Structure and evolution of teleost mitochondrial control regions

We amplified and sequenced the mitochondrial control region from 23 species representing six families of teleost fish. The length of this segment is highly variable among even closely related species due to the presence of tandemly repeated sequences and large insertions. The position of the repetitive sequences suggests that they arise during replication both near the origin of replication and at the site of termination of the D-loop strand. Many of the conserved sequence blocks (CSBs) observed in mammals are also found among fish. In particular, the mammalian CSB-D is present in all of the fish species studied. Study of potential secondary structures of RNAs from the conserved regions provides little insight into the functional constraints on these regions. The variable structure of these control regions suggests that particular care should be taken to identify the most appropriate segment for studies of intraspecific variation. Correspondence to: T.D. Kocher     

Tempo and mode of sequence evolution in mitochondrial DNA of HawaiianDrosophila

Summary Sequence comparisons were made for up to 667 bp of DNA cloned from 14 kinds of HawaiianDrosophila and five other dipteran species. These sequences include parts of the genes for NADH dehydrogenase (subunits 1, 2, and 5) and rRNA (from the large ribosomal subunit). Because the times of divergence among these species are known approximately, the sequence comparisons give insight into the evolutionary dynamics of this molecule. Transitions account for nearly all of the differences between sequences that have diverged by less than 2%; for these sequences the mean rate of divergence appears to be about 2%/Myr. In comparisons involving greater divergence times and greater sequence divergence, relatively more of the sequence differences are due to transversions. Specifically, the fraction of these differences that are counted as transversions rises from an initial value of less than 0.1 to a plateau value of nearly 0.6. The time required to reach half of the plateau value, about 10 Myr, is similar to that for mammalian mtDNA. The mtDNAs of flies and mammals are also alike in the shape of the curve relating the percentage of positions at which there are differences in protein-coding regions to the time of divergence. For both groups of animals, the curve has a steep initial slope ascribable to fast accumulation of synonymous substitutions and a shallow final slope resulting from the slow accumulation of substitutions causing amino acid replacements. However, the percentage of all sites that can experience a high rate of substitution appears to be only about 8% for fly mtDNA compared to about 20% for mammalian mtDNA. The low percentage of hypervariable sites may be a consequence of a functional constraint associated with the low content of guanine and cytosine in fly mtDNA.     

Diversity and evolution of T-cell receptor variable region genes in mammals and birds

 The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes. Received: 20 May 1999 / Revised: 13 July 1999     

中华攀雀线粒体基因组全序列测定与分析

该研究使用长PCR扩增和引物步移法测定了中华攀雀(Remiz consobrinus)线粒体基因组全序列,在对序列进行拼接和注释的基础上,分析了其结构、序列组成及蛋白编码基因密码子使用情况等,并对22个tRNA和2个rRNA的二级结构以及控制区结构进行了预测及系统发育分析,为雀形目鸟类的系统发育研究提供了新信息。中华攀雀线粒体基因组全长16737bp,GenBank登录号KC463856,碱基A、T、C、G的含量分别为27.8%、21.5%、35.4%及15.3%,37个基因排列顺序与已报道的其他鸟类基本一致,包含13个蛋白编码基因、22个tRNA基因、2个rRNA基因及1个非编码的控制区(D-loop),有18对基因间共存在77bp的间隔,7对基因间共存在30bp的重叠。除ND3基因的起始密码子为ATT外,其余均为标准的ATG,11个蛋白编码基因的终止密码子为TAA、TAG、AGA或AGG,2个为不完全终止密码子T(COⅢ、ND4)。除tRNASer-AGNDHU臂缺失外,其余21个tRNA均可形成典型的三叶草结构,在出现的27处碱基错配中有19处为常见的G-U错配。SrRNA和LrRNA二级结构分别包含3个结构域47个茎环结构和6个结构域60个茎环结构,与所发表的其他鸟类rRNA二级结构大体一致。中华攀雀控制区发现了同样存在于其他鸟类控制区的保守框F-box、D-box、C-box、B-box、Bird similarity-box和CSB1-box。该研究支持将攀雀科作为独立的科,同时,支持莺总科与攀雀科的单系性。     

Molecular characterization and mitochondrial sequence variation in two sympatric species of Proechimys (Rodentia: Echimyidae) in French Guiana

Variations in mitochondrial DNA characters were used to characterize two morphologically similar and sympatric species of Neotropical terrestrial rodents of the genus Proechimys (Mammalia: Echimyidae). We sequenced both cytochrome b (1140 pb) and part of the control region (445 pb) from four individuals of P. cuvieri and five of P. cayennensis from French Guiana, which allowed us to depict intra- and inter-specific patterns of variation. The phylogenetic relationships between the nine sequences evidence the monophyly of each species, and illustrate that more polymorphism might exist within P. cuvieri than within P. cayennensis. By developing species-specific primers to amplify a fragment of the cytochrome b gene, we were able to identify 50 individuals of Proechimys spp. caught in two localities of French Guiana. In both sites of primary rainforests, we showed that the two species live in syntopy, and this observation emphasizes the need to document ecological differences which should exist in order to diminish inter-specific competition.     

安徽汉族群体mtDNA高变区I序列多态性分析

以Anderson标准序列作为对照,用GeneDOC软件确定42个安徽汉族无关个体的mtDNA高变区I序列在线粒体基因组中的位置,通过序列比对软件clustalX分析安徽汉族群体mt DNA高变区I序列多态性,共检测到38种单倍型和57个变异位点.在mtDNA高变区I序列中14个bp的高变结构域中,安徽汉人16183位点变异率高达38%,在16187位点的变异率为4.8%.同时发现,安徽汉人与成都汉人在mtDNA高变区I 16183和16189位点的变异率接近,明显高于广东汉人.     

The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): great difference in the A+T-rich region compared to Liriomyza trifolii

The complete mitochondrial genome sequence of Liriomyza sativae Blanchard (15,551 bp) was determined and analyzed in this study. The circular genome contained 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and an A + T-rich region. The initiation codons of COI and ND1 were ‘ATCA’ and ‘GTG’, respectively. ND2 gene used the truncated termination codon ‘T’. All the tRNA genes had the typical cloverleaf secondary structures except for tRNA^Ser(AGN) gene, which was found with the absence of a DHU arm. In addition, a tRNA-like secondary structure (tRNA^Met) was found in the A + T-rich region. The great difference was that the length of L. sativae A + T-rich region was 597 bp shorter than that of Liriomyza trifolii (Burgess). Meanwhile, some minor differences such as ‘TATA’ block were also observed in L. sativae in contrast to ‘TACA’ block in L. trifolii. There were also some essential structure elements such as ‘TATA’ block, ‘G(A)_nT’ block, poly-T stretch and stem-and-loop structure in the A + T-rich region of L. sativae mitochondrial genome.     

Evolutionary Relationships in the Sand-Dwelling Cichlid Lineage of Lake Tanganyika Suggest Multiple Colonization of Rocky Habitats and Convergent Origin of Biparental Mouthbrooding

The cichlid species flock of Lake Tanganyika is comprised of seven seeding lineages that evolved in step with changes of the lake environment. One seeding lineage diversified into at least six lineages within a short period of time. Our study focuses on the diversification of one of these lineages, the Ectodini, comprising highly specialized, sand- and rock-dwelling species. They display two distinct breeding styles: maternal and biparental mouthbrooding. By analyzing three mtDNA gene segments in 30 species representing all 13 described genera, we show that the Ectodini rapidly diversified into four clades at the onset of their radiation. The monotypic genus Grammatotria is likely to represent the most ancestral split, followed by the almost contemporary origin of three additional clades, the first comprising the benthic genus Callochromis, the second comprising the benthic genera Asprotilapia, Xenotilapia, Enantiopus, and Microdontochromis, and the third comprising the semi-pelagic genera Ophthalmotilapia, Cardiopharynx, Cyathopharynx, Ectodus, Aulonocranus, Lestradea, and Cunningtonia. Our study confirms the benthic and sand-dwelling life-style as ancestral. Rocky habitats were colonized independently in the Xenotilapia- and Ophthalmotilapia-clade. The Xenotilapia-clade comprises both maternal and biparental mouthbrooders. Their mode of breeding appears to be highly plastic: biparental mouthbrooding either evolved once in the common ancestor of the clade, to be reverted at least three times, or evolved at least five times independently from a maternally mouthbrooding ancestor. Furthermore, the genera Xenotilapia, Microdontochromis, Lestradea, and Ophthalmotilapia appeared paraphyletic in our analyses, suggesting the need of taxonomic revision.     

Sequence variation and evolution of the mitochondrial DNA control region in the musk shrew, Suncus murinus

The complete mitochondrial DNA (mtDNA) control region was cloned and sequenced in the musk shrew, Suncus murinus, Insectivora. The general aspect was similar to that found in other mammals. We have found in two locations of this region the presence of arrays of tandem repeats like those in other shrew species. One array was located in the left domain containing the termination-associated sequences (TAS) and the length of a copy was 77 bp. The other repeats were situated upstream from the recognition site for the end of H-strand replication in the right domain and were 20 bp long. The left halves of the control region containing the former repeats were sequenced and compared in several laboratory lines and wild animals from different localities, variations in copy number of repeated sequences were found both among individuals and within an individual. A comparative study of repeated sequences provides useful indication for the origin and evolution of tandem repeated sequences. Strand slippage and mispairing during replication of mtDNA with concerted manner is currently regarded as a dominant theory to account molecular mechanism for tandemly repeated sequences, and the pattern of sequence and length variation in our study supports this theory. Our results, however, suggest that the evolution of the repeated sequences containing the TAS in the musk shrew might go through the process of two steps; at the first step one complete repeated and several incomplete repeated sequences had reproduced in common ancestor of the shrew, and the second stage step-up of complete repeated sequences occurred with concerted evolution after differentiation into continental and insular groups.     

Ancient Divergence in Bathypelagic Lake Tanganyika Deepwater Cichlids: Mitochondrial Phylogeny of the Tribe Bathybatini

The cichlid species flock of Lake Tanganyika represents a polyphyletic assemblage of eight ancestral lineages, which colonized the emerging lake independently. Our study is focused on one of these lineages, the Bathybatini, a tribe of specialized piscivorous cichlids of the deep pelagic zone. By analyzing three mtDNA gene segments of all eight species of the tribe and two species of the closely related Trematocarini, we propose on the basis of a linearized tree analysis that the Bathybatini comprise two distinct lineages, the genera Hemibates and Bathybates, that seeded the primary lacustrine Tanganyika radiation independently. The genus Hemibates is likely to represent a distinct lineage that emerged simultaneously with the tribe Trematocarini and the genus Bathybates and should be therefore treated as a distinct tribe. Within the genus Bathybates, B. minor clearly represents the most ancestral split and is likely to have diverged from the remaining species in the course of the primary lacustrine Tanganyika radiation during which also the radiations of the Lamprologini and the H-lineage took place. The remaining large Bathybates species also diversified almost simultaneously and in step with the diversification of other Tanganyikan lineages—the Limnochromini and Cyprichromini—with B. graueri occupying the most ancestral branch, suggesting that these were induced by the same environmental changes. The lack of geographic color morphs suggests that competition and resource partitioning, rather than allopatric speciation, promoted speciation within the genus Bathybates.Reviewing Editor: Dr. Axel Meyer     

Structure and patterns of sequence variation in the mitochondrial DNA control region of the great cats

Mitochondrial DNA control region structure and variation were determined in the five species of the genus Panthera. Comparative analyses revealed two hypervariable segments, a central conserved region, and the occurrence of size and sequence heteroplasmy. As observed in the domestic cat, but not commonly seen in other animals, two repetitive sequence arrays (RS-2 with an 80-bp motif and RS-3 with a 6-10-bp motif) were identified. The 3' ends of RS-2 and RS-3 were highly conserved among species, suggesting that these motifs have different functional constraints. Control region sequences provided improved phylogenetic resolution grouping the sister taxa lion (Panthera leo) and leopard (Panthera pardus), with the jaguar (Panthera onca).     

Phylogeny of leafcutter ants in the genus Atta Fabricius (Formicidae: Attini) based on mitochondrial and nuclear DNA sequences

Leafcutting ants of the genus Atta are the most conspicuous members of the tribe Attini, the fungus-growing ants. Atta species have long attracted the attention of naturalists, and have since become a common model system for the study of complex insect societies as well as for the study of coevolutionary dynamics due to their numerous interactions with fungi and other microbes. Nevertheless, systematics and taxonomy of the 15 species in the genus Atta have proven challenging, due in part to the extreme levels of worker polymorphism these species display, leading to disagreements about the validity of as many as five different subgenera and calling into question the monophyly of the genus. Here, we use DNA sequence information from fragments of three mitochondrial genes (COI, tRNA leucine and COII) and one nuclear gene (EF1-αF1), totaling 1070 base pairs, to reconstruct the phylogenetic relationships of Atta species using maximum parsimony, maximum likelihood and Bayesian inference techniques. Our results provide support for monophyly of the genus Atta, and suggest that the genus is divided into four monophyletic groups, which correspond to four of the five previously erected Atta subgenera: Atta sensu stricto and Archeatta, each with species composition identical to earlier proposals; Neoatta and Epiatta, with major differences in species composition from earlier proposals. The current geographic ranges of these species suggest that the historical separation of South America from Central and North America has played a role in speciation within this genus.     

Parallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae)

Summary Analysis of mitochondrial DNAs (mtDNAs) from parthenogenetic lizards of theHeteronotia binoei complex with restriction enzymes revealed an 5-kb addition present in all 77 individuals. Cleavage site mapping suggested the presence of a direct tandem duplication spanning the 16S and 12S rRNA genes, the control region and most, if not all, of the gene for the subunit 1 of NADH dehydrogenase (ND1). The location of the duplication was confirmed by Southern hybridization. A restriction enzyme survey provided evidence for modifications to each copy of the duplicated sequence, including four large deletions. Each gene affected by a deletion was complemented by an intact version in the other copy of the sequence, although for one gene the functional copy was heteroplasmic for another deletion. Sequencing of a fragment from one copy of the duplication which encompassed the tRNA^leu(UUR) and parts of the 16S rRNA and ND1 genes, revealed mutations expected to disrupt function. Thus, evolution subsequent to the duplication event has resulted in mitochondrial pseudogenes. The presence of duplications in all of these parthenogens, but not among representatives of their maternal sexual ancestors, suggests that the duplications arose in the parthenogenetic form. This provides the second instance inH. binoei of mtDNA duplication associated with the transition from sexual to parthenogenetic reproduction. The increased incidence of duplications in parthenogenetic lizards may be caused by errors in mtDNA replication due to either polyploidy or hybridity of their nuclear genomes.     

Nucleotide sequence and molecular evolution of the gene coding for glyceraldehyde-3-phosphate dehydrogenase in the thermoacidophilic archaebacteriumSulfolobus solfataricus

ASulfolobus solfataricus genomic library cloned in the EMBL3 phage was screened using as probes synthetic oligonucleotides designed from the known amino acid sequence of a peptide obtained from the purified glyceraldehyde-3-phosphate dehydrogenase (aGAPD) protein. The screening led to the isolation of six recombinant phages (G1–G6) and one of them (G4) contained the entire GAPD gene. The deduced amino acid sequence accounts for a protein made of 341 amino acids and the initial methionine is encoded by a GTG triplet. Alignment of theS. solfataricus aGAPD sequence versus GAPD from archaea, eukarya, and bacteria showed that aGAPD is very similar to other archaebacterial but not to eukaryotic or eubacterial GAPD. For known archaebacterial GAPD sequences, the rate of nucleotide substitutions per site per year showed that these sequences are homologous not only at the amino acid but also at the nucleotide level. The evolutionary rates are nearly similar to those reported for other eukaryotic genes.This work was supported by grants from the CNR, Target Project on Biotechnology and Bioinstrumentation, and MURST (Rome).     

Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea starPisaster ochraceus

Summary We have cloned and sequenced over 9 kb of the mitochondrial genome from the sea starPisaster ochraceus. Within a continuous 8.0-kb fragment are located the genes for NADH dehydrogenase subunits 1, 2, 3, and 4L (ND1, ND2, ND3, and ND4L), cytochrome oxidase subunits I, II, and III (COI, COII, and COIII), and adenosine triphosphatase subunits 6 and 8 (ATPase 6 and ATPase 8). This large fragment also contains a cluster of 13 tRNA genes between ND1 and COI as well as the genes for isoleucine tRNA between ND1 and ND2, arginine tRNA between COI and ND4L, lysine tRNA between COII and ATPase 8, and the serine (UCN) tRNA between COIII and ND3. The genes for the other five tRNAs lie outside this fragment. The gene for phenylalanine tRNA is located between cytochrome b and the 12S ribosomal genes. The genes for tRNA^glu and tRNA^thr are 3 to the 12S ribosomal gene. The tRNAs for histidine and serine (AGN) are adjacent to each other and lie between ND4 and ND5. These data confirm the novel gene order in mitochondrial DNA (mtDNA) of sea stars and delineate additional distinctions between the sea star and other mtDNA molecules.     

中国大陆梅花鹿mtDNA控制区序列变异及种群遗传结构分析

测定了37只中国大陆梅花鹿(Cervus nippon)不同种群mtDNA控制区5′端351 bp的序列，共发现23个变异位点，定义了5种单元型。分子变异分析表明，中国大陆梅花鹿出现了显著的种群分化(Φm＝0．45，Fst＝0．60，P＜0．001)，支持把分布于东北、华南和四川的梅花鹿种群归入各自独立的管理单元。中国大陆、日本南部和日本北部之间无共享单元型，且有25个鉴别位点。最小跨度网络图(Minimum spannlng network，MSN)和基于最大似然法和邻接法的系统发生分析均把单元型聚类为对应于中国大陆、日本南部和日本北部的三个单系，其中中国大陆和日本南部梅花鹿有相对较近的亲缘关系，支持日本梅花鹿的祖先通过至少两个大陆桥从亚洲迁移到日本的观点。     

Phylogeography of the common pandora Pagellus erythrinus in the central Mediterranean Sea: sympatric mitochondrial lineages and genetic homogeneity

The distribution of the genetic diversity and the population structure of Pagellus erythrinus were analysed using mitochondrial control region sequences and cytochrome b restriction profiles in a total of 128 and 508 individuals, respectively, that were collected from 15 sampling sites in the central Mediterranean Sea and from one site in the Atlantic Ocean. No population genetic structure was detected within the central Mediterranean and thus, the commonly recognized transition zones in the area do not seem to affect population connectivity. The comparison between the Mediterranean samples and the single Atlantic sample suggests weak differentiation between the two basins. Three mitochondrial lineages were identified, each including individuals from almost every sampling site. The haplotype and nucleotide diversity values, mismatch distribution and demographic parameters indicate that the sympatry of these lineages can be ascribed to a period of isolation followed by genetic divergence, population expansion and secondary contact, all of which are likely to be associated with climatic oscillations that occurred during the middle and late Pleistocene.     

Diffusion of nuclear and mitochondrial genes across a zone of secondary contact in the maritime shrew, Sorex maritimensis: implications for the conservation of a Canadian endemic mammal

The maritime shrew, Sorex maritimensis, is a Canadian endemic species with a limited distribution in two provinces in eastern Canada. Phylogeographic analysis of mitochondrial DNA control region and cytochrome b sequences revealed two clades, one found in New Brunswick and the other primarily in Nova Scotia, Canada. We propose that these clades have come back into secondary contact following the Wisconsin glaciation via wetlands on the narrow Isthmus of Chigneto that connects these provinces. Despite evidence of an historic separation of maritime shrew subpopulations in Nova Scotia and New Brunswick, we conclude that shrews in these two regions should be considered a single evolutionary significant unit but separate, semi-isolated management units that should be recognized as such for conservation purposes. The susceptibility of this stenotopic species with limited dispersal capabilities raises concerns about its long-term persistence if climate-change induced habitat fragmentation increases. Maintenance of contiguous wetland habitats is needed to ensure connectivity and gene flow among populations of the maritime shrew.     

Discrepancy in divergence of the mitochondrial and nuclear genomes ofDrosophila teissieri andDrosophila yakuba

Summary Restriction sites were compared in the mitochondrial DNA (mtDNA) molecules from representatives of two closely related species of fruit flies: nine strains ofDrosophila teissieri and eight strains ofDrosophila yakuba. Nucleotide diversities amongD. teissieri strains and amongD. yakuba strains were 0.07% and 0.03%, respectively, and the nucleotide distance between the species was 0.22%. Also determined was the nucleotide sequence of a 2305-nucleotide pari (ntp) segment of the mtDNA molecule ofD. teissieri that contains the noncoding adenine+thymine (A+T)-rich region (1091 ntp) as well as the genes for the mitochondrial small-subunit rRNA, tRNA^f-met, tRNA^gln, and tRNA^ile, and portions of the ND2 and tRNA^val genes. This sequence differs from the corresponding segment of theD. yakuba mtDNA by base substitutions at 0.1% and 0.8% of the positions in the coding and noncoding regions, respectively. The higher divergence due to base substitutions in the A+T-rich region is accompanied by a greater number of insertions/deletions than in the coding regions. From alignment of theD. teissieri A+T-rich sequence with those ofD. yakuba andDrosophila virilis, it appears that the 40% of this sequence that lies adjacent to the tRNA^ile gene has been highly conserved. Divergence between the entireD. teissieri andD. yakuba mtDNA molecules, estimated from the sequences, was 0.3%; this value is close to the value (0.22%) obtained from the restriction analysis, but 10 times lower than the value estimated from published DNA hybridization results. From consideration of the relationships of mitochondrial nucleotide distance and allozyme genetic distance found among seven species of theDrosophila melanogaster subgroup, the mitochondrial nucleotide distance observed forD. teissieri andD. yakuba is anomalously low in relation to the nuclear genetic distance.