Repetitive sequences in Eurasian lynx (Lynx lynx L.) mitochondrial DNA control region

Mitochondrial DNA (mtDNA) control region (CR) of numerous species is known to include up to five different repetitive sequences (RS1-RS5) that are found at various locations, involving motifs of different length and extensive length heteroplasmy. Two repetitive sequences (RS2 and RS3) on opposite sides of mtDNA central conserved region have been described in domestic cat (Felis catus) and some other felid species. However, the presence of repetitive sequence RS3 has not been detected in Eurasian lynx (Lynx lynx) yet. We analyzed mtDNA CR of 35 Eurasian lynx (L. lynx L.) samples to characterize repetitive sequences and to compare them with those found in other felid species. We confirmed the presence of 80 base pairs (bp) repetitive sequence (RS2) at the 5' end of the Eurasian lynx mtDNA CR L strand and for the first time we described RS3 repetitive sequence at its 3' end, consisting of an array of tandem repeats five to ten bp long. We found that felid species share similar RS3 repetitive pattern and fundamental repeat motif TACAC.     

Genetic diversity of Besermyans inferred from mitochondrial DNA polymorphism

The first data are presented on mtDNA diversity in Besermyans, the Finno-Ugric ethnic group related to Udmurts. An analysis of mtDNA polymorphism showed that Besermyans stood out from the other populations of Volga-Ural region due to the presence of a large proportion of the Mongoloid component. The sample of Besermyans contained East Eurasian haplotypes not detected in ethnic populations of the Volga region and Cisurals, while they were detected in South Siberia, mostly among Turkic-speaking populations. An analysis of the genetic distances between Besermyans and the neighboring ethnic groups showed that Besermyans were distant from other populations of Volga-Ural region and close to Turkic-speaking populations of South Siberia. Thus, the data obtained favor the suggestion on the mixed Udmurto-Turkic origin of Besermyans.     

Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region

Forest musk deer ( Moschus berezovskii ) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity ( π  = 0.0568), haplotype diversity ( h  =   0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species.     

Genetic diversity analysis of Arius manillensis (Siluriformes: Ariidae) using the mitochondrial control region

Arius manillensis is a Philippine endemic species and is an economically important fishery resource in Laguna de Bay, the largest lake in the country. Drastic reduction in population sizes of A. manillensis has been recorded in the past, which may have resulted in genetic bottleneck. In this study, the genetic diversity and population structure of A. manillensis in Laguna de Bay were assessed using the mitochondrial DNA control region. Specimens were obtained from three localities along Laguna de Bay, namely Binangonan (n?=?27), Tanay (n?=?29), and Calamba (n?=?30). Of the 86 DNA sequences generated, 22 distinct haplotypes were observed. There were four unique haplotypes for Binangonan, six for Calamba, and five for Tanay. There were two haplotypes common to the three sites. The maximum likelihood tree and median-joining network showed little geographic separation among the haplotypes. Chi-square test showed no significant differentiation in A. manillensis from the three sites. The overall computed F(ST) was 0.0144, indicating small genetic differentiation in A. manillensis from the three localities sampled. Likewise, analysis of molecular variance showed a greater percentage of variation within population (98.62%) than variation among populations (1.38%; P?=?0.21). Total haplotype diversity and nucleotide diversity among the specimens from the three sites were 0.775 and 0.013, respectively. The high haplotype diversity coupled with low nucleotide diversity observed in this study confirms that genetic bottleneck occurred in A. manillensis which was followed by population expansion. This is also supported by the non-significant values for both Tajima's D and Fu's F. Furthermore, multimodal mismatch distribution plots were generated, which is consistent with the model of spatial range expansion followed by demographic expansion.     

Genetic diversity of Setipinna taty (Engraulidae) populations from the China Sea based on mitochondrial DNA control region sequences

The genetic diversity of Setipinna taty, which is commercially fished in the China Sea, was studied based on mitochondrial DNA control region sequences. PCR was used to amplify the control region fragment in 100 individuals of S. taty collected from Weihai (WH), Yantai (YT), Zhoushan (ZS), Xiangshan (XS), and Ninghai (NH) in China. A control region fragment of 656 bp was successfully sequenced in these 100 individuals. The A+T content of this S. taty control region was 71.7%; 172 variable sites and 62 haplotypes were found. Nucleotide diversity in the WH, YT, ZS, XS, and NH groups was 0.0228, 0.0247, 0.0441, 0.0126, and 0.0238, respectively. The haplotype diversity was 0.984, 0.911, 0.989, 0.926, and 0.979, respectively. Analysis of molecular variance showed that 97.95% of genetic variation was within populations, and only 2.05% among populations. The neighbor-joining phylogenetic tree obtained based on genetic distance showed that no significant genealogical structure exists throughout this range of S. taty. These results indicate no apparent geographical differentiation in the comparison of Yellow Sea and East China Sea populations of S. taty. Within the control region, we identified an extended termination-associated sequence domain, a central conserved sequence block domain and a conserved sequence block domain; insertions of short tandem repeat sequence segments were found at the 5' end of the control region.     

Genetic diversity and population history of two related seabird species based on mitochondrial DNA control region sequences

Geographical variation in two related seabird species, the razorbill (Alca torda) and common guillemot (Uria aalge), was investigated using sequence analysis of mitochondrial DNA (mtDNA) control regions. We determined the nucleotide sequence of the variable 5' segment of the control region in razorbills and common guillemots from breeding colonies across the Atlantic Ocean. The ecology and life history characteristics of razorbill and common guillemot are in many respects similar. They are both considered highly philopatric and have largely overlapping distributions in temperate and subarctic regions of the North Atlantic, yet the species were found to differ widely in the extent and spatial distribution of mtDNA variation. Moreover, the differences in genetic differentiation and diversity were in the opposite direction to that expected from a consideration of traditional classifications and current population sizes. Indices of genetic diversity were highest in razorbill and varied among colonies, as did genotype frequencies, suggestive of restrictions to gene flow. The distribution of genetic variation suggests that razorbills originated from a refugial population in the south-western Atlantic Ocean through sequential founder events and subsequent expansion in the east and north. In common guillemots, genetic diversity was low and there was a lack of geographical structure, consistent with a recent population bottleneck, expansion and gene flow. We suggest that the reduced level of genetic diversity and differentiation in the common guillemot is caused by an inherent propensity for repeated population bottlenecks and concomitantly unstable population structure related to their specialized feeding ecology.     

Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism

We used sequence polymorphism of the mitochondrial DNA D-loop (968 bp excluding the tandem repeat region) to determine genetic diversity of horses inhabiting Cheju (a southern island of Korea). Seventeen haplotypes with frequencies from 1.5 to 21.5% were found among 65 Cheju horse samples. Genetic diversity (h) of the 17 haplotypes was calculated to be 0.91, indicating that the extant Cheju horse population consists of diverse genetic groups in their maternal lineage. Phylogenetic analysis showed that 17 types of Cheju (D-loop sequences determined), 5 Mongolian, 6 Arabian, 3 Belgian, 2 Tsushima, 2 Yunnan, 1 Przewalskii, and 3 Thoroughbred horses (published sequences for the latter seven breeds) showed that Cheju horses were distributed into many different clusters in the tree. Four Mongolian horses clustered with separate Cheju horse groups, showing that some Cheju horses are clearly of Mongolian origin. The analysis of partial sequences (284 bp) of the D-loop of 109 horses showed that Thoroughbred, Mongolian, Lipizzan, and Arabian breeds are as diverse as Cheju horses. Our data together with others' suggest that most horse breeds tested with reasonably sufficient numbers of samples are diverse in their maternal lineages and also are not uniquely different from each other.     

Genetic diversity of wild reindeer (<Emphasis Type="Italic">Rangifer tarandus</Emphasis>) of Taimyr: Analysis of polymorphism of the control region of mitochondrial DNA

Based on an analysis of the polymorphism of nucleotide sequences (n = 111) of the mtDNA control region (left domain), the genetic diversity of the largest population of wild reindeer Rangifer tarandus in Eurasia, which inhabits Taimyr peninsula, was studied. High levels of haplotype (H) and nucleotide (π) diversity (0.987 and 0.018, respectively) were revealed, which indicate the long existence and the sufficiently stable growth of this population. The absence of long periods of abrupt decrease in the number of the Taimyr wild reindeer population and/or facts of formation of its genetic diversity as a result of mixing of genetically distant conspecific populations is supported by the data on the pattern of mismatch distributions and the topology of the phylogenetic tree. The low level of genetic differences between reindeer from the western, central, and eastern groups reflects their common origin and close relationship.     

Genetic structure of brown trout (Salmo trutta, L.) populations from south-western France: data from mitochondrial control region variability

The genetic relationships between several French Atlantic populations of brown trout were analysed using polymerase chain reaction-single-strand conformation polymorphism and sequencing of two parts of the mitochondrial control region. Ten mitochondrial haplotypes were identified, separated by a small number of mutations. The distribution of these haplotypes confirmed our hypothesis of the existence of two genetically well-differentiated groups of populations in this area, which has already been suggested using nuclear markers. Nuclear and mitochondrial markers, however, show different patterns of genetic differentiation: some populations which belong to one group according to allozyme results appear to be part of the other when using mitochondrial DNA. The origin of these different forms is discussed; they seem to belong to the Atlantic grouping. Nevertheless, the hypothesis of an ancestral and a modern form suggested for northern populations does not appear valid in this particular case.     

Genetic diversity and phylogenetic relationships of Malayan tapir (Tapirus indicus) populations in the Malay Peninsula based on mitochondrial DNA control region

Biodiversity and Conservation - The Malayan tapir (Tapirus indicus) is an endangered species in Southeast Asia (SEA). Over the years, there has only been a few reports on its population genetic...     

舟山小黄鱼线粒体DNA D-loop区序列变异的遗传多样性分析

小黄鱼(Pseudosciaena polyactis)为我国重要海产经济鱼类之一,过度捕捞和环境污染等因素造成其资源日益衰退。研究小黄鱼种群遗传结构对其资源的保护及其可持续利用有十分重要的意义。该研究采用聚合酶链式反应(PCR)技术对浙江舟山附近海域小黄鱼种群53个个体的mtDNA D-loop区全序列进行扩增,序列长度在795~801bp之间,长度差异不大。采用ClustalX1.83、MEGA3.1、DnaSP4.0等生物信息学软件进行遗传多样性分析,结果显示:53条小黄鱼线粒体DNA D-loop区的T、C、A和G碱基平均含量分别为30.3%、23.1%、32.3%和14.3%,排除13处核苷酸的插入或缺失后,共检测到93处转换和颠换位点,约占分析序列总长度的11.6%,其中包括53个单一多态位点和40个简约信息位点,共确定了52种单倍型,单倍型多样性(hd)为0.9993,单倍型间的平均遗传距离为0.012,转换/颠换平均值为4.305,平均核苷酸差异数(k)为9.73875,核苷酸多样性(π)为0.01233,表明舟山小黄鱼遗传多样性处于中等水平。     

基于线粒体DNA控制区的斑翅草螽不同地理种群遗传分化研究

采用PCR扩增结合DNA克隆测序技术,分析了斑翅草螽Conocephalus maculates 9个地理种群mtDNA控制区序列的变异及遗传多样性。切除侧翼RNA基因序列后,最终获得的斑翅草螽mtDNA控制区比对后全长为676 bp,平均碱基组成T(37.8%),C(11.7%),A(41.3%)和G(9.1%)。共检测到98个可变位点,占总位点数的14.5%,其中,9处碱基插入/缺失,74处转换(40个T/C,34个A/G),50处颠换(18个A/T,11个T/G,15个A/C,6个C/G)。共定义46个单倍型,其中,4个为种群间共享单倍型(H02、H05、H08和H10),其余42个为各种群独有单倍型,包括6个种群内共享单倍型(H09、H11、H15、H18、H26和H38)。单倍型总数占实验个体总数的69.7%,除四川峨眉山外,其余种群单倍型百分比均﹥50%。通过两两地理种群间的FST值差异显著性检验,将这些群体分为4组,分别为SC+CQ,GX+FLB+HN+YN,XZ和HB。以长瓣草螽C.gladiatus、峨眉草螽C.emeiensis、悦鸣草螽C.melaenus、竹草螽C.bambusanus为外群,构建的斑翅草螽mtDNA控制区单倍型NJ法系统树形成3个自举支持度较高的分支,其中,分支A由28种单倍体组成,包括本研究中除四川峨眉山(SC)和重庆万州(CQ)以外的7个种群;分支B由12种单倍体组成,包含除菲律宾拉乌尼翁(FLB)和江西南昌(JX)以外的7个种群;分支C由6种单倍型组成,全部来自西藏林芝(XZ)的单倍型。聚类结果表明,斑翅草螽不同地理种群间的遗传分化并不明显,即使是两两群体间FST值差异显著的群体,也未能形成完全独立的分支。     

Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region

The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.     

Spread of mitochondrial DNA haplotypes in population of scots pine (Pinus sylvestris L.) in northern European Russia

The variability of the first intron of the nad7 gene of Scots pine mitochondrial DNA was investigated in 15 populations in northeast of European Russia and in three populations in Belarus, Sweden, and the Voronezh region. Restriction Fragments Length Polymorphism of the PCR product (PCR-RFLP) and sequencing were used. The investigated samples were compared with the populations studied previously [1, 2]. The haplotype, which is absolutely dominant in the eastern part of the Scots pine range [1, 2], was fixed in the Kirov, Arkhangelsk, and Kostroma regions; Komi; and Chuvashia. The extreme northeastern discovery of an alternative haplotype that is present in most European populations and occurs the most frequently in eastern Scandinavia was made in the Vologda region. These results support the hypothesis that the population of Scots pine in northeast Russia and Fennoscandia originated from different glacial refugia.     

Genetic diversity and population structure of miiuy croaker populations in East China Sea revealed by the mitochondrial DNA control region sequence

The genetic diversity and population structure of the miiuy croaker (Miichthys miiuy) were investigated. Seventy-six individuals were sampled from six localities of the East China Sea. Genetic variation in DNA sequences was examined from the 5′-end of the mitochondrial DNA control region. High levels of haplotype diversity (h = 0.99333) in the control region were detected, indicating a high level of genetic diversity. A total of 81 polymorphic sites were found, and 65 haplotypes were defined. The results of AMOVA analysis indicated that 97.9% of the genetic variation contained within populations and 2.14% occurred among populations. No significant genealogical branches or clusters were recognized on the NJ tree. Tests of neutral evolution and analysis of mismatch distribution suggested that miiuy croaker might have undergone a population expansion. The knowledge on genetic diversity and genetic structure will be crucial to establish appropriate fishery management stocks for the species.     

Genetic diversity of silver pomfret (Pampus argenteus) populations from the China Sea based on mitochondrial DNA control region sequences

The genetic diversity of silver pomfret (Pampus argenteus) from the Bohai, East China, and South China Seas was investigated using mitochondrial DNA (mtDNA) control region sequence data. We found high levels of variation with 17 haplotypes among the 45 individuals (h = 0.88, π = 0.006). AMOVA analysis detected significant structuring among China Sea silver pomfret (P < 0.05, F_ST = 0.050), which indicates significant genetic differentiation. No significant differentiation between Bohai Sea and East China Sea samples was detected (P > 0.05). Whether silver pomfret from the South China Sea exhibit a different demographic history than those from the Bohai and East China Seas remains to be determined.     

Genetic diversity of moose (Alces alces L.) in Eurasia

Polymorphism of nucleotide sequence of D-loop fragment of the mitochondrial DNA was studied in 20 moose from several local populations on the territory of Eurasia. Three main haplotype variants of D-loop were detected by molecular phylogenetic method, which formed three clusters named European, Asian and American. Intraspecies variation in the length of HVSI of D-loop of the mitochondrial DNA of moose was revealed. In the Far Eastern and Yakutian moose, haplotypes with a 75-bp deletion were found, which were most similar with haplotypes (also with the deletion), earlier observed in North American moose [1]. The highest diversity of the haplotypes of mitochondrial DNA is characteristic of Yakutia and the Far East (where three haplotype variants were found), which demonstrates the probable role of the region as the center of the species or as the region of ancient population mixture. The geographic region might be considered as a probable source of ancient moose migrations from Asia to America, basing on the data of distribution of mitochondrial haplotypes of D-loop and alleles of MhcAlal-DRB1. Divergence of nucleotide sequences of haplotypes with the 75-bp deletion (forming the American cluster on the phylogenetic tree) was the lowest (0.4%), which evidences respectively recent origin of the group of haplotypes. In Europe, only haplotypes of mitochondrial DNA referred to European variant were observed. Basing on analysis of variation of nucleotide sequences of D-loop, exon 4 of kappa-Casein and exon 2 of MhcALal-DRB1, we demonstrated that Eurasian moose studied belong to the unique species, which has probably passed through a bottle neck. The time of the origin of modern diversity of D-loop haplotypes of the species was estimated as 0.075-0.15 Myr ago.     

Study of chloroplast DNA polymorphism in the sunflower (Helianthus L.)

Russian Journal of Genetics - The polymorphism of microsatellite loci of chloroplast genome in six Helianthus species and 46 lines of cultivated sunflower H. annuus (17 CMS lines and 29 Rf-lines)...