Phylogeography and Evolution of the Tanganyikan Cichlid Genus Tropheus Based upon Mitochondrial DNA Sequences

Abstract Lake Tanganyika harbors the oldest and most diverse species flock of cichlid fish. Many species are subdivided into numerous genetically and phenotypically distinct populations. Their present distribution and genetic structure were shaped by a series of lake level fluctuations which caused cycles of isolation and admixis and promoted dispersal events. One of the best examples of this phenomenon is the genus Tropheus. We present a comprehensive mtDNA phylogeny based upon 365 individuals of 55 populations from all over Lake Tanganyika, which suggests an almost-contemporaneous origin of eight major mitochondrial lineages about 700 Ka ago. While the distribution of seven lineages is restricted to particular sections of the lake shore, one lineage was found to have a much more widespread distribution. This particular lineage is subdivided into four sublineages which seem to have originated from a single dispersal event about 400 Ka. By using a molecular clock estimate in combination with geological data we derived a hypothetical scenario for the colonization history of Tropheus. Thereby we show a high degree of concordance between major changes of the lake level in the recent history of Lake Tanganyika and three distinct diversification events in this genus.     

Homogenization of Tandemly Repeated Nucleotide Sequences by Distance-Dependent Nucleotide Sequence Conversion

Previous work revealed that recurrent mutations (= mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the likelihood of heteroduplex formation decreases with increasing distance between the repeats and one assuming that it is constant. Patterns of mutation distribution obtained in computer simulations were compared with the distribution of mutations found in the repeated arrays in the NTS of seven rDNA clones. The patterns of mutations generated by the models assuming that the likelihood of heteroduplex formation decreases as distance between the repeats increases agreed with the patterns observed in rDNA; the patterns generated by the model assuming that the likelihood is independent of distance between repeats disagreed with the patterns observed in the rDNA clones. The topology of the heteroduplex formed between DNA in adjacent repeats predicts that the most frequently occurring conversions in the NTS repeated arrays will be shorter than the length of the repeat. The topology of the heteroduplex also predicts that if the heteroduplex leads to crossing over a circular repeat is excised. It is speculated that the circle can transpose or can be amplified via rolling circle replication and subsequently transpose. It is also shown that homogenization of the NTS repeated arrays proceeds at different rates in different species.     

西藏小型猪的线粒体DNA控制区分析

目的研究西藏小型猪的遗传标记以及与其他国内地方猪的亲缘关系。方法扩增102头西藏小型猪以及16头巴马小型猪、17头贵州香猪的线粒体DNA控制区,测序并与国内其他猪进行比较。结果西藏小型猪线粒体DNAD-loop区分三个区域。串联重复序列区处于中间位置,包含有15～29个10 bp的重复片段,分为A、B两种类型。D-loop 3′端340 bp,与国内其他猪的序列相同比较保守;5′端704 bp,共有22个变异位点。由22个变异位点中归纳出25个单倍型,其中有两种主要的单倍型,分别占34.4%和36.6%。根据三个转换位点：305、500、691,将西藏小型猪分成了两组,几乎与串联重复序列所分的A、B两组类型相对应。与西藏小型猪相比,巴马小型猪和贵州香猪D-loop 5′端变异位点较少,分别只有4种和2种单倍型,串联重复区也只有一个类型。结论西藏小型猪可能有两个母系祖先并且与我国西南地区的品种猪有较近的亲缘关系;不同的串联重复片段类型和5′端的变异位点可以联合组建西藏小型猪的遗传标记。     

Discriminating between Ixodes Ticks by Means of Mitochondrial DNA Sequences

Ticks of the genus Ixodes have recently assumed prominence because they frequently serve as vectors of important zoonoses, including Lyme disease and babesiosis. The morphological characteristics that have been used in their identification often are ambiguous and are useful solely at a particular stage of development. Here we report the DNA sequence of the mitochondrially encoded 16S rRNA gene of nine different Ixodes ticks and an outgroup from another genus, Dermacentor. The sequences readily discriminate between these ticks. Samples of I. dammini from the northeastern and upper midwestern United States differ from southeastern I. scapularis at about 2% of the nucleotides. This difference is about half that separating other members of the I. ricinus group of species, but exceeds typical levels of intraspecific variation. Two major clades exist within the I. ricinus complex. One includes I. cookei , I. hexagonus,and I. angustus. The other includes I. persulcatus, I. pacificus, I. muris, I. ricinus, I. scapularis, and I. dammini. We conclude that mtDNA sequences are useful for unravelling the systematics of these important vectors of human disease.     

Chromatin Packing,Repeated DNA Sequences and Gene Control

Neutralization of DNA by basic proteins promotes packing into a regular “crystalline” form. This model can explain the structure and functional organization of chromatins.     

鳄龟科和平胸龟科线粒体控制区序列分析和结构比较

本文参照龟类近缘种的线粒体DNA(mitochondrial DNA,mtDNA)控制区(control region,CR)及邻接序列,设计了二对特异引物,采用PCR和测序技术,获得了大鳄龟(Macroclemys temminckii)、小鳄龟(Chelydra serpentina)和平胸龟(Platysternon megacephalum)mtDNA CR区序列,其长度分别为1062bp、1124bp和1119bp;A T的含量分别为68.93%、69.34%和69.44%。序列分析显示,三种龟CR区3'末端均存在丰富的微卫星序列,其中大鳄龟和小鳄龟各有一段2bp的TA序列分别重复20和15次;小鳄龟另有一段5bp的TATAT序列重复13次;平胸龟则是一段10bp的AGTATGTTAT序列重复4次和一段17bp的GTTGTTATATAACATAT序列重复13次。本文还结合GenBank中已发表的其他6种龟鳖类动物的控制区序列,探讨了龟鳖类动物微卫星序列的类型及分布,结果表明:9种龟鳖类动物都存在丰富的微卫星序列,且微卫星所在位置及序列存在很大差异。     

Evolution of Repeated Sequence Arrays in the D-Loop Region of Bat Mitochondrial DNA

Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, θ and π, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites.     

新疆3种雅罗鱼线粒体DNA控制区序列的差异和系统进化关系

对分布在新疆的准噶尔雅罗鱼(Leuciscus merzbacheri)、贝加尔雅罗鱼(Leuciscus leuciscus baicalensis)和高体雅罗鱼(Leuciscus idus)3个鱼种共24尾个体的线粒体DNA D-loop控制区核苷酸序列进行了测定,获得24条长度为667—669bp的同源基因序列。3种雅罗鱼之间的序列差异在6．39％—9．89％之间,贝加尔雅罗鱼与高体雅罗鱼种间序列同源性高,变异程度小;贝加尔雅罗鱼与准噶尔雅罗鱼种间序列同源性最低,变异程度最大。所采集的贝加尔雅罗鱼两个地理群体(赛里木湖和额尔齐斯河)内mtDNA的平均核苷酸碱基序列差异为1．07％和1．08％;两群体间的序列差异为1．07％,显示两个地理群体间无明显分化。DNA序列数据显示,这3种鱼类线粒体DNAD-loop序列变异丰富,24尾个体呈现独自的单倍型。同源基因序列平均含AT碱基64．1％,GC碱基35．9％,显示准噶尔雅罗鱼、贝加尔雅罗鱼、高体雅罗鱼的线粒体DNAD-loop区核苷酸组成的不均一性。分子系统树提示,贝加尔雅罗鱼与高体雅罗鱼亲缘关系较近,准噶尔雅罗鱼是3种雅罗鱼中较古老的鱼种。     

Tandemly Repeated Sequence Families in Micronuclear DNA of the Ciliate Stylonychia pustulata1

One third of a collection of cloned Stylonychia pustulata micronuclear DNA PstI fragments were found to be of a similar size, consistent with their being members of a repetitious sequence family with a repeat size of about 160 base pairs. Cross-hybridization experiments confirmed that these small cloned fragments are related by sequence homology. Hybridization of the cloned repetitious sequences to PstI digested micronuclear DNA revealed a “ladder” of bands (step size = 160 base pairs), indicating that the repeats are found in tandem arrays. This is the first demonstration of highly repetitious, tandemly repeated sequences in a ciliated protozoan.     

基于叶绿体DNA非编码序列的蒙古扁桃谱系地理学研究

该研究选取中国西北干旱区第三纪孑遗植物蒙古扁桃（Amygdalus mongolica）,基于叶绿体DNA非编码trnH psbA序列对蒙古扁桃17个居群324个个体进行了谱系地理学研究。结果表明：（1）蒙古扁桃trnH psbA序列长度350 bp,变异位点63个,共有9种单倍型,居群间总遗传多样性为（H_t）为0.758,居群内平均遗传多样性为（H_s）为0.203,贺兰山东麓及阴山南麓边缘的居群具有较高的单倍型多样性及核苷酸多样性并固定较多特有单倍型,推测这2个地区是蒙古扁桃在第四纪冰期时的重要避难所。（2）AMOVA分析表明,居群间的遗传变异为83.84%,居群内的遗传变异为16.16%,居群间遗传分化系数N_st>G_st（N_st=0.733, G_st=0.655, P>0.05）,表明蒙古扁桃不存在明显的谱系地理结构;根据单倍型地理分布及网络关系图,把蒙古扁桃自然地理居群分为东、西两大地理组群,而且东、西地理组群没有共享单倍型;居群遗传结构分析表明,两大地理组群遗传分化较大。（3）蒙古扁桃居群在间冰期或冰期后经历了近期的居群扩张,由于奠基者效应使得多数居群只固定了单一的单倍型。     

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。     

黄海伪虎鲸mtDNA控制区序列的测定和初步分析

测定了黄海7 头伪虎鲸mtDNA 控制区5’端533 bp 的序列, 共发现54 个变异位点, 定义了4 种单元型。最大似然法和邻接法的系统树均把单元型聚为2 分支。两支之间没有共享单元型且无姊妹关系。分支间的核苷酸序列差异显著地超过了其它海豚类种间的序列差异水平, 提示传统意义上的伪虎鲸可能包括了具有显著遗传差别的不同物种, 迫切需要开展进一步的研究。     

Structure and Evolution of the Mitochondrial DNA Complete Control Region in the Lizard Lacerta dugesii (Lacertidae, Sauria)

Abstract We sequenced the complete control region (CR) and adjacent tRNAs, partial 12S rRNA, and cytochrome b (over 3100 bp) from eight individuals of Madeiran wall lizards, Lacerta dugesii, from four distinct island populations. The tRNAs exhibit a high degree of intraspecific polymorphisms compared to other vertebrates. All CR sequences include a minisatellite that varies in length between populations but is apparently fixed within them. Variation in minisatellite length appears between populations separated by apparently very short evolutionary time spans. Many motifs identified in the CR of other vertebrates are not highly conserved, although conserved blocks are identifiable between the few published reptile CR sequences. Overall there are extensive differences in the internal organization of the reptile CR compared to the more widely studied mammals and birds. Variability in the CR is lower than in cytochrome b, but higher than in 12S rRNA. Phylogenetic analysis of these sequences produces a well-resolved estimate of relationships between populations.     

动物mtDNA控制区及保守与异质

本文通过文献综述,对动物线粒体DNA控制区进行了阐述.从线粒体控制区（control region）基因组的研究出发,重点介绍了动物线粒体控制区基因组结构特点.主要结论：由于碱基替换、插入和缺失以及重复序列数目的变异致使D-loop成为mtDNA中变异最多的区域,但突变和结构重排并不是发生在整个D-loop区域,而是在高变区;大多研究集中在mtDNA D-loop保守区和异质方面：对D-loop序列分析,能较好地阐明动物的起源,在动物亲缘关系鉴定、系统进化和物种形成方式的研究等领域具有广阔的研究和应用前景.     

Polymorphisms in the Mitochondrial DNA Control Region and Frailty in Older Adults

Background

Mitochondria contribute to the dynamics of cellular metabolism, the production of reactive oxygen species, and apoptotic pathways. Consequently, mitochondrial function has been hypothesized to influence functional decline and vulnerability to disease in later life. Mitochondrial genetic variation may contribute to altered susceptibility to the frailty syndrome in older adults.

Methodology/Principal Findings

To assess potential mitochondrial genetic contributions to the likelihood of frailty, mitochondrial DNA (mtDNA) variation was compared in frail and non-frail older adults. Associations of selected SNPs with a muscle strength phenotype were also explored. Participants were selected from the Cardiovascular Health Study (CHS), a population-based observational study (1989–1990, 1992–1993). At baseline, frailty was identified as the presence of three or more of five indicators (weakness, slowness, shrinking, low physical activity, and exhaustion). mtDNA variation was assessed in a pilot study, including 315 individuals selected as extremes of the frailty phenotype, using an oligonucleotide sequencing microarray based on the Revised Cambridge Reference Sequence. Three mtDNA SNPs were statistically significantly associated with frailty across all pilot participants or in sex-stratified comparisons: mt146, mt204, and mt228. In addition to pilot participants, 4,459 additional men and women with frailty classifications, and an overlapping subset of 4,453 individuals with grip strength measurements, were included in the study population genotyped at mt204 and mt228. In the study population, the mt204 C allele was associated with greater likelihood of frailty (adjusted odds ratio = 2.04, 95% CI = 1.07–3.60, p = 0.020) and lower grip strength (adjusted coefficient = −2.04, 95% CI = −3.33– −0.74, p = 0.002).

Conclusions

This study supports a role for mitochondrial genetic variation in the frailty syndrome and later life muscle strength, demonstrating the importance of the mitochondrial genome in complex geriatric phenotypes.     

Fingerprinting of Cyanobacteria Based on PCR with Primers Derived from Short and Long Tandemly Repeated Repetitive Sequences

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.     

鲹科鱼类线粒体DNA控制区结构及系统发育关系

采用PCR技术获得了9种鲹科鱼类的线粒体DNA控制区全序列,并结合从GenBank中下载的3种鲹科鱼类的相应序列采用ClustalW排序后,对控制区结构进行分析,识别了其终止序列区、中央保守区和保守序列区3个区域,指出了终止相关序列的主体是TACAT与其反向互补序列ATGTA以及一系列保守序列(CSB-F、CSB-E、CSB-D和CSB-1、CSB-2、CSB-3),并给出了它们的一般形式,同时在康氏似鲹控制区的5′和3′两端发现重复序列。以尖吻鲈作为外类群,应用邻接法构建的分子系统树表明:鲹科鱼类分为鲹亚科、鰤亚科、鲳鲹亚科和鰆鲹亚科4个亚科,各自形成单系群;鲹亚科与鰤亚科形成姐妹群,鲳鲹亚科再与他们聚在一起,鰆鲹亚科处于鲹科鱼类的基部,与前面3个亚科聚在一起。     

A Gene with Specific and Global Effects on Recombination of Sequences from Tandemly Repeated Genes in Saccharomyces Cerevisiae

The preservation of sequence homogeneity and copy number of tandemly repeated genes may require specific mechanisms or regulation of recombination. We have identified mutations that specifically affect recombination among natural repetitions in the yeast Saccharomyces cerevisiae. The rrm3 mutation stimulates mitotic recombination in the naturally occurring tandem repeats of the rDNA and copper chelatin (CUP1) genes. This mutation does not affect recombination of several other types of repeated genes tested including Ty elements, mating type information and duplications created by transformation. In addition to stimulating exchange among the multiple CUP1 repeats at their natural chromosomal location, rrm3 also increases recombination of a duplication of CUP1 units present at his4. This suggests that the RRM3 gene may encode a sequence-specific factor that contributes to a global suppression of mitotic exchange in sequences that can be maintained as tandem arrays.     

Structure Analysis of Mitochondrial DNA Control Region Sequences and its Applications for the Study of Population Genetic Diversity of Acanthogobius ommaturus

Russian Journal of Marine Biology - Acanthogobius ommaturus, which belongs to the family Gobiidae, is a euryhaline, demersal fish widely distributed in coastal areas, harbors, and estuaries of...     

Frequency and Pattern of Heteroplasmy in the Control Region of Human Mitochondrial DNA

In this work, we present the results of the screening of human mitochondrial DNA (mtDNA) heteroplasmy in the control region of mtDNA from 210 unrelated Spanish individuals. Both hypervariable regions of mtDNA were amplified and sequenced in order to identify and quantify point and length heteroplasmy. Of the 210 individuals analyzed, 30% were fully homoplasmic and the remaining presented point and/or length heteroplasmy. The prevalent form of heteroplasmy was length heteroplasmy in the poly(C) tract of the hypervariable region II (HVRII), followed by length heteroplasmy in the poly(C) tract of hypervariable region I (HVRI) and, finally, point heteroplasmy, which was found in 3.81% of the individuals analyzed. Moreover, no significant differences were found in the proportions of the different kinds of heteroplasmy in the population when blood and buccal cell samples were compared. The pattern of heteroplasmy in HVRI and HVRII presents important differences. Moreover, the mutational profile in heteroplasmy seems to be different from the mutational pattern detected in population. The results suggest that a considerable number of mutations and, particularly, transitions that appear in heteroplasmy are probably eliminated by drift and/or by selection acting at different mtDNA levels of organization. Taking as a whole the results reported in this work, it is mandatory to perform a broad-scale screening of heteroplasmy to better establish the heteroplasmy profile which would be important for medical, evolutionary, and forensic proposes.