基于线粒体DNA的中国亚洲象种群遗传多样性及种群遗传结构

亚洲象是我国国家一级保护动物.本文利用非损伤性取样法,以亚洲象粪便中脱落的肠道上皮细胞为DNA来源,选用线粒体DNA作为分子标记,对分布于我国境内的亚洲象种群的遗传结构和种群遗传多样性进行研究.本研究得到mtDNA序列片段长度为556 bp,经对178个个体进行扩增结果分析,共得到24个单倍型.在5个地理种群中,除南滚河种群外,其他4个种群中的114个个体共享同一单倍型,南滚河种群与其他种群间未观察到共享单倍型.系统发生分析,观察到中国境内现有亚洲象种群在进化上分为两大分支,α和β.其中分支α中包含除南滚河种群外的4个地理种群,分支β仅含有南滚河种群,表明南滚河种群与其他4个地理种群间存在明显分化.遗传多样性分析结果表明,中国境内的亚洲象种群的遗传多样性水平较低,分析原因认为是栖息地破碎化阻断了种群间有效的基因交流.     

Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): taxonomic implications for the Great Lakes species flock

Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco ( Coregonus zenithicus ). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens of C. zenithicus and the related species C. artedi , C. hoyi , C. kiyi , and C. clupeaformis . DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.     

Population structure and speciation in the genus Tursiops based on microsatellite and mitochondrial DNA analyses

Bottlenose dolphins (Tursiops truncatus) have a world-wide distribution, and show morphotypic variation among regions. Distinctions between coastal and pelagic populations have been documented; however, regional patterns of differentiation had not been previously investigated in a wider geographic context. We analysed up to nine different populations from seven different areas of the world by mitochondrial DNA and microsatellite DNA markers, and found differentiation among all putative regional populations. Both mtDNA and microsatellite DNA data show significant differentiation, suggesting restricted gene flow for both males and females. Dolphins in coastal habitat showed less variability and were in most cases differentiated from a pelagic lineage, which could suggest local founder events in some cases. Two coastal populations recently classified as belonging to a new species, T. aduncus, were each highly differentiated from populations of the truncatus morphotype, and from each other, suggesting a possible third species represented by the South African aduncus type.     

Population biology ofHortaea werneckii based on restriction patterns of mitochondrial DNA

Fifteen isolates ofHortaea werneckii, causative agent of tinea nigra in man, were examined with respect to restriction fragment length polymorphisms of mitochondrial DNA. Seven types of mtDNA, interpreted as populations, could be distinguished, with similarities between the restriction patterns ranging from 32 to 79%. Much of the variance originated from length mutations. Of the seven populations four represented isolates from man, two of which also comprised isolates from other sources. This makes adaptation ofH. werneckii towards association with man in its evolution unlikely; similarity in the chemical and/or physical characteristics of the different isolation sources, viz. salinity, seems more probable. mtDNA types were not correlated with geographic origin. Isolates with the same mtDNA type are widely geographically distributed.     

Genetic diversity and structuring of the grey wolf population from the Central Balkans based on mitochondrial DNA variation

The Dinaric-Balkan grey wolf population used to be at a border between the large remaining Eastern European populations and the largely eradicated Western European populations. During the last few decades we have witnessed the Western European wolf population recovery. Substantial genetic variation has previously been reported in the Balkan wolf population, but rigorous genetic characterization has not been done for its central parts. The aims of this research were to determine genetic diversity based on mtDNA sequence variability, to infer possible population structuring, to find genetic signals of population expansions or bottlenecks and to evaluate phylogenetic position of the grey wolf population from the Central Balkans. Six haplotypes were detected, of which three have only been found in the Balkan region. These haplotypes belong to both haplogroups previously determined in Europe. Based on our mtDNA sequence analyses, the Dinaric-Balkan wolf population is vertically differentiated into “western” (Croatia/Bosnia and Herzegovina) and “eastern” (Serbia/Macedonia) subpopulations. None of the results support assumption of population expansion. Instead, significantly positive values for Tajima's D and Fu's Fs may suggest recent population bottleneck. Obtained data may be helpful in observation to which extent gene pool from the Balkans contribute to newly founded populations in Western Europe.     

Genetic diversity of longtail macaques (Macaca fascicularis) on the island of Mauritius: an assessment of nuclear and mitochondrial DNA polymorphisms

BACKGROUND: Individuals from an introduced population of longtail macaques on Mauritius have been extensively used in recent research. This population has low MHC gene diversity, and is thus regarded as a valuable resource for research. METHODS: We investigated the genetic diversity of this population using multiple molecular markers located in mitochondrial DNA and microsatellite DNA loci on the autosomes and the Y chromosome. We tested samples from 82 individuals taken from seven study sites. RESULTS AND CONCLUSIONS: We found this population to be panmictic, with a low degree of genetic variability. On the basis of an mtDNA phylogeny, we inferred that these macaques' ancestors originated from Java in Asia. Weak gametic disequilibrium was observed, suggesting decay of non-random associations between genomic genes at the time of founding. The results suggest that macaques bred in Mauritius are valuable as model animals for biomedical research because of their genetic homogeneity.     

Gene diversity analysis of mitochondrial DNA, microsatellites and allozymes in landlocked Atlantic salmon

This study investigates the patterns of genetic diversity detected in allozymes, mtDNA, and microsatellites, in order to assess their relative efficacy to differentiate sympatric landlocked salmon populations and to estimate changes in genetic diversity between wild and first-generation hatchery fish. Overall, the three genetic markers indicated a genetic differentiation between two sympatric populations of Lake Saint-Jean, Québec. MtDNA and microsatellites also showed significant differences between wild and first-generation hatchery fish originating from the same river. Allozyme analysis was the most limited approach due to the low genetic diversity detected and the necessity to kill specimens. Although low polymorphism was found in mtDNA, it was the most discriminant marker between wild populations. Microsatellite analysis appears to be a promising approach due to its high sensitivity in differentiating wild populations, in detecting changes in allele composition between wild and first-generation hatchery fish and its potential for increased resolution by augmenting the number of polymorphic loci. Given the benefits and disadvantages of the three methods, the combination of mtDNA and microsatellite analyses will best address our research objectives.     

Population structure and local differentiation in the delicate loach, Niwaella delicata, as revealed by mitochondrial DNA and morphological analyses

Population structures of the delicate loach, Niwaella delicata, were inferred from morphology and restriction fragment length polymorphism (RFLP) analysis of part of the mitochondrial DNA (mtDNA) of 25 populations, representing the species range in central Honshu Island. The existence of two types of morphological variation corresponding to regional distributions, the "Pacific slope type" and "Sea of Japan slope type," has been known in N. delicata. Our morphological reexamination of the two types revealed some discrepancies in their distribution pattern. Therefore, we reclassified two new color types corresponded to their distribution areas as "gathered spots type (G type)" and "scattered spots type (S type)," respectively. The present classification of G and S types is closely related to the mtDNA divergence pattern. The current analysis also indicated that each G and S type population was further divided into two genetic groups, corresponding to geographic proximity. In spite of marked morphological differentiation, the genetic diversity between G and S type populations (1.153%) was comparable only to that reported for intraspecific levels in most freshwater fishes. Moreover, in the population of which the color patterns of all fish were characterized to the S type, mtDNA haplotypes corresponding to G and S types were sympatrically detected. This result indicates secondary contact between the two type populations and the possibility that they are not reproductively isolated. Received: June 11, 1999 / Revised: September 30, 2000 / Accepted: January 16, 2001     

Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease

The mitochondrial genome (mtDNA) represents a tiny fraction of the whole genome, comprising just 16.6?kilobases encoding 37 genes involved in oxidative phosphorylation and the mitochondrial translation machinery. Despite its small size, much interest has developed in recent years regarding the role of mtDNA as a determinant of both aging and age-associated diseases. A number of studies have presented compelling evidence for key roles of mtDNA in age-related pathology, although many are correlative rather than demonstrating cause. In this review we will evaluate the evidence supporting and opposing a role for mtDNA in age-associated functional declines and diseases. We provide an overview of mtDNA biology, damage and repair as well as the influence of mitochondrial haplogroups, epigenetics and maternal inheritance in aging and longevity.     

The influence of past and present climate on the biogeography of modern mammal diversity

Within most terrestrial groups of animals, including mammals, species richness varies along two axes of environmental variation, representing energy availability and plant productivity. This relationship has led to a search for mechanistic links between climate and diversity. Explanations have traditionally focused on single mechanisms, such as variation in environmental carrying capacity or evolutionary rates. Consensus, though, has proved difficult to achieve and there is growing appreciation that geographical patterns of species richness are a product of many interacting factors including biogeographic history and biological traits. Here, we review some current hypotheses on the causes of gradients in mammal richness and range sizes since the two quantities are intimately linked. We then present novel analyses using recent datasets to explore the structure of the environment-richness relationship for mammals. Specifically, we consider the impact of glaciation on present day mammalian diversity gradients. We conclude that not only are multiple processes important in structuring diversity gradients, but also that different processes predominate in different places.     

Inferring Pongo conservation units: a perspective based on microsatellite and mitochondrial DNA analyses

In order to define evolutionarily significant and management units (ESUs and MUs) among subpopulations of Sumatran (Pongo pygmaeus abelii) and Bornean (P. p. pygmaeus) orangutans we determined their genetic relationships. We analyzed partial sequences of four mitochondrial genes and nine autosomal microsatellite loci of 70 orangutans to test two hypotheses regarding the population structure within Borneo and the genetic distinction between Bornean and Sumatran orangutans. Our data show Bornean orangutans consist of two genetic clusters—the western and eastern clades. Each taxon exhibits relatively distinct mtDNA and nuclear genetic distributions that are likely attributable to genetic drift. These groups, however, do not warrant designations as separate conservation MUs because they demonstrate no demographic independence and only moderate genetic differentiation. Our findings also indicate relatively high levels of overall genetic diversity within Borneo, suggesting that observed habitat fragmentation and erosion during the last three decades had limited influence on genetic variability. Because the mtDNA of Bornean and Sumatran orangutans are not strictly reciprocally monophyletic, we recommend treating these populations as separate MUs and discontinuing inter-island translocation of animals unless absolutely necessary.     

Population evolution of western Canary Island lizards (Gallotia galloti): 4-base endonuclease restriction fragment length polymorphisms of mitochondrial DNA

The mitochondrial DNA evolution of the western Canary Island lacertid, Galloti galloti , was studied using six restriction enzymes ( Hae III, Mva I, Hin fl, Taq I, Msp I and Dsa V). The population phytogeny ( G. stehlini , from the adjacent island of Gran Canada, was used as an outgroup) based on 56 restriction fragments from the first two enzymes indicates two distinct lineages; a 'northern' lineage of La Palma, north Tenerife and south Tenerife populations and a 'southern' lineage of populations from Gomera and Hierro. The relationships within the northern lineage are also supported by an additional analysis of 132 restriction fragments from the remaining four enzymes. This molecular phylogeny argues for the recognition of two subspecies corresponding to the two main lineages and against the recognition of the six current subspecies which are based on inadequate 'conventional' criteria.     

Population genetic structure, phylogeography and spawning philopatry in walleye (Stizostedion vitreum) from mitochondrial DNA control region sequences

Mitochondrial (mt) DNA control region sequences were used to test the genetic and phylogeographic structure of walleye Stizostedion vitreum populations at different geographical scales: among spawning sites, lake basins, lakes, and putative glacial refugia in the Great Lakes region. Sequencing 199 walleye revealed nucleotide substitutions and tandemly repeated sequences that varied in copy number, as well as in sequence composition, in 1200 bp of the mtDNA control region. Variable numbers of copies of an 11-bp tandem repeat showed no geographical patterning and were not used in further analyses. Substitutions in the other areas of the control region yielded 19 haplotypes, revealing phylogeographic structure and significant differences among glacial refugia, lakes, basins and some spawning sites. Differences among spawning populations were consistent with reduced gene flow, philopatry and possible natal homing. Analysis of spawning populations showed consistency of genotypic frequencies among years and between males and females, supporting philopatry in both sexes. The unglaciated plateau in southern Ohio, USA housed a very different haplotype that diverged prior to the Missouri, Mississippi and Atlantic glacial refugia types. Haplotypes from the three refugia colonized the Great Lakes after retreat of the Wisconsin glaciers, and their present distribution reflects the geography of their prior isolation and differential colonization. Populations that became associated with spawning localities appear to have diverged further due to philopatry, resulting in fine-scale phylogeographic structuring.     

Genetic discrimination of wild and hatchery populations of brook charr, Salvelinus fontinalis (Mitchill), in Ontario using mitochondrial DNA analysis

Two brood stocks of brook charr, Sulvelinus fontinalis , are currently maintained by the Ontario Ministry of Natural Resources. The Nipigon brood stock originated from Lake Nipigon, in north-central Ontario, while the Hills Lake stock is believed to have been produced by hybridizing several strains (including charr from a Pennsylvania hatchery as well as charr from Ontario) in the past. The mitochondrial DNA (mtDNA) variability of these brood stocks was characterized using 51 hexanucleotide restriction enzymes. Eleven restriction enzymes, Acc I, Am I, Bun I, Bun II, Hind III, Nco I, Nde I, Nhe I, Nsi I, Pst I and Sph I, were polymorphic between the two brood stocks. Eight hatchery mtDNA haplotypes were detected showing a maximum of 0.41 % sequence divergence. Seven haplotypes are present in the Hills Lake strain, and two in the Nipigon strain. These mtDNA haplotypes are useful markers to determine the degree of reproductive success between planted and native fish. In one comparison in southern Ontario, less than 20% of the wild fish sampled from the head water regions of a small drainage entering Lake Erie could have resulted from random introgression with hatchery fish planted further downstream, because most of these fish possessed a unique Acc 1 cut site. This is one of the few examples in stock analysis studies where such a high degree of genetic discrimination is evident between hatchery and native fish.     

Population structure and gene flow of the Atlantic walrus (Odobenus rosmarus rosmarus) in the eastern Atlantic Arctic based on mitochondrial DNA and microsatellite variation

The population structure of the Atlantic walrus, Odobenus rosmarus rosmarus , was studied using 11 polymorphic microsatellites and restriction fragment length polymorphism detected in the NADH-dehydrogenase ND1, ND2 and ND3/4 segments in mtDNA. A total of 105 walrus samples were analysed from northwest (NW) Greenland, east (E) Greenland, Svalbard and Franz Joseph Land. Two of the 10 haplotypes detected in the four samples were diagnostic for the NW Greenland sample, which implied that the group of walruses in this area is evolutionary distinct from walruses in the other three areas. One individual sampled in E Greenland exhibited a Pacific haplotype, which proved a connection between the Pacific walrus and walruses in eastern Greenland. The Franz Joseph Land, Svalbard and E Greenland samples shared the most common haplotype, indicating very little differentiation at the mtDNA level. Gene flow ( Nm ) estimates among the four areas indicated a very restricted exchange of female genes between NW Greenland and the more eastern Atlantic Arctic samples, and a closer relationship between the three samples composing the eastern Atlantic Arctic. The genetic variation at 11 polymorphic microsatellite loci grouped individuals into three populations, NW Greenland, E Greenland and a common Franz Joseph Land–Svalbard population, which were connected by moderate gene flow.     

The investigation and diagnosis of pathogenic mitochondrial DNA mutations in human urothelial cells

Patients with mitochondrial DNA disease are amongst the most challenging to diagnose and manage given the striking phenotypic and genetic heterogeneity, which characterise these conditions. Recently, we and others have demonstrated the m.3243A>G mutation, one of the most common mitochondrial DNA pathogenic mutations, is present at clinically relevant levels in urinary epithelium, thus providing a practical, non-invasive test for diagnosis and mutation screening. In this study we further evaluate the use of these cells in detecting the m.3243A>G mutation, other mtDNA tRNA gene point mutations including the m.8344A>G mutation and single large-scale mtDNA deletions. We observe a robust relationship between m.3243A>G levels in urothelial cells and clinically affected tissues that does not change with time. Conversely, single large-scale mtDNA deletions can be detected in urothelial cells, with higher levels present in younger patients with more severe disease, but generally mtDNA deletion levels are not representative of those seen in a clinically affected tissue. Our results have implications for the diagnosis, management and counselling of families with mtDNA disease.     

Population biology and stock assessment of Pristipomoides filamentosus on the Mahe Plateau, Seychelles

The population of P. filamentosus around the periphery of the Mahe Plateau was studied using data derived from commercial handline fishing operations between November 1989 and December 1990. Sex ratio was close to one. Fork length was in the range 25.6–79.8 cm: at first sexual maturity, 36–38 cm for females and 40–42 cm for males. Spawning occurred from October to April peaking between February and April and in November.
The length ( f.l. , cm)–weight (kg) relationship was W =0.00005353 × f.l. ^2.7004. The von Bertalanffy growth parameters, estimated from length frequency data, were K =0.2875 and L _inf=81.7 cm. Mortality rates, estimated from length converted catch curve analysis, were Z =0.811, F =0.277 with M =0.534 derived from Pauly's empirical formula. Jones' length cohort analysis gave an estimate of F= 0.294 for the fully exploited part of the stock, and a density of 2.59 t km⁻² for the periphery of the plateau from 75 to 150 m depth. The Lesley constant catchability model, applied to the results of intensive fishing around isolated banks, derived a mean density estimate of 2.99t km⁻². The sustainable yield was estimated to be 233–268 tonnes per annum and the catch in 1990 was 200 tonnes.     

Chloroplast and mitochondrial DNA diversity in Theobroma cacao

The variability of cocoa (Theobroma cacao) cytoplasmic genomes has been investigated. A total of 177 cocoa clones was surveyed for restriction fragment length polymorphism (RFLP) in chloroplast DNA and in mitochondrial DNA using two restriction endonucleases and various heterologous cytoplasmic probes. A high level of polymorphism was found for the mitochondrial genome. This study points up a structuring of the species that fits with the distinction between the Criollo and Forastero populations. In contrast to all previous analyses, a higher level of polymorphism is found among the Criollo clones while the Forastero clones form quite a homogeneous group.     

Ovine mitochondrial DNA: restriction enzyme analysis, mapping and sequencing data

Restriction endonuclease fragment patterns of mitochondrial DNA (mtDNA) in sheep were analysed with 11 enzymes. Four breeds (Merinolandschaf, Rhoenschaf, Schwarzkoepfiges Fleischschaf and Skudde) of domestic sheep and European Mouflon were examined. A restriction map with 28 cleavage sites of seven enzymes was established. KpnI and PstI do not cut ovine mtDNA. Two EcoRI fragments of Merinolandschaf, Rhoenschaf and Mouflon each were cloned and partially sequenced. Intraspecific nucleotide sequence differences within 1.101 kb ranged from 0.09 to 0.27%. Hybridization analysis with a fragment of porcine mtDNA along with sequencing data from cloned fragments was used for orientation of the restriction map along the bovine sequence. Ovine mtDNA sequences encompassing parts of the Cyt.b-, ND5-, CoIII- and ATPase6 genes were compared with the corresponding sequences of the bovine mtDNA.