四种犬科（Canidae）动物线粒体DNA分子进化

以９种限制性内切酶分析家犬,狼,赤狐,貉共７只动物的一粒体ＤＮＡ限制性片段长度多态性（ｍｔＤＮＡＲＦＬＰ）,通过双酶解法构建各种动物的限制性内切酶图谱,用ＵＰＧ法,ＮＪ法和简略法分析这些动物之间的遗传关系。结果表明,１．犬的个体差异小,而赤弧的个体间遗传分化程度非常高;２．犬和狼的亲缘关系很近,应是同一种动物;３．在属间关系中,犬属与狐属的关系较接近,貉属是一个较早分化的独立分支。     

中国牦牛线粒体DNA多态性及遗传分化

用２０种限制性内切酶分析了我国５个牦牛群体９０个个体的限制性片段长度多态性,其中ＡｖａＩ,ＡｖａＩＩ、ＢｇｌＩＩ、ＥｃｏＲＩ．ＨｉｎｄＩＩＩ、ＨｐａＩ６个酶切类型具有多态性,共发现５种ｍｔＤＮＡ单倍型,每种单倍型中检出５０－５５个位点,并利用双酶切制定出其物理图谱。我国牦牛群体ｍｔＤＮＡ多样度ＨＴ为０．１０６５,群体内的平均一致性概率为０．８９６６,表明我国牦牛群体ｍｔＤＮＡ多态性较贫乏,群体间的平均净遗传距离Ｐｅｔ为０．０００２０１,群体基因分化系数Ｇｓｔ为０．０２９１,我国牦牛群体ｍｔＤＮＡ变异只有２．９１％来自群体间的差异,群体间的分化程度较低。并根据报道,比较了牦牛和其他家养牛种的ｍｔＤＮＡ遗传分化,估计出牦牛和普通牛、瘤牛的分化时间大约分别在１．１－２．２百万年和１．０１－１．０２百万年之间。     

中国貉随机扩增多态DNA及其亚种分化关系

对来自陕西、云南、越南、安徽和广西等地的８只中国貉（Ｎｙｃｔｅｒｅｕｔｅｓｐｒｏｃｙｏｎｉｄｅｓ）进行随机扩增多态ＤＮＡ分析。应用２８个１０ｂｐ的随机引物,平均每只貉获得的ＲＡＰＤ标记数约为１３０条。遗传距离计算结果显示,中国貉个体间的平均遗传距离指数值为１１．２０％,最大值为１４．９３％,最小值为２．９４％。以赤狐（Ｖｕｌｐｅｓｖｕｌｐｅｓ）为外群,应用ＰＨＹＬＩＰ３．０计算软件包中的ＵＰＧＭＡ和ＮＪ聚类方法构建分子系统树。结果表明,不同地理群体间的中国貉存在遗传分化;中国貉可分为４组：（１）广西貉,（２）安徽貉,（３）陕西貉,（４）云南貉和越南貉。其中安徽貉和广西貉间的关系稍近,陕西貉则与云南貉－越南貉稍近。对合中国貉的形态分类、地理分布、ｍｔＤＮＡ多态分析以及进化遗传学的观点,认为陕西貉、广西貉和安徽貉可能与云南貉－越南貉具有等同的分类地位。     

板齿鼠线粒体DNA的研究

本文应用ＡｐａＩ、ＢａｍＨＩ、ＢｃｌＩ、ＢｇｌＩ、ＣｌａＩ、ＥｃｏＲＩ、ＥｃｏＲＶ、ＨｉｎｄＩＩ、ＰｓｔＩ、ＰｖｕＩＩ、ＳａｃＩ、ＳｃａＩ和ＸｂａＩ等１３种限制性内切酶对板齿鼠线粒体ＤＮＡ（ｍｔＤＮＡ）进行限制性片段长度多态（ＲＦＬＰ）分析,并用双酶解法构建其限制性内切酶图谱。结果表明板齿鼠存在３种ｍｔＤＮＡ单倍型,可通过限制酶ＰｖｕＩＩ、ＨｉｎｄＩＩ和ＡｐａＩ区分,呈现ＤＮＡ多态性和种内遗传变异。与小家鼠、褐家鼠ｍｔＤＮＡ限制性片段的数据相比较,板齿鼠和这两种鼠ｍｔＤＮＡ存在明显差异。板齿鼠ｍｔＤＮＡ限制性内切酶图谱的建立,为进一步系统研究鼠科动物的遗传分化提供了依据。     

线粒体DNA和人类进化

线粒体ＤＮＡ（ｍｔＤＮＡ）由于自身比较独特的遗传特性（母系遗传、缺乏重组和进化速率高）而被广泛地应用于人类群体的起源和演化研究。通过对其全序列的限制性酶切和Ｄ－环高变区序列数据的分析,ｍｔＤＮＡ较好地阐明了人类学中诸如现代人类起源、人群过去动态的估计以及单个人群的区域性微分化和人口历史学等问题。综述了近年来世界各人群ｍｔＤＮＡ的研究进展、研究方法的改进、ｍｔＤＮＡ与核基因标记结果的异同、ｍｔＤＮＡ     

中国大陆若干群体的黑果蝇的线粒体DNA多态性研究

本文研究了果蝇Ｄ．ｖｉｒｉｌｉｓ种群Ｄ．ｖｉｒｉｌｉｓ线粒体ＤＮＡ（ｍｉｔｏｃｈｏｎｄｒｉａｌＤＮＡ,ｍｔＤＮＡ）的多态性。用９种限制性内切酶ＸｂａⅠ,ＥｃｏＲⅠ,ＰｓｔⅠ,ＨｉｎｄⅢ,ＢｇｌⅡ,ＳａｃⅠ,ＳｃａⅠ,ＥｃｏＲＶ和ＰｕｖⅡ,对青岛、南京、上海、宁波与泉州５个Ｄ．ｖｉｒｉｌｉｓ群体的ｍｔＤＮＡ进行了限制性片段长度多态性（ｒｅｓｔｒｉｃｔｉｏｎｆｒａｇｍｅｎｔｓｌｅｎｇｔｈｐｏｌｙｍｏｒｐｈｉｓｍ,ＲＦＬＰ）的研究。在５群体中,发现５种不同的酶切图谱,它们彼此之间的遗传差异π为０．４６％－１．７６％,群体内遗传差异πｉｊ为０．００％－０．３３％,群体间的差异ｄｘｙ,为０．００％－０．８２％。分布于中国大陆的Ｄ．ｖｉｒｉｌｉｓ的群体间遗传差异在总遗传差异中所占比例γｓｔ值为２４．６２％。我们发现,Ｄ．ｖｉｒｉｌｉｓ的栖息环境对ｍｔＤＮＡ的遗传变异有十分明显的影响,而不同地理纬度的群体之间其遗传距离并无倾群（ｃｌｉｎｅ）表现。     

黑果蝇（D.virilis）自然群体遗传多态研究

利用９种限制性内切酶对Ｄ．ｖｉｒｉｌｉｓ兰州群体作了ｍｔＤＮＡ的ＲＦＬＰ分析,结合其他地区Ｄ．ｖｉｒｉｌｉｓ群体的ｍｔＤＮＡ的ＲＦＬＰ数据,用ＵＰＧＭＡ法构建了聚类图。发现大陆Ｄ．ｖｉｒｉｌｉｓ聚成明显的３支：兰州和青岛群体、华东群体、福建群体,呈一纬度梯度分布。单纯以地理隔离不能解释Ｄ．ｖｉｒｉｌｉｓ自然群体间的遗传差异。温度依赖性的选择可能是纬度梯度分布的维持机制。     

银鲴自然群体线粒体DNA的遗传分化

运用２１种限制性内切酶对银鲴自然群体进行了ｍｔＤＮＡ的限制性片断长度多态性（ＲＦＬＰ）分析。发现银鲴自然群体存在丰富的ｍｔＤＮＡ多态性,从４个群体３９个个体中,共检测到１２种单倍型,对这一现象的成成因进行了探讨。依据单倍型和群体的系统发育关系,结合地理分布的资料,对其现今分布区相互间的历史联系及其对银鲴起源和分化的影响进行了分析。     

树鼠mtDNA限制性内切酶图谱及其与小家鼠褐家鼠的新缘关系

本实验用Ａｐａ Ｉ,ＡＶａ Ｉ,Ｂａｍ ＨＩ＜ＢｃｌＩ,Ｃｌａ Ｉ,Ｅｃｏ ＲＩＥｃｏ ＲＶ,Ｈｐａ Ｉ,Ｐｓｔ Ｉ,Ｐｖｕ Ⅱ,ＳｃａＩ,ＸｂａＩ等１３种限制性内切酶分析树鼠的ｍｔＤＮＡ限制性片段长度多态性,并用双酶解法构建了其中８种酶的限制性内切酶图谱。根据限制性片段差异法和分子钟,计算并讨论树鼠和小家鼠、褐家鼠的ｍｔＤＮＡ遗传距离和亲缘关系。结果表明树鼠与褐家鼠的关系较接近,两者的分歧时间在     

DNA似近距离及进化时间的估算

在似近分析和Ｎｅｉ氏遗传距离的基础上,给出了ＤＮＡ似近距离计算公式,并以ＤＮＡ似近距离估算类群间的分歧时间（进化时间）,应用１０种限制内切酶对猕猴属（ｇｅｎｕｓ Ｍａｃａｃａ）内５个种ｍｔＤＮＡ的切点数据计算了这５个种的ＤＮＡ似近距离和进化时间,比较由ＤＮＡ似近距,遗传距离构建的歧化树和Ｆｏｏｄｅｎ及Ｄｅｌｓｏｎ的形态歧化树表明,除遗传距离的歧化树外,其它三种歧化树都有一个共同点,就是熊猴（Ｍ．ａ     

Population structure and genetic diversity of metamorphic and paedomorphic populations of the tiger salamander,Ambystoma tigrinum

Genetic relationships, population subdivision and genetic diversity were estimated from mtDNA and allozyme data for two subspecies of tiger salamander, one of which is obligately metamorphic and the other polymorphic for paedomorphosis (larval reproduction). Far greater genetic differentiation exists between subspecies than within subspecies, suggesting that the subspecies have evolved in allopatry. Values of F_st calculated from both mtDNA and allozymes were greater than 0.400 for each subspecies. Significant population subdivision was detected even on a microgeographic scale. This extensive population subdivision indicates that populations can respond to extremely localized selection pressures. In the case of paedomorphosis, populations in permanent water should evolve paedomorphosis as long as the appropriate genes exist. For both mtDNA and allozymes, comparisons of population structure within the polymorphic subspecies and between polymorphic and metamorphic subspecies reveal no discernible effects of paedomorphosis. However, a comparison of paedomorphic and metamorphic populations of the polymorphic subspecies showed significantly higher mtDNA diversity in paedomorphic populations. The discrepancy between the allozyme and mtDNA results may be due to the lower effective population size of mtDNA compared to autosomal genes.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

Evolutionary history of the honey bee Apis mellifera inferred from mitochondrial DNA analysis

Variability of mitochondrial DNA (mtDNA) of the honey bee Apis mellifera L. has been investigated by restriction and sequence analyses on a sample of 68 colonies from ten different subspecies. The 19 mtDNA types detected are clustered in three major phylogenetic lineages. These clades correspond well to three groups of populations with distinct geographical distributions: branch A for African subspecies (intermissa, monticola, scutellata, andansonii and capensis), branch C for North Mediterranean subspecies (caucasica, carnica and ligustica) and branch M for the West European populations (mellifera subspecies). These results partially confirm previous hypotheses based on morphometrical and allozymic studies, the main difference concerning North African populations, now assigned to branch A instead of branch M. The pattern of spatial structuring suggests the Middle East as the centre of dispersion of the species, in accordance with the geographic areas of the other species of the same genus. Based on a conservative 2% divergence rate per Myr, the separation of the three branches has been dated at about 1 Myr BP.     

Genetic variation and bill size dimorphism in a passerine bird, the reed bunting Emberiza schoeniclus

In passerine birds morphological differentiation in bill size within species is not commonly observed. Bill size is usually associated with a trophic niche, and strong differences in it may reflect the process of genetic differentiation and, possibly, speciation. We used both mitochondrial DNA (mtDNA) and nuclear microsatellites to study genetic variation between two subspecies of reed bunting, Emberiza schoeniclus schoeniclus and E.s. intermedia , along their distributional boundary in western Europe. These two subspecies are characterized by a high dimorphism in bill size and, although breeding populations of the two subspecies are found very close to each other in northern Italy, apparently no interbreeding occurs. The observed morphological pattern between the two subspecies may be maintained by geographically varying selective forces or, alternatively, may be the result of a long geographical separation followed by a secondary contact. MtDNA sequences of cytochrome b and ND5 (515 bp) showed little variation and did not discriminate between the two subspecies, indicating a divergence time of less than 500 000 years. The analysis of four microsatellite loci suggested a clear, although weak, degree of genetic differentiation in the large- and small-billed populations, as indicated by F _ST and R _ST values and genetic distances. The correlation between bill size and genetic distance between populations remained significant after accounting for the geographical distances between sampling localities. Altogether, these results indicate a very recent genetic differentiation between the two bill morphs and suggest that a strong selection for large bills in the southern part of the breeding range is probably involved in maintaining the geographical differentiation of this species.     

MtDNA COI‐COII marker and drone congregation area: An efficient method to establish and monitor honeybee (Apis mellifera L.) conservation centres

Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of nonlocal subspecies of bees which has had an adverse impact on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. To restore the original diversity of this local honeybee subspecies, different conservation centres were set up in Europe. In this study, we established a black honeybee conservation centre Conservatoire de l'Abeille Noire d'Ile de France (CANIF) in the region of Ile‐de‐France, France. CANIF's honeybee colonies were intensively studied over a 3‐year period. This study included a drone congregation area (DCA) located in the conservation centre. MtDNA COI‐COII marker was used to evaluate the genetic diversity of CANIF's honeybee populations and the drones found and collected from the DCA. The same marker (mtDNA) was used to estimate the interactions and the haplotype frequency between CANIF's honeybee populations and 10 surrounding honeybee apiaries located outside of the CANIF. Our results indicate that the colonies of the conservation centre and the drones of the DCA show similar stable profiles compared to the surrounding populations with lower level of introgression. The mtDNA marker used on both DCA and colonies of the conservation centre seems to be an efficient approach to monitor and maintain the genetic diversity of the protected honeybee populations.     

Phylogeny of mitochondrial DNA clones in tassel-eared squirrels Sciurus aberti

The tassel-eared squirrel, Sciurus aberti , includes six subspecies which occupy restrictive and apparently identical habitats in Ponderosa pine forests in the south-western United States and Mexico; the strict habitat requirement of this species is based on dietary requirements which are only fulfilled in these forests. To examine evolutionary relationships among certain subspecies of S. aberti , we obtained estimates of nucleotide diversity within subspecies as well as nucleotide divergence between subspecies using mitochondrial DNA (mtDNA) analysis. Restriction site polymorphisms were identified in samples of the four US subspecies: S. a. aberti (Abert), S. a. kaibabensis (Kaibab), S. a. ferreus (Ferreus), and S. a. chuscensis (Chuska) Fourteen mtDNA clones were resolved that were, with one exception, uniquely subspecific. Dendrograms constructed by neighbour-joining and maximum parsimony methods revealed two major assemblages: (1) an Abert/Kaibab group; and (2) a Ferreus/Chuska group. The Abert vs. Ferreus clones exhibited the greatest net nucleotide divergence, with a lineage separation estimate approximating 572 000 years ago assuming a nucleotide substitution rate of 7.15 × 10^-9/year/site. Five out of ten Chuska squirrels shared a clone with one Abert sample; the relative sizes of these two populations and their respective ranges as well as their close proximity support the proposal for relatively recent intermixing of Abert and Chuska populations resulting in what appears to be Abert → Chuska migration. Nucleotide diversity within subspecies ranked as Kaibab < Ferreus < Abert < Chuska; the relatively high diversity for the Chuska sample is based on the apparent introgression of Abert mtDNA. The relative diversity exhibited by Kaibab, Ferreus and Aberti samples corresponds to the range size of the respective subspecies.     

Phylogeography of white-spotted Charr (Salvelinus leucomaenis) inferred from mitochondrial DNA sequences

The white-spotted charr (Salvelinus leucomaenis) is a coldwater-adapted fish distributed in far-eastern Asia. To assess phylogeographic patterns of this species over most of its range in the Japanese archipelago and Sakhalin Island, Russia, we examined nucleotide sequences of the mitochondrial DNA (mtDNA) cytochrome b region (557 bp) in 141 individuals from 50 populations. A total of 33 (5.5%) nucleotide positions were polymorphic and defined 29 haplotypes. Phylogenetic analysis assigned the observed haplotypes to four main clades, which were characterized by the idiosyncrasies and discontinuity of geographic distributions. The nested clade analyses revealed that the geographical distribution patterns of some haplotypes and clades were explained by historical event such as past fragmentation. Although substantial genetic differentiation was found among the four main clades, their geographic distributions overlapped extensively in several regions. Since white-spotted charr can potentially use both freshwater and marine environments, coexistence among different lineages can be attributed to secondary contact through range expansion by migratory individuals during multiple glacial periods after interglacial isolation. Finally, our data demonstrate that the current subspecies designation does not reflect the phylogeography of this species based on mtDNA analysis. Hierarchical analysis (AMOVA) also showed that genetic variation was far more pronounced within subspecies than among subspecies (i.e., among discrete regions). These results suggest that each population, rather than each subspecies, must be treated as an evolutionarily significant unit.     

A genetic comparison of two alleged subspecies of Philippine cynomolgus macaques

Two subspecies of cynomolgus macaques (Macaca fascicularis) are alleged to co‐exist in the Philippines, M. f. philippensis in the north and M. f. fascicularis in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies M. f. fascicularis to warrant the subspecies distinction M. f. philippensis. Am J Phys Anthropol 155:136–148, 2014. © 2014 Wiley Periodicals, Inc.     

The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis)

During the last glacial age, Afro-alpine habitats were widespread across the highlands of Ethiopia. A wolf-like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf-like ancestor, around 100,000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation approximately 15,000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation.     

Mitochondrial DNA polymorphisms in the two subspecies of Drosophila sulfurigaster: relationship between geographic structure of population and nucleotide diversity.

Recent empirical and theoretical studies on mitochondrial DNA (mtDNA) variation in higher animals have suggested that the extent of mtDNA polymorphism is largely affected by spatial population subdivision. To examine this we studied mtDNA polymorphism in two subspecies of Drosophila sulfurigaster: D. s. albostrigata and D. s. bilimbata. Drosophila sulfurigaster albostrigata is mainly distributed on the mainland of Southeast Asia. In contrast, D. s. bilimbata forms discontinuous populations on many islands scattered in the Pacific Ocean. Because of the difference in their distribution patterns, the two subspecies are thought to be different in the extent of spatial population subdivision. mtDNA was isolated from greater than 50 isofemale strains for each subspecies and were analyzed by eight restriction endonucleases. Nucleotide diversity within a population was higher in D. s. albostrigata than in D. s. bilimbata. However, haplotype diversity was 1.6 times greater in D. s. bilimbata (0.85) than in D. s. albostrigata (0.53). The large difference in overall heterogeneity was attributed to the difference in interpopulational nucleotide diversity. For the two subspecies the proportion of interpopulational gene diversity in a subdivided population was calculated to be 0.54 in D. s. bilimbata and 0.40 in D. s. albostrigata. These observations indicate that spatial population subdivision is a major factor in determining mtDNA polymorphism in these subspecies. The extent of mtDNA divergence between the subspecies was very high. The average nucleotide divergence between them was 7.6%, which is almost the interspecific level reported for other Drosophila species. The cause of the high degree of mtDNA divergence is discussed.