基于线粒体控制区序列的猕猴属系统发育研究

通过线粒体部分控制区DNA序列数据探讨7种猕猴属物种的分子系统发育关系。结果表明熊猴的核苷酸多样度最高,而藏酋猴核苷酸多样度较低。基于控制区序列数据所构建的最大似然树,不考虑食蟹猴的位置,7种猕猴物种可粗略地分为3个种组,即狮尾猴组(包括北平顶猴)、头巾猴组(包括红面猴、熊猴和藏酋猴)和食蟹猴组(包括恒河猴和台湾猴)。与前人(Fooden＆Lanyon,1989;Tosi et al,2003a;Deinard＆Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales＆Melnick,1998)的结果不同,我们的结果支持食蟹猴比北平顶猴分化早的假设;东部恒河猴(相对于台湾猴)和东部熊猴(相对于藏酋猴)出现并系。与Y染色体、等位酶、核基因以及部分形态学数据推测的结果(Delson,1980;Fooden＆Lanyon。1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard＆Smith,2001)一致,红面猴应归于头巾猴组,但此结论与前人(Hayasaka et al,1996;Morales＆Melnick,1998;Tosi et al,2003a)依据线粒体得到的结果有较大分歧。     

Radiation and phylogeography in the Japanese macaque, Macaca fuscata

The Japanese macaque (Macaca fuscata) presumably differentiated from eastern rhesus macaque (Macaca mulatta) populations during the Pleistocene and the two species are closely related. In order to analyse speciation and subspeciation events in the Japanese macaque and to describe historical and current relationships among their populations, we sequenced and analysed a fragment of 392bp of mitochondrial DNA (mtDNA) control region in 50 individuals belonging to six populations of Japanese macaque and compared these sequences with 89 eastern rhesus macaque control region sequences from GenBank/EMBL database. There were high genetic similarities between both species and only two positions were fixed within each species, which supports the inclusion of the Japanese macaque in a single species with eastern populations of rhesus macaques. Japanese macaque ancestors colonised Japan after the separation of the two species, estimated at between 0.31 and 0.88 million years ago (Mya). The star-like phylogeny, multimodal mismatch distribution, and lack of correlation between geographic and genetic distances are in accordance with a rapid dispersion of macaques throughout the archipelago after the arrival into Japan. The species shows low genetic variation within populations and high levels of genetic differentiation among populations with no mtDNA haplotype shared across populations. Genetic distances between Yakushima macaques (Macaca fuscata yakui) and any other population of Macaca fuscata fuscata subspecies are comparable to the distances between populations of Honshu, Awajishima, and Kyushu, not supporting the classification of Yakushima macaques as a different subspecies.     

Phylogenetic relationships among Japanese, rhesus, Formosan, and crab- eating monkeys, inferred from restriction-enzyme analysis of mitochondrial DNAs [published erratum appears in Mol Biol Evol 1988 Sep;5(5):601]

Mitochondrial DNA (mtDNA) polymorphisms in four species of macaques, i.e., Japanese monkey (Macaca fuscata), rhesus monkey (M. mulatta), Formosan monkey (M. cyclopis), and crab-eating monkey (M. fascicularis), were analyzed to study phylogenetic relationships. When 17 restriction enzymes of 6-bp recognition were used, 42-49 sites were observed in the samples. The estimated number of nucleotide substitutions per site among Japanese, rhesus, and Formosan monkeys ranges from 0.0318 to 0.0396, and that between the crab-eating monkey and the other monkeys from 0.0577 to 0.0653. These findings suggest that the crab-eating monkey diverged from the other three approximately 1.5-3.0 Myr before the present (Mybp) and that the Japanese, rhesus, and Formosan monkeys diverged approximately 0.9-1.8 Mybp, although the branching order cannot be determined conclusively.      

猕猴属中的基因流研究

本文以我们修改的方法从猕猴肝脏组织中提取ｍｔＤＮＡ。用限制性片段长度多态分析为手段研究恒河猴,台湾省的台湾猴,日本猴和食蟹猴的ｍｔＤＮＡ多态。根据ｍｔＤＮＡ遗传距离计算了４个种间的分歧年代,其范围为１．８－３．２百万年。根据蛋白质多态资料,同样计算了这４个种间的分歧年代,其范围为０．４－１．５百万年。结合化石,行为,动物地理等方面的资料,我们的结果提示：在猕猴属的进化过程中,恒河猴,食蟹猴,日本猴     

Molecular dating of a marine species,Eriocheir japonica (Decapoda: Grapsidae), corroborates cenozoic tectonic events and sea level fluctuation

Changes of coastal topography for Cenozoic Himalayan orogeny complicated the phylogeographical structure of marine species and deepened their divergences. To test the association between divergence and Cenozoic tectonic events, we analyzed the phylogeographical structure of Eriocheir japonica by combining molecular data and geographical environment events. The four distinct lineages obtained through phylogenetic reconstruction and network analysis demonstrated the significant genetic divergence among geographical populations. Furthermore, the divergence time between E. j. japonica in Japan and E. j. sinensis in China was about 10.5–11.5 mya, which was coincident with the opening of the Sea of Japan. The north-south divergence time (15.5–17.5 mya) was in the range of the occurrence of the Himalaya movement. We hypothesize that coastal topography, including the formation of Taiwan in the Himalaya movement and the opening of the Sea of Japan, contributed to the geographical subspeciation of marine species. Mitten crabs were inferred to originate from one ancient population with the oldest haplotype H6 and subsequently divide into northern and southern populations. Furthermore, the Japan lineage derived from northern population in China for the opening of the Sea of Japan.     

Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques

An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was sequenced to characterize genetic variation within and among 1,053 samples comprising five regional populations each of longtail macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta), and one sample each of Japanese (M. fuscata) and Taiwanese (M. cyclopis) macaques. The mtDNA haplotypes of longtail macaques clustered in two large highly structured clades (Fas1 and Fas2) of a neighbor-joining tree that were reciprocally monophyletic with respect to those representing rhesus macaques, Japanese macaques, and Taiwanese macaques. Both clades exhibited haplotypes of Indonesian and Malaysian longtail macaques widely dispersed throughout them; however, longtail macaques from Indochina, Philippines, and Mauritius each clustered in a separate well-defined clade together with one or a few Malaysian and/or Indonesian longtail macaques, suggesting origins on the Sunda shelf. Longtail macaques from Malaysia and Indonesia were far more genetically diverse, and those from Mauritius were far less diverse than any other population studied. Nucleotide diversity between mtDNA sequences of longtail macaques from different geographic regions is, in some cases, greater than that between Indian and Chinese rhesus macaques. Approximately equal amounts of genetic diversity are due to differences among animals in the same regional population, different regional populations, and different species. A greater proportion of genetic variance was explained by interspecies differences when Japanese and Taiwanese macaques were regarded as regional populations of rhesus macaques than when they were treated as separate species. Rhesus macaques from China were more closely related to both Taiwanese and Japanese macaques than to their own conspecifics from India.     

Genetic distinctness of isolated populations of an endangered marsupial, the mountain pygmy-possum, Burramys parvus

The mountain pygmy-possum, Burramys parvus, exists in isolated and fragmented populations in the Australian alps. To examine the degree of interpopulation divergence, mitochondrial cytochrome b and NADH dehydrogenase subunit 2 (NADH2) sequences were obtained from samples representing all populations of B. parvus. Three divergent mitochondrial DNA (mtDNA) lineages were identified which exhibited strong phylogeographical structure. This indicates the presence of three maternal clades corresponding to populations in the northern, central and southern Australian alps. Molecular clock estimates suggest that the mtDNA lineages diverged from one another 420-680 thousand years ago. On this basis it is argued that B. parvus populations have probably been isolated since the mid-Pleistocene, and that management should focus on maintaining viable B. parvus populations in each of the three regional localities.     

Mito‐nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)

Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW–NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW–NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito‐nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within‐species discord. Male‐mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation.     

Human-type ABO,MN, and Lewis blood groups,and Gm and Inv factors in several species of macaques

More than 1,000 blood samples were collected from macaques of speciesM. fuscata, M. cyclopis, M. irus, M. mulatta, M. nemestrina, andM. speciosa, and all or a part of them were tested for human-type ABO, MN, and Lewis blood groups, and Gm and Inv factors. Differences between and/or within species analogous to racial differences in man were markedly noted in the distribution of the ABO and Lewis blood groups. Saliva samples from a small number ofM. fuscata were tested quantitatively for the presence of H and Lewis substances, and it was found that almost all the animals were secretors of H, Le^a, and Le^b, independently of the Lewis blood groups of their red cells. Red cells of all macaques tested contained M or M-like, but not N^v(V), antigens, and no polymorphism of MN blood groups was present. Selected plasma samples fromM. fuscata, M. cyclopis, M. irus, andM. nemestrina were found to be negative for all Gm(1), Gm(2), Gm(4), and Inv(1) factors tested.This study was supported in part by the Japan Society for Promotion of Science Grant B-54 and by National Science Foundation Grant FJ 4.11. 1 as part of the Japan-U.S. Cooperative Science Program.     

Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes

The phylogeographical patterns and population genetic structures of Varicorhinus barbatulus in Taiwan were investigated based on genetic diversity of 34 allozyme loci and nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mtDNA. Allozyme and mtDNA analyses revealing evident geographical structuring suggest limited gene flow between populations (F(ST)=0.511 and 0.791, respectively). Low genetic variability within populations (P=5.56%; He=0.018) based on allozymes and significantly negative Tajima's D statistics based on mtDNA suggest that most populations in Taiwan may have originated from a small number of founders followed by demographic expansion. The gene genealogy of mtDNA identified six lineages corresponding to major drainages that were separated by the geological barriers due to vicariant events. A minimum spanning network based on nucleotide substitutions reflects divergence from populations of the Miao-li Plateau to northern and southern regions of the island. In contrast to a previous hypothesis that suggests an early invasion to eastern part of Taiwan prior to the lifting of central mountain range some one million years ago, the mtDNA genealogy and molecular dating reveal very recent colonization of the eastern population. Nested clade analyses revealing significant associations between genetic structure and geographical division identify past fragmentation and range expansion as major phylogeographical events that shaped the geographical distribution of this species in Taiwan.     

Genetic surfing,not allopatric divergence,explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern—local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation—not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male‐biased dispersal.     

Cloning and sequencing of rhesus monkey pepsinogen A cDNA

The complete nucleotide sequence of Rhesus monkey (Macaca mulatta) pepsinogen A (PGA) cDNA was determined from two partially overlapping cDNA clones, covering the whole coding sequence and part of the flanking sequences. The nucleotide and deduced amino acid sequences were compared to known PGA sequences from other species. The degree of similarity with human PGA appeared to be 96% at the nucleotide sequence level and 94% at the amino acid sequence level. In the coding region the divergence was highest in the activation peptide. The amino acid sequence similarity between Japanese monkey (Macaca fuscata) PGA and Rhesus monkey PGA was shown to be 99%. Using the cDNA as probe in Southern hybridization of EcoRI-digested human and Rhesus monkey genomic DNAs, PGA patterns with inter-individual differences were observed. The hybridization patterns are compatible with the existence of a PGA multigene family in both species.     

Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis)

We studied the mitochondrial DNA (mtDNA) polymorphism of 304 Macaca fascicularis fascicularis (M. f. fascicularis) individuals, representative of 4 cynomolgus macaque populations (Indochina, Indonesia, Philippines, and Mauritius). By sequencing a 590-bp fragment in the hypervariable II region of the D-loop region, we defined 70 haplotypes. The homologous region was also characterized in 22 Chinese Macaca mulatta and 2 Macaca sylvanus. The phylogenetic analysis confirms the monophyly of M. f. fascicularis and defines 2 haplotype groups inside the M. f. fascicularis clade: one "insular," encompassing 6 Philippines, 2 Mauritius, and 31 Indonesian haplotypes, the other "continental" that contains all Indochinese and 6 Indonesian haplotypes. Continental and insular group divergence time was estimated to be approximately 10(6) years before present (BP). Among Indonesian haplotypes, some have a continental origin. This suggests either direct migration from mainland to Indonesia or that remnant lineages from an ancient population genetically close to the mainland (i.e., in the Sunda Shelf, <550 000 years BP) were subsequently brought southward to Indonesia. The low nucleotide diversity in the Philippines population suggests a bottleneck following colonization by Indonesian individuals, around 110 000 years BP. mtDNA and further observations of nuclear genetic data corroborate the mixed origin (Indonesian/continental) hypothesis of Mauritius individuals and a population bottleneck.     

Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island

Ameiva chrysolaema is distributed across the island of Hispaniola in the West Indies. The species is restricted to dry lowlands between major mountain ranges and along the southern and eastern coasts. Phylogenetic and phylogeographic analyses of mtDNA sequence variation from 14 sampling localities identify at least three independent evolutionary lineages, separated from one another by major mountain ranges. Nested clade phylogeographic analysis (NCPA) suggests a complex history of population fragmentation, consistent with geological evidence of seawater incursions into the Azua and Enriquillo basins during the Pliocene/Pleistocene (approximately 1.6 mya). Significantly negative Fu's F(S) values and parameters of mismatch distributions suggest that formerly fragmented populations have recently expanded their ranges. Significantly large average population clade distances (APCD) for two sampling localities in the Azua basin suggest secondary contact at these localities of previously separated populations. The distribution of haplotypes among polymorphic populations of A. chrysolaema suggests that variation in dorsal pattern represents a polymorphism within evolutionary lineages. Ameiva leberi is ecologically indistinguishable from and syntopic with A. chrysolaema. Genetic data suggest that A. leberi is a junior synonym of A. chrysolaema.     

Extreme levels of intra-specific divergence among Cape Peninsula populations of the Cape galaxias,Galaxias zebratus Castelnau 1861, reveals a possible species complex

The Cape galaxias, Galaxias zebratus, is part of the paleao-endemic fauna characteristic of the south-western Cape, South Africa, and is the only galaxiid found in continental Africa. A 284-bp fragment of the cytochrome b region of the mtDNA was sequenced from 48 individual galaxiids, representing 10 populations from the Cape Peninsula. Five sequences, for four additional populations sampled at the extremes of the species range, were obtained from the literature. Analysis of cyt b mtDNA from these 14 populations of G. zebratus revealed five distinct and highly divergent lineages with low levels of intra-population mtDNA haplotype diversity. A new and distinct genetic lineage is described from the southern part of the Cape Peninsula. Estimates of genetic divergence between populations ranged from <1% to >17%. The observed level of sequence divergence represents the largest yet reported for any single fish species. The distribution of these lineages and their degree of sequence divergence refutes a model of isolation by distance. Results suggest that periods of low sea level may have been important in creating opportunities and alternative routes for dispersal and migration for Cape Peninsula populations.     

Phylogeography of Bufo marinus from its natural and introduced ranges.

The marine toad, Bufo marinus, has a broad natural distribution extending from the south-west of the USA to southern Peru and the central Amazon. It was introduced to several localities in the Caribbean and Pacific Oceans to control sugar cane pests. We sequenced 468 bp of mitochondrial DNA (mtDNA) containing the ND3 gene, and flanking tRNA genes from toads spanning the broad natural and introduced ranges. Consistent with the known history of introductions and expected effects of serial bottlenecks, mtDNA within introduced populations in Hawaii and Australia was uniform and most closely related to samples from eastern Venezuela and French Guiana. However, mtDNA nucleotide diversity in the geographic region spanning the source areas is also relative low (0.18-0.46%) and the absence of variation in the introduced populations precludes quantitative assessment of the reduction in genetic diversity. Unexpectedly, there was a large phylogeographic break (5.4% sequence divergence) within the natural range separating populations east and west of the Venezuelan Andes. We hypothesize that the two major lineages of B. marinus were isolated by the uplift of the eastern Andean cordillera which was completed approximately 2.7 Ma. Another species of the marinus group, B. paracnemis, had mtDNA paraphyletic, with marinus, being nested within the eastern lineage. Thus, at least one speciation event within the marinus group postdates the split within marinus. These findings suggest that the taxonomy of B. marinus should be re-evaluated and that the search for pathogens to control Australian populations should be conducted in populations from both lineages in the natural range.     

The divergence of two independent lineages of an endemic Chinese gecko,Gekko swinhonis,launched by the Qinling orogenic belt

The genetic structure and demographic history of an endemic Chinese gecko, Gekko swinhonis, were investigated by analysing the mitochondrial cytochrome b gene and 10 microsatellite loci for samples collected from 27 localities. Mitochondrial DNA data provided a detailed distribution of two highly divergent evolutionary lineages, between which the average pairwise distance achieved was 0.14. The geographic division of the two lineages coincided with a plate boundary consisting of the Qinling and Taihang Mts, suggesting a historical vicariant pattern. The orogeny of the Qinling Mts, a dispersal and major climatic barrier of the region, may have launched the independent lineage divergence. Both lineages have experienced recent expansion, and the current sympatric localities comprised the region of contact between the lineages. Individual‐based phylogenetic analyses of nucDNA and Bayesian‐clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level at localities outside of the contact region can be explained by the different inheritance patterns and male‐biased dispersal in this species. High genetic divergence, long‐term isolation and ecological adaptation, as well as the morphological differences, suggest the presence of a cryptic species.     

Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus

The grasshopper Oedaleus decorus is a thermophilic insect with a large, mostly south-Palaearctic distribution range, stretching from the Mediterranean regions in Europe to Central-Asia and China. In this study, we analyzed the extent of phylogenetic divergence and the recent evolutionary history of the species based on 274 specimens from 26 localities across the distribution range in Europe. Phylogenetic relationships were determined using sequences of two mitochondrial loci (ctr, ND2) with neighbour-joining and Bayesian methods. Additionally, genetic differentiation was analyzed based on mitochondrial DNA and 11 microsatellite markers using F-statistics, model-free multivariate and model-based Bayesian clustering approaches. Phylogenetic analyses detected consistently two highly divergent, allopatrically distributed lineages within O. decorus. The divergence among these Western and Eastern lineages meeting in the region of the Alps was similar to the divergence of each lineage to the sister species O. asiaticus. Genetic differentiation for ctr was extremely high between Western and Eastern grasshopper populations (F(ct)=0.95). Microsatellite markers detected much lower but nevertheless very significant genetic structure among population samples. The nuclear data also demonstrated a case of cytonuclear discordance because the affiliation with mitochondrial lineages was incongruent in Northern Italy. Taken together these results provide evidence of an ancient separation within Oedaleus and either historical introgression of mtDNA among lineages and/or ongoing sex-specific gene flow in this grasshopper. Our study stresses the importance of multilocus approaches for unravelling the history and status of taxa of uncertain evolutionary divergence.     

Phylogeography of the flathead mullet Mugil cephalus in the north-west Pacific as inferred from the mtDNA control region

The population genetic structure and historical demography of the flathead mullet Mugil cephalus were investigated using the mtDNA control region (CR) sequences (909–1015 bp) of 126 individuals collected from seven locations in the north-west Pacific between 2005 and 2007. Haplotype diversity ( h = 0·9333–1·000) and nucleotide diversity (π = 0·0046–0·1467) varied greatly among the sampling locations. Phylogenetic analysis of the CR sequences indicated that M. cephalus in the north-west Pacific belongs to two highly divergent lineages (lineages 1 and 2), with the inferred population structure being closely associated with the distribution of both lineages. Two populations were identified, one from the East China Sea and the other from the South China Sea. The former samples were obtained from Taiwan and Qingdao of north China and associated with lineage 1 haplotypes. The latter samples were collected from the Philippines, Pearl River of South China and two samples from Japan, all of which were associated with lineage 2. Japanese samples from Okinawa and Yokosuka had different degrees of mixing between lineages 1 and 2. Historical demographic variables in both populations indicated that Pleistocene glaciations had a strong impact on M. cephalus in the north-west Pacific, resulting in a recent demographic decline of the East China Sea population but in demographic equilibrium for the South China Sea population. Japan appears to be a contact zone between lineages 1 and 2, but it may also be indicative of coexistence between resident and migratory populations. Further global studies are required to clarify the taxonomic status of this cosmopolitan species.