with published sequences from OWM and hominoids, our analysis demonstrates that multiple gene duplications and several gene conversion events both occurred in the evolutionary history of this gene family in OWM/hominoids. The episode of recent duplications of CSH-like genes in gibbon is accompanied with rapid sequence evolution likely resulting from relaxation of purifying selection. GHN genes in both hominoids and OWM are under strong purifying selection. In contrast, CSH genes in both lineages are probably not. GHV genes in OWM and hominoids evolved at different evolutionary rates and underwent different selective constraints. Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events.

Animals↗

PubMed2005

Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals.

Pheromones are chemicals emitted and sensed by conspecifics to elicit social and sexual responses and are perceived in terrestrial vertebrates primarily by the vomeronasal organ (VNO). Pheromone receptors in the mammalian VNO are encoded by the V1R and V2R gene superfamilies. The V1R superfamily contains 187 and 102 putatively functional genes in the mouse and rat, respectively. To investigate whether this large repertoire size is typical among mammals with functional VNOs, we here describe the V1R repertoires of dog, cow, and opossum based on their draft genome sequences. The dog and cow have only 8 and 32 intact V1R genes, respectively. Thus, the intact V1R repertoire size varies by at least 23-fold among placental mammals with functional VNOs. To our knowledge, this size ratio represents the greatest among-species variation in gene family size of all mammalian gene families. Phylogenetic analysis of placental V1R genes suggests multiple losses of ancestral genes in carnivores and artiodactyls and gains of many new genes by gene duplication in rodents, manifesting massive gene births and deaths. We also identify 49 intact opossum V1R genes and discover independent expansions of the repertoire in placentals and marsupials. We further show a concordance between the V1R repertoire size and the complexity of VNO morphology, suggesting that the latter could indicate the sophistication of pheromone communications within species. In sum, our results demonstrate tremendous diversity and rapid evolution of mammalian V1R gene inventories and caution the generalization of VNO biology from rodents to all mammals.

Animals↗

PubMed2005

Adaptive diversification of vomeronasal receptor 1 genes in rodents.

The vomeronasal receptor 1 (V1R) are believed to be pheromone receptors in rodents. Here we used computational methods to identify 95 and 62 new putative V1R genes from the draft rat and mouse genome sequence, respectively. The rat V1R repertoire consists of 11 subfamilies, 10 of which are shared with the mouse, while rat appears to lack the H and I subfamilies found in mouse and possesses one unique subfamily (M). The estimations of the relative divergence times suggest that many subfamilies originated after the split of rodents and primates. The analysis also reveals that these clusters underwent an expansion very close to the split of mouse and rat. In addition, maximum likelihood analysis showed that the nonsynonymous and synonymous rate ratio for most of these clusters was much higher than one, suggesting the role of positive selection in the diversification of these duplicated V1R genes. Because V1R are thought to mediate the process of signal transduction in response to pheromone detection, we speculate that the V1R genes have evolved under positive Darwinian selection to maintain the ability to discriminate between large and complex pheromonal mixtures.

Adaptation, Physiological↗

PubMed2005

Episodic evolution of prolactin receptor gene in mammals: coevolution with its ligand.

Divergence of proteins in signaling pathways requires ligand and receptor coevolution to maintain or improve binding affinity and/or specificity. In this paper we show a clear case of coevolution between the prolactin (PRL) gene and its receptor (prolactin receptor, PRLR) in mammals. First we observed episodic evolution of the extracellular and intracellular domains of the PRLR, which is closely consistent with that seen in PRL. Correlated evolution was demonstrated both between PRL and its receptor and between the two domains of the PRLR using Pearson's correlation coefficient. On comparing the ratio of the nonsynonymous substitution rate to synonymous substitution rate (omega = d(N)/d(S)) for each branch of the star phylogeny of mammalian PRLRs, separately for the extracellular domain (ECD) and the transmembrane domain/intracellular domain (TMD/ICD), we observed a lower omega ratio for ECD than TMD/ICD along those branches leading to pig, dog and rabbit but a higher ratio for ECD than TMD/ICD on the branches leading to primates, rodents and ruminants, on which bursts of rapid evolution were observed. These observations can be best explained by coevolution between PRL and its receptor and between the two domains of the PRLR.

Amino Acid Sequence↗

PubMed2004

Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes.

The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ two nuclear single-copy gene segments, the partial exon 1 from gene encoding interphotoreceptor retinoid binding protein (IRBP) and the complete intron 1 from transthyretin (TTR) gene, in conjunction with previously published mt data, to clarify these enigmatic problems. The combined analyses of nuclear IRBP and TTR datasets not only corroborated prior hypotheses, positioning the spectacled bear most basally and grouping the brown and polar bear together but also provided new insights into the bear phylogeny, suggesting the sister-taxa association of sloth bear and sun bear with strong support. Analyses based on combination of nuclear and mt genes differed from nuclear analysis in recognizing the sloth bears as the earliest diverging species among the subfamily ursine representatives while the exact placement of the sun bear did not resolved. Asiatic and American black bears clustered as sister group in all analyses with moderate levels of bootstrap support and high posterior probabilities. Comparisons between the nuclear and mtDNA findings suggested that our combined nuclear dataset have the resolving power comparable to mtDNA dataset for the phylogenetic interpretation of the bear family. As can be seen from present study, the unanimous phylogeny for this recently derived family was still not produced and additional independent genetic markers were in need.

Animals↗

PubMed2004

Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes.

Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon 1 of the IRBP gene (approximately 1.3 kb) and first intron of the TTR gene (approximately 1 kb). These data were used to analyze carnivoran phylogeny at the family and generic level as well as the interspecific relationships within recently derived Felidae. Phylogenetic results using a combined IRBP+TTR dataset strongly supported within the superfamily Califormia, the red panda as the closest lineage to procyonid-mustelid (i.e., Musteloidea) clade followed by pinnipeds (Otariidae and Phocidae), Ursidae (including the giant panda), and Canidae. Four feliform families, namely the monophyletic Herpestidae, Hyaenidae, and Felidae, as well as the paraphyletic Viverridae were consistently recovered convincingly. The utilities of these two gene segments for the phylogenetic analyses were extensively explored and both were found to be fairly informative for higher-group associations within the order Carnivora, but not for those of low level divergence at the species level. Therefore, there is a need to find additional genetic markers with more rapid mutation rates that would be diagnostic at deciphering relatively recent relationships within the Carnivora.

Animals↗

PubMed2004

Phylogenetic relationships of Drosophila melanogaster species group deduced from spacer regions of histone gene H2A-H2B.

Nucleotide sequences of the spacer region of the histone gene H2A-H2B from 36 species of Drosophila melanogaster species group were determined. The phylogenetic trees were reconstructed with maximum parsimony, maximum likelihood, and Bayesian methods by using Drosophila pseudoobscura as the out group. Our results show that the melanogaster species group clustered in three main lineages: (1). montium subgroup; (2). ananassae subgroup; and (3). the seven oriental subgroups, among which the montium subgroup diverged first. In the third main lineage, suzukii and takahashii subgroups formed a clade, while eugracilis, melanogaster, elegans, ficusphila, and rhopaloa subgroups formed another clade. The bootstrap values at subgroup levels are high. The phylogenetic relationships of these species subgroups derived from our data are very different from those based on some other DNA data and morphology data.

Animals↗

PubMed2004

Phylogenetic relationships of 12 penaeoidea shrimp species deduced from mitochondrial DNA sequences.

DNA sequences of an 847 bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene and a 514 bp fragment of 16s rRNA gene were determined to examine the phylogenetic relationships of 12 Penaeoidea shrimp species (Penaeus chinensis, Penaeus japonicus, Penaeus penicillatus, Penaeus vannamei, Penaeus canaliculatus, Trachypenaeus curvirostris, Metapenaeus affinis, Metapenaeus ensis, Metapenaeopsis barbata, Parapenaeus fissuroides, Parapenaeopsis hardiwickii, Solenocera crassicomis). Both fragments of the swimming crab Portunus trituberculaus chosen as the outgroup were also sequenced. Intraspecific sequence divergence of 0.24-1.2% in the COI gene was found in 5 species, while no intraspecific variation was observed in the 16s rRNA gene. Three phylogenetic trees based on the 1361 bp combined sequences of COI and 16s rRNA were concordant in indicating the following suggestions: (1) phylogenetic relationship of the 11 Penaeidae species based on our result support the opinion of Burkenroad (Burkenroad, M.D. (1983). Crustacean Issues 3:279-290) on the basis of morphological features; (2) it seems more reasonable to class Solenocera crassicorni in the family Penaeidae; (3) the fragment of the COI gene chosen here appears to be a good marker for speciation studies and population analysis in Crustaceans, while the 16s rRNA gene fragment here seems suitable for examining phylogenetic relationships at the species or genus levels in Crustaceans. Our time estimates suggest that Penaeus and Metapenaeus might have separated about 6.38 x 10(6)-7.98 x 10(6) years BP in the post-Miocene, and the species separation within Metapenaeus and Penaeus might occur 0.08 x 10(6)-0.4 x 10(6) years BP in the late Pleistocene.

Animals↗

PubMed2004

[Relationship between the locus 16 geontype of beta 2 adrenergic receptor and the nocturnal asthma phenotype].

OBJECTIVE: To investigate the relationship between the polymorphism of beta 2 adrenergic receptor (beta 2 AR) at loci 16, 27 and the nocturnal asthma phenotype. METHODS: Forty-nine asthmatic patients were divided into nocturnal asthmatic group (n = 25) and non-nocturnal asthmatic group(n = 24) by their peak expiratory flow rates (PEFR). The genotypes at loci 16, 27 of beta 2 AR were delineated by PCR product sequencing. Then the relationships of beta 2 AR genotypes with the PEFR, FEV1 and the situation of drug use in the two groups were analyzed. RESULTS: By the criteria of overnight decrements in PEFR, the nocturnal asthma group had a mean overnight decrement in PEFR of 33.6%, compared to 7.0% for the non-nocturnal asthma group (P < 0.001). The mean values of daytime baseline percent predicted forced expiratory volume in 1 s (FEV1) were 73.7% and 85.8% for the nocturnal and non-nocturnal cohorts, respectively (P < 0.001). The frequency of the Gly16 allele was 56.0% in the nocturnal group, compared to 22.9% in the non-nocturnal group (P < 0.05). The results from comparison of the two cohorts as to homozygosity for Gly16, homozygosity for Arg16, or heterozygosity were also consistent with the segregation of Gly16 with nocturnal asthma. There was no significant difference in the frequency of polymorphisms at locus 27 (Gln27 or Glu27). CONCLUSION: The Gly16 polymorphism of beta 2 AR appears to be associated with nocturnal asthma.

Alleles↗

PubMed2003

Intra- and interspecific variation of the CCR5 gene in higher primates.

We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light on its functional role. The comparison of differences between intraspecific polymorphisms and interspecific fixed substitutions provides useful information regarding modes of selection during the course of evolution. There is marked polymorphism in the CCR5 gene sequence within different primate species, whereas sequence divergence between different species is small. By using contingency tests, we compared synonymous (SS) and nonsynonymous (NS) CCR5 mutations occurring within and between a broad range of primates. Our results demonstrate that CCR5 evolution did not follow expectations of strict neutrality at the level of the whole gene. The proportion of NS to SS at the intraspecific level was significantly higher than that observed at the interspecific level. These results suggest that most CCR5 NS polymorphisms are slightly deleterious. However, at domains more closely correlated with its known biological functions, there was no obvious evidence to support deviation from neutrality.

Animals↗

PubMed2003

Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey.

Physiological functions of human genes may be studied by gene-knockout experiments in model organisms such as the mouse. This strategy relies on the existence of one-to-one gene orthology between the human and mouse. When lineage-specific gene duplication occurs and paralogous genes share a certain degree of functional redundancy, knockout mice may not provide accurate functional information on human genes. Angiogenin is a small protein that stimulates blood-vessel growth and promotes tumor development. Humans and related primates only have one angiogenin gene, while mice have three paralogous genes. This makes it difficult to generate angiogenin-knockout mice and even more difficult to interpret the genotype-phenotype relation from such animals should they be generated. We here show that in the douc langur (Pygathrix nemaeus), an Asian leaf-eating colobine monkey, the single-copy angiogenin gene has a one-nucleotide deletion in the sixth codon of the mature peptide, generating a premature stop codon. This nucleotide deletion is found in five unrelated individuals sequenced, and therefore is likely to have been fixed in the species. Five colobine species that are closely related to the douc langur have intact angiogenin genes, suggesting that the pseudogenization event was recent and unique to the douc langur lineage. This natural knockout experiment suggests that primate angiogenin is dispensable even in the wild. Further physiological studies of douc langurs may offer additional information on the role of this cancer-related gene in normal physiology of primates, including humans. Our findings also provide a strong case for the importance of evolutionary analysis in biomedical studies of gene functions.

Amino Acid Sequence↗

PubMed2003

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences.

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.

Animals↗