Recombination and Evolution of Duplicate Control Regions in the Mitochondrial Genome of the Asian Big-Headed Turtle,Platysternon megacephalum

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3′ end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.     

Evolution of duplicate control regions in the mitochondrial genomes of metazoa: a case study with Australasian Ixodes ticks

To investigate the evolution pattern and phylogenetic utility of duplicate control regions (CRs) in mitochondrial (mt) genomes, we sequenced the entire mt genomes of three Ixodes species and part of the mt genomes of another 11 species. All the species from the Australasian lineage have duplicate CRs, whereas the other species have one CR. Sequence analyses indicate that the two CRs of the Australasian Ixodes ticks have evolved in concert in each species. In addition to the Australasian Ixodes ticks, species from seven other lineages of metazoa also have mt genomes with duplicate CRs. Accumulated mtDNA sequence data from these metazoans and two recent experiments on replication of mt genomes in human cell lines with duplicate CRs allowed us to re-examine four intriguing questions about the presence of duplicate CRs in the mt genomes of metazoa: (1) Why do some mt genomes, but not others, have duplicate CRs? (2) How did mt genomes with duplicate CRs evolve? (3) How could the nucleotide sequences of duplicate CRs remain identical or very similar over evolutionary time? (4) Are duplicate CRs phylogenetic markers? It appears that mt genomes with duplicate CRs have a selective advantage in replication over mt genomes with one CR. Tandem duplication followed by deletion of genes is the most plausible mechanism for the generation of mt genomes with duplicate CRs. Once duplicate CRs occur in an mt genome, they tend to evolve in concert, probably by gene conversion. However, there are lineages where gene conversion may not always occur, and, thus, the two CRs may evolve independently in these lineages. Duplicate CRs have much potential as phylogenetic markers at low taxonomic levels, such as within genera, within families, or among families, but not at high taxonomic levels, such as among orders.     

Phylogeography of Asparagopsis taxiformis revisited: Combined mtDNA data provide novel insights into population structure in Japan

Six intraspecific lineages (Lineages 1–6) of Asparagopsis taxiformis have been previously established based on mitochondrial cox2‐cox3 intergenic spacer and a partial cox1 sequences. ‘Lineage 2’ (L2) was suggested to be a recent introduction to the Mediterranean Sea, but its source population has not yet been identified. In order to clarify the nature of northwestern Pacific populations, we performed extensive sampling in Japan (60 individuals from 16 locations) and molecular phylogenetic analyses based on mitochondrial sequences. Sixteen additional individuals, collected from eight locations in the Indo‐Pacific, Caribbean, and Mediterranean regions, were also analyzed. Combined sequence analyses revealed that the Japanese populations only consisted of L2. Out of 19 combined haplotypes identified within L2, two are shared between Japan and the Mediterranean Sea and the Hawaiian Islands, and 12 were identified as endemic to Japan. Genetic analyses of population differentiation suggested that Japanese populations are genetically isolated from the Mediterranean and the Hawaiian populations. A genetic disjunction appears to separate two subpopulations within Japan: one between Toi and Kagoshima and the other between Ojikajima Island and Kagoshima in the Kyushu area.     

Phylogenetic Relationships among Holarctic Populations of Chironomus entis and Chironomus plumosus in View of Possible Horisontal Transfer of Mitochondrial Genes

In eight Holarctic populations of two typical chironomid sibling species of the plumosus group, Chironomus entisandChironomus plumosus, nucleotide sequences of mitochondrial (cytb) and nuclear (gb2b) gene regions were examined. The phylogenetic trees reflecting the evolutionary histories of the nuclear and mitochondrial markers exhibited significant differences. On the tree based on the nuclear gene sequences the populations clustered according to their species affiliation, whereas on the tree based on the mitochondrial gene sequences the populations were grouped according to their geographic position. This discrepancy is probably explained by mitochondrial gene flow between sympatric species with incomplete reproductive isolation (sibling species). Based on our results together with the earlier data on nuclear and mitochondrial gene sequences of some other species from the phylogenetic group plumosus, a scheme of phylogenetic relationships within this group is proposed. This scheme is in many ways different from the traditional view on the evolutionary relationships among species of the plumosus group.     

Phylogenetic relationships among holarctic populations of Chironomus entis and Chironomus plumosus in view of possible horizontal transfer of mitochondrial genes

In eight Holarctic populations of two typical chironomid sibling species of the plumosus group, Chrionomus entis and Chironomus plumosus, nucleotides sequences of mitochondrial (cytb) and nuclear (gb2b) gene regions were examined. The phylogenetic trees reflecting the evolutionary histories of the nuclear and mitochondrial markers exhibited significant differences. On the tree based on the nuclear gene sequences the populations clustered according to their species affiliation, whereas on the tree based on the mitochondrial gene sequences the populations were grouped according to their geographic position. This discrepancy is probably explained by mitochondrial gene flow between sympatric species with incomplete reproductive isolation (sibling species). Based on our results together with the earlier data on nuclear and mitochondrial gene sequences of some other species from the phylogenetic group plumosus, a scheme of phylogenetic relationships within this group is proposed. This scheme is in many ways different from the traditional view on the evolutionary relationships among species of the plumosus group.     

A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes)

Background

Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements.

Results

In the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained.

Conclusions

We propose a “Double Replications and Random Loss” model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-352) contains supplementary material, which is available to authorized users.     

Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar

In Malagasy frogs of the family Mantellidae, the genus Mantellais known to possess highly reorganized mitochondrial (mt) genomeswith the following characteristics: 1) some rearranged genepositions, 2) 2 distinct genes and a pseudogene correspondingto the transfer RNA gene for methionine (trnM), and 3) 2 controlregions (CRs) with almost identical nucleotide sequences. Theseunique genomic features were observed concentrated between theduplicated CRs surrounding cytochrome b (cob) and nicotinamideadenine dinucleotide dehydrogenase subunit 2 (cnad2) genes.To elucidate the mechanisms and evolutionary pathway that yieldedthe derived genome condition, we surveyed the reorganized genomicportion for all 12 mantellid genera. Our results show that themt genomes of 7 genera retain the ancestral condition. In contrast,adding to Mantella, 4 genera of the subfamily Mantellinae, Blommersia,Guibemantis, Wakea, and Spinomantis, share several derived genomiccharacters. Furthermore, mt genomes of these mantellines showedadditional structural divergences, resulting in different genomeconditions between them. The high frequency of genomic reorganizationdoes not correlate with nucleotide substitution rate. The encounteredmt genomic conditions also suggest the occurrences of stepwisegene duplication and deletion events during the evolution ofmantellines. Simultaneously, the majority of duplication eventsseems to be mediated by general (homologous) or illegitimaterecombination, and general recombination also plays a role inconcerted sequence evolution between multiple CRs. Consideringour observations and recent conditional evidences, the followingoutlines can be expected for recombination processes in mt genomereorganization. 1) The CR is the "hot spot" of recombination;2) highly frequent recombination between CRs may be mediatedby a replication fork barrier lying in the CR; 3) general recombinationhas a potential to cause gene rearrangement in upstream regionsof multiple CRs as the results of gene conversion and unequalcrossing over processes. Our results also suggest that recombinationactivity is not a direct cause of convergent gene rearrangement;rather, homoplasious gene rearrangement seems to be mediatedby persistence of a copied genomic condition through severallineage splits and subsequent parallel deletions.     

Population structure of mitochondrial genomes in Saccharomyces cerevisiae

Background

Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences.

Results

To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae.

Conclusions

Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.     

High cryptic diversity and persistent lineage segregation in endemic Romecytheridea (Crustacea,Ostracoda) from the ancient Lake Tanganyika (East Africa)

Ostracods form a substantial part of the endemic fauna of ancient lakes. Here, we have investigated the phylogenetic and phylogeographic patterns and genetic diversities of species of the endemic genus Romecytheridea from the Southern and Central part of Lake Tanganyika. We found that ostracod populations from four different localities are genetically highly differentiated from each other when analyzing the mitochondrial 16S region, while they are almost identical with genetic markers from the nuclear genome (D1-D2 from the large ribosomal subunit (LSU) and ITS). The criteria of the K/θ method for the evolutionary species concepts are fulfilled when analyzing 16S DNA sequence data, indicating that these populations are in fact different (cryptic) species with allopatric distribution. We discuss various hypotheses on how this high diversity could have originated. The complete lineage segregation can partly be explained by geographic isolation during periods of low lake level stands. But, other factors must have contributed to genetic isolation and speciation, as the two closest populations (Chimba and Katoto) from shallow parts of the Southern basin of Tanganyika are also geographically fully segregated.     

Hierarchical organization of genetic variation in the Costa Rican livebearing fish Brachyrhaphis rhabdophora (Poeciliidae)

I examined the geographic distribution of genetic variation in the livebearing freshwater fish Brachyrhaphis rhabdophora in northwestern Costa Rica as revealed by allozymes and mitochondrial DNA sequences. Allelic variability at 11 enzyme-coding loci surveyed across 12 localities revealed marked genetic differentiation among populations within drainages (0_P= 0.36) and among drainages within regions (0_D=0.17), but not between northern and southern geographic regions (0_R=– 0.02). Allozyme variation was hierarchically organized such that populations found within stream drainages were more similar to each other than to populations found in adjacent drainages, a result confirmed by cluster analysis. In contrast to the allozyme data, there was extremely little DNA sequence variation among populations in the mitochondrial control region (3 variable nucleotide positions out of 444 bp examined). The difference in genetic divergence between allozyme and mtDNA markers was unexpected and is discussed in terms of biogeographical colonization events and a molecular selective swéep on the mitochondrial genome, both processes that could explain the lack of mitochondrial variability in this highly subdivided species.     

关于中国香鱼分类地位的线粒体DNA基因序列分析

测定了辽宁和广东香鱼的Cytb基因序列,与GenBank中日本和韩国香鱼分子数据合并比较。结果表明11尾香鱼402个碱基序列中变异位点8个,信息简约位点有2个,A+T与G+C含量分别为51.4%和48.6%,转换/颠换比为4.9。运用Kimura-2parameter模型,采用邻接法构建的分子系统树,发现中国香鱼与日本和韩国香鱼聚类在一起,不同地理种群的香鱼均未单独分群,表明中国和日、韩香鱼亲缘关系相当近。根据日、韩香鱼的地理分布,推测所分析的辽宁和广东种群可能亦为香鱼指名亚种,但该推论尚需与琉球香鱼亚种的序列进行比较后才能确定。研究虽未发现辽宁香鱼和广东香鱼间存在明显的种群结构差异,但由于中国海域辽阔,生境多样,中国沿海是否会有其它种下群体发生,则需要采用进化速度适中的线粒体和核基因标记,对中国香鱼不同的地理种群进行广泛的大样本分析来确定。     

The legacy of ice ages in mountain species: post‐glacial colonization of mountain tops rather than current range fragmentation determines mitochondrial genetic diversity in an endemic Pyrenean rock lizard

Aim The genetic impact of Quaternary climatic fluctuations on mountain endemic species has rarely been investigated. The Pyrenean rock lizard (Iberolacerta bonnali) is restricted to alpine habitats in the Pyrenees where it exhibits a highly fragmented distribution between massifs and between habitats within massifs. Using mitochondrial DNA markers, we set out: (1) to test whether several evolutionary units exist within the species; (2) to understand how the species persisted through the Last Glacial Maximum and whether the current range fragmentation originates from distribution shifts after the Last Glacial Maximum or from more ancient events; and (3) to investigate whether current mitochondrial diversity reflects past population history or current habitat fragmentation. Location The Pyrenees in south‐western France and northern Spain. Methods We used variation in the hypervariable left domain of the mitochondrial control region of 146 lizards collected in 15 localities, supplemented by cytochrome b sequences downloaded from GenBank to cover most of the species’ distribution range. Measures of population genetic diversity were contrasted with population isolation inferred from topography. Classical (F‐statistics) and coalescence‐based methods were used to assess the level of gene flow and estimate divergence time between populations. We used coalescence‐based simulations to test the congruence of our genetic data with a scenario of simultaneous divergence of current populations. Results Coalescence‐based analyses suggested that these peripheral populations diverged simultaneously at the end of the last glacial episode when their habitats became isolated on mountain summits. High mitochondrial diversity was found in peripheral, isolated populations, while the populations from the core of the species’ range were genetically impoverished. Where mitochondrial diversity has been retained, populations within the same massif exhibited high levels of genetic differentiation. Main conclusions As suggested for many other mountain species, the Pyrenean rock lizard survived glacial maxima through short‐distance range shifts instead of migration or contraction in distant southern refugia. Most of the main Pyrenean range has apparently been re‐colonized from a single or a few source populations, resulting in a loss of genetic diversity in re‐colonized areas. As a result, current levels of intra‐population mitochondrial diversity are better explained by post‐glacial population history than by current habitat fragmentation. Genetic population differentiation within massifs implies severe reduction in female‐mediated gene flow between patches of habitats.     

澜沧江老挝纹胸鮡Cytb基因的序列变异与遗传结构分析

老挝纹胸鮡是分布于澜沧江流域的一种特有鱼类,喜激流底栖生活。为了解其各地理种群间的遗传结构与遗传变异,文章分析了129尾采自澜沧江8条支流水系的老挝纹胸鮡mtDNA细胞色素b基因1 138 bp的序列变异,共发现16个多态性位点,定义了15个单倍型。澜沧江老挝纹胸鮡遗传变异较低,平均单倍型多样性指数和核苷酸多样性指数分别是h=0.299,π=0.299,有3个种群甚至没有变异,分子变异方差分析结果表明各种群内变异大于各种群间变异,种群间没有差异。对老挝纹胸鮡所有种群进行的单倍型错配分布呈现单峰型,中性检验结果均为负值(Tajima’s D=?2.36965,P<0.02;Fu’s Fs=?20.975,P<0.05)表明,澜沧江老挝纹胸鮡自然种群可能经历过近期的种群扩张事件。     

Intraspecific diversity of mitochondrial DNA in the land snail Euhadra peliomphala (Bradybaenidae)

Exceptionally high levels of intraspecific variation of mitochondrial DNA (mtDNA) sequences encoding 16S ribosomal RNA (16SrRNA) were detected in populations of the land snail Euhadra peliomphala from the eastern part of Japan. Geographical isolation has occurred within small areas and has created many genetically distinct local populations. These are morphologically segregated into two groups: the first consists of populations from the southern part of the Izu Peninsula, and the second of populations from other areas within the peninsula. They are separated by mountains in the middle of the peninsula. Sequence divergences between these two groups were 7.6–9.5%. The sequence divergences and geological ages of the Izu peninsula and its mountains suggest that the divergence rate of mitochondrial 16SrRNA sequences of this species is extremely rapid, approximately 10% per million years. This rapid evolutional")' rate of mtDNA and vicariance events due to tectonic events and sea level changes has also contributed to creating exceptional geographical variation in the mtDNA of this species.     

The Use of Restriction Endonucleases to Measure Mitochondrial DNA Sequence Relatedness in Natural Populations. I. Population Structure and Evolution in the Genus Peromyscus

In this study we introduce to natural population analysis a molecular technique that involves the use of restriction endonucleases to compare mitochondrial DNA (mtDNA) sequences. We have examined the fragment patterns produced by six restriction endonucleases acting upon mtDNA isolated from 23 samples of three species of the rodent Peromyscus. Our observations confirm the following conclusions derived from previous experiments with laboratory animals: (1) mtDNA within an individual homogeneous; (2) at least the majority of mtDNA present in an individual is inherited from the female parent. Our experiments demonstrate for the first time that there is detectable heterogeneity in mtDNA sequences within and among natural geographic populations of a species and that this heterogeneity can readily be used to estimate relatedness between individuals and populations. Individuals collected within a single locale show less than 0.5% sequence divergence, while those collected from conspecific populations separated by 50 ti 500 miles differ by approximately 1.5%. The mtDNAs of the closely related sibling species P. polionotus and P. maniculatus differ from each other by 13 to 17%; nonsibling species differ by more than 20%. Qualitative and quantitative approaches to analysis of digestion patterns are suggested. The results indicate that restriction analysis of mtNDA may become the most sensitive and powerful technique yet available for reconstructing evolutionary relationships among conspecific organisms.     

The influence of landscape on population structure of four invertebrates in groundwater springs

1. The unique aquatic fauna of the island‐like groundwater springs of arid inland Australia raises important questions as to how aquatic species persist in very isolated and fragmented habitats and the role that dispersal may play in mitigating/mediating the influence of landscape structure and determining population structure. By determining the relationship between genetics and geography (i.e. phylogeography), the historical processes responsible for population structure can be determined. 2. We undertook comparative phylogeographic studies of invertebrates from springs south of Lake Eyre. Clusters of springs lying within and between surface drainage catchments (which provide a potential connection between springs) were sampled, and the phylogeographic structure of four coexisting species, an ostracod Ngarwa dirga, a snail Fonscochlea accepta, an isopod Phreatomerus latipes and an amphipod Wangiannachiltonia guzikae, was examined. 3. Clear differences in the geographic patterns of genetic structure were found amongst the four species. No discernable genetic structure was found in ostracod and snail populations, even amongst springs lying 20 km apart in separate surface catchments; isopod populations were highly genetically structured amongst springs located in separate catchments, but not within catchments, whilst amphipod populations were highly genetically structured amongst springs both within and between catchments. 4. The results suggest that differences in dispersal ability of each species, and not the overall fragmented nature of the springs, may have led to large differences in phylogeographic history. Interestingly, the relative dispersal ability of these species may be related to their vulnerability to and recovery from large‐scale flood events. Therefore, despite the highly isolated and fragmented nature of the springs, the landscape has not strongly influenced the population structure of the aquatic invertebrate community as a whole nor has it led to the evolution of common life histories.     

Phylogeographic analysis of the green python,Morelia viridis,reveals cryptic diversity

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.