Phylogeny ofMuntiacus (Cervidae) based on mitochondrial DNA restriction maps

Mitochondrial DNA restriction maps for 12 restriction enzymes of four species of muntjacs—Indian muntjac(M. muntjak), Gongshan muntjac(M. gongshanensis), black muntjac(M. crinifrons), and Chinese muntjac(M. reevesi)—were compared to estimate the phylogenetic relationships among them. Phylogenetic trees were constructed by both distance and parsimony methods. The two resulting trees share a similar topology, which indicates that the black muntjac and the Gongshan muntjac are closely related, followed by the Chinese muntjac; the Indian muntjac is the sister taxon to all the other muntjacs.     

Phylogeny of African fruit bats (Chiroptera,Pteropodidae) based on complete mitochondrial genomes

Members of the family Pteropodidae, also known as Old World fruit bats, are represented in Africa by 14 genera and 44 species. Here, we sequenced 67 complete mitochondrial genomes from African and Asian pteropodids to better understand the evolutionary history of the subfamily Rousettinae, which includes most of the African species. An increased frequency of guanine to adenine transitions is detected in the mtDNA genomes of Macroglossus sobrinus and all species of Casinycteris and Scotonycteris. Our phylogenetic and molecular dating analyses based on 126 taxa and 15,448 characters indicate a low signal for deep relationships within the family, suggesting a rapid diversification during the Late Oligocene period of “warming.” Within the subfamily Rousettinae, most nodes are highly supported by our different analyses (all nucleotide sites, SuperTRI analyses of a sliding window, transversions only, coding genes only, and amino acid sequences). The results indicate the existence of four tribes: Rousettini—distributed from Africa through Mediterranean region and South Asia to South-East Asia; Eonycterini—found in Asia; and Epomophorini and Scotonycterini—restricted to sub-Saharan Africa. Although most interspecies relationships are highly supported, three parts of the Rousettinae mitochondrial tree are still unresolved, suggesting rapid diversification: (a) among the three subtribes Epomophorina (Epomophorus sensu lato, i.e., including Micropteropus, Epomops, Hypsignathus, Nanonycteris), Plerotina (Plerotes), and Myonycterina (Myonycteris, Megaloglossus) in the Late Miocene; (b) among Epomops, Hypsignathus, and other species of Epomophorina at the Pliocene–Pleistocene boundary; and (c) among Myonycteris species in the Early Pleistocene. Within the Epomophorini, Stenonycteris lanosus emerged first, suggesting that lingual echolocation may have appeared in the common ancestor of Epomophorini and Rousettini. Our analyses suggest that multiple events of mtDNA introgression occurred within the Epomophorus species complex during the Pleistocene.     

Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of five individual caecilians (Amphibia: Gymnophiona) representing five of the six recognized families: Rhinatrema bivittatum (Rhinatrematidae), Ichthyophis glutinosus (Ichthyophiidae), Uraeotyphlus cf. oxyurus (Uraeotyphlidae), Scolecomorphus vittatus (Scolecomorphidae), and Gegeneophis ramaswamii (Caeciliidae). The organization and size of these newly determined mitogenomes are similar to those previously reported for the caecilian Typhlonectes natans (Typhlonectidae), and for other vertebrates. Nucleotide sequences of the nuclear RAG1 gene were also determined for these six species of caecilians, and the salamander Mertensiella luschani atifi. RAG1 (both at the amino acid and nucleotide level) shows slower rates of evolution than almost all mt protein-coding genes (at the amino acid level). The new mt and nuclear sequences were compared with data for other amphibians and subjected to separate and combined phylogenetic analyses (Maximum Parsimony, Minimum Evolution, Maximum Likelihood, and Bayesian Inference). All analyses strongly support the monophyly of the three amphibian Orders. The Batrachia hypothesis (Gymnophiona, (Anura, Caudata) receives moderate or good support depending on the method of analysis. Within Gymnophiona, the optimal tree (Rhinatrema, (Ichthyophis, Uraeotyphlus), (Scolecomorphus, (Gegeneophis Typhlonectes) agrees with the most recent morphological and molecular studies. The sister group relationship between Rhinatrematidae and all other caecilians, that between Ichthyophiidae and Uraeotyphlidae, and the monophyly of the higher caecilians Scolecomorphidae+Caeciliidae+Typhlonectidae, are strongly supported, whereas the relationships among the higher caecilians are less unambiguously resolved. Analysis of RAG1 is affected by a spurious local rooting problem and associated low support that is ameliorated when outgroups are excluded. Comparisons of trees using the non-parametric Templeton, Kishino-Hasegawa, Approximately Unbiased, and Shimodaira-Hasegawa tests suggest that the latter may be too conservative.     

A reevaluation of rice mitochondrial evolution based on the complete sequence of male-fertile and male-sterile mitochondrial genomes

Plant mitochondrial genomes have features that distinguish them radically from their animal counterparts: a high rate of rearrangement, of uptake and loss of DNA sequences, and an extremely low point mutation rate. Perhaps the most unique structural feature of plant mitochondrial DNAs is the presence of large repeated sequences involved in intramolecular and intermolecular recombination. In addition, rare recombination events can occur across shorter repeats, creating rearrangements that result in aberrant phenotypes, including pollen abortion, which is known as cytoplasmic male sterility (CMS). Using next-generation sequencing, we pyrosequenced two rice (Oryza sativa) mitochondrial genomes that belong to the indica subspecies. One genome is normal, while the other carries the wild abortive-CMS. We find that numerous rearrangements in the rice mitochondrial genome occur even between close cytotypes during rice evolution. Unlike maize (Zea mays), a closely related species also belonging to the grass family, integration of plastid sequences did not play a role in the sequence divergence between rice cytotypes. This study also uncovered an excellent candidate for the wild abortive-CMS-encoding gene; like most of the CMS-associated open reading frames that are known in other species, this candidate was created via a rearrangement, is chimeric in structure, possesses predicted transmembrane domains, and coopted the promoter of a genuine mitochondrial gene. Our data give new insights into rice mitochondrial evolution, correcting previous reports.     

Phylogeny and comparative genomic analysis of Pteriomorphia (Mollusca: Bivalvia) based on complete mitochondrial genomes

The subclass Pteriomorphia is a morphologically diverse and economically important group of Mollusca. We retrieved 42 mitochondrial genomes (mtGenomes) of Pteriomorphia and concatenated protein-coding genes, rRNAs and tRNAs to assess phylogenetic relationships and divergence times among the families with maximum likelihood (ML) and Bayesian inference (BI) analyses. Both ML and BI analyses strongly support the same topology except for the position of Atrina pectinata. Our study confirms the monophyly of the families Arcidae, Mytilidae, Pteriidae, Ostreidae and Pectinidae. Within Pteriomorphia, we recovered two clusters, one comprising Mytilidae, Arcidae and Pectinidae, the other consisting of Ostreidae, Pteriidae and Pinnidae, but we did not confirm a basal position for any family. The phylogenetic trees suggest that Ostreidae, Pteriidae and Pinnidae should be grouped as the order Ostreoida. Divergence times of major families are estimated as follows: Arcidae, 315.9 Ma; Pectinidae, 384.4 Ma; Ostreidae, 240.8 Ma; Mytilidae, 390.8 Ma. Comparative analysis indicates a low-level codon usage bias (with an average of 50.29) in mtGenomes of Pteriomorphia. In Mytilidae and Ostreidae, the codon usage bias was under mutation pressure rather than selection. Contrastingly, mutation is not the main factor in defining the codon usage in Pectinidae and Pteriidae. Among Ostreidae, Pectinidae and Mytilidae, Ka/Ks ratios range from 0.00 to 1.22 and most values (89.11%) are less than 0.20, indicating that most genes are under strong negative or purifying selection. The protein-coding gene orders show dramatically different patterns in Pteriomorphia. There is no gene block even consisting of two genes that is shared by five families.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

Phylogenetic analysis of diprotodontian marsupials based on complete mitochondrial genomes

Australidelphia is the cohort, originally named by Szalay, of all Australian marsupials and the South American Dromiciops. A lot of mitochondria and nuclear genome studies support the hypothesis of a monophyly of Australidelphia, but some familial relationships in Australidelphia are still unclear. In particular, the familial relationships among the order Diprotodontia (koala, wombat, kangaroos and possums) are ambiguous. These Diprotodontian families are largely grouped into two suborders, Vombatiformes, which contains Phascolarctidae (koala) and Vombatidae (wombat), and Phalangerida, which contains Macropodidae, Potoroidae, Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae. Morphological evidence and some molecular analyses strongly support monophyly of the two families in Vombatiformes. The monophyly of Phalangerida as well as the phylogenetic relationships of families in Phalangerida remains uncertain, however, despite searches for morphological synapomorphy and mitochondrial DNA sequence analyses. Moreover, phylogenetic relationships among possum families (Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae) as well as a sister group of Macropodoidea (Macropodidae and Potoroidae) remain unclear. To evaluate familial relationships among Dromiciops and Australian marsupials as well as the familial relationships in Diprotodontia, we determined the complete mitochondrial sequence of six Diprotodontian species. We used Maximum Likelihood analyses with concatenated amino acid and codon sequences of 12 mitochondrial protein genomes. Our analysis of mitochondria amino acid sequence supports monophyly of Australian marsupials+Dromiciops and monophyly of Phalangerida. The close relatedness between Macropodidae and Phalangeridae is also weakly supported by our analysis.     

Phylogeny of Neotropical Seirinae (Collembola,Entomobryidae) based on mitochondrial genomes

Seirinae is one of the most diverse subfamilies of Collembola. To date no detailed phylogeny of Seirinae has been proposed, which leads to difficulties in the understanding of evolutionary patterns regarding this taxon. The main aim of this study is to clarify the phylogenetic relationships within the Neotropical Seirinae, by generating and analysing the mitochondrial genomes of 26 terminal taxa of Entomobryidae, and one species of Paronellidae. Specifically, we first generated Illumina HiSeq 2000 shotgun sequence data from each species, then reconstructed the mitochondrial genome of each species using two methods: MitoZ and MIRA/MITOBim. Using these data, we were able to generate a well-supported phylogeny that combined all the above species as well as three publicly available mitogenomes from other species. Bayesian and maximum likelihood methods were applied using all 13 protein coding genes. In this way, monophyly for the internal groups of Seirinae was obtained based on molecular evidence for the first time, as was the potential validity of three main internal taxa of the subfamily. We furthermore validated that Tyrannoseira is a distinct lineage and propose the elevation of Lepidocyrtinus to genus. Lastly, we anticipate that these newly available mitogenomes will serve as a useful dataset for future studies on the evolution of the Collembola and Hexapoda.     

Sequencing complete mitochondrial and plastid genomes

Organelle genomics has become an increasingly important research field, with applications in molecular modeling, phylogeny, taxonomy, population genetics and biodiversity. Typically, research projects involve the determination and comparative analysis of complete mitochondrial and plastid genome sequences, either from closely related species or from a taxonomically broad range of organisms. Here, we describe two alternative organelle genome sequencing protocols. The "random genome sequencing" protocol is suited for the large majority of organelle genomes irrespective of their size. It involves DNA fragmentation by shearing (nebulization) and blunt-end cloning of the resulting fragments into pUC or BlueScript-type vectors. This protocol excels in randomness of clone libraries as well as in time and cost-effectiveness. The "long-PCR-based genome sequencing" protocol is specifically adapted for DNAs of low purity and quantity, and is particularly effective for small organelle genomes. Library construction by either protocol can be completed within 1 week.     

Phylogeny of the Tachycineta genus of New World swallows: insights from complete mitochondrial genomes

The Tachycineta genus of swallows is comprised of nine species that range from Alaska to southern Chile. We sequenced the entire mitochondrial genome of each member of Tachycineta and generated a completely resolved phylogenetic hypothesis for the corresponding mitochondrial gene tree. Our analyses confirm the presence of two sub-clades within Tachycineta that are associated with geography: a North American/Caribbean clade and a South/Central American clade. We found considerable variation among regions of the mitochondrial genome in both substitution rates and the level of information that each region supplied for phylogenetic reconstruction. We found no evidence of positive directional selection within mitochondrial coding regions, but we identified numerous sites under purifying selection. This finding suggests that, despite differences in life history traits and distributions, mitochondrial genes in Tachycineta are predominantly under purifying selection for conserved function.     

Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes

Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous ( approximately 69Ma) or Middle Eocene ( approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea ( approximately 29Ma).     

鳜类系统发育的线粒体Cytb基因全序列分析

测定了鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜、中国少鳞鳜等7种鳜类12个个体的线粒体细胞色素b基因全序列。结合GenBank中的同源序列,共分析了9种鳜类的系统发育关系。序列分析表明,鳜属鱼类属内种间的遗传距离(0.015～0.093)明显小于少鳞鳜属鱼类属内种间的遗传距离(0.152～0.178)。在分子系统发育树上,长体鳜与鳜属的鳜、大眼鳜、斑鳜、波纹鳜、暗鳜聚合成一分支,少鳞鳜属的种类聚成另一分支;支持将长体鳜归入鳜属,鳜类分为鳜属和少鳞鳜属等二个属的分类处理。在鳜属鱼类中,鳜和大眼鳜亲缘关系十分密切;斑鳜与波纹鳜亲缘较近;长体鳜与鳜属其它5个种的亲缘关系较远。在少鳞鳜属鱼类中,中国少鳞鳜和日本少鳞鳜的亲缘关系较远,韩国少鳞鳜的系统位置较不明确。鳜类的单系性及其鳜类的系统位置仍有待进一步研究。     

Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

Efforts have been made to investigate the phylogeny of the family Bovidae; however, the relationships within this group still remain controversial. To further our understanding of the relationships, we sequenced the mitochondrial genome of the Himalayan goral, Naemorhedus goral, an IUCN Redlist near threatened conservation dependent species. Then we conducted molecular phylogenetic relationships of the Bovidae based on Bayesian and Maximum Likelihood methods. The results indicate that the basal divergence within the Bovidae is between the Bovinae and a strongly supported clade of the remaining Bovidae species. The two Neotragus species (the suni and pygmy antelope) clustered with the impala, Aepyceros melampus (Aepycerotinae), and together they formed the most basal of the non-Bovinae. All the genera of the Antilopinae clustered together except Neotragus, which suggested that the Antilopinae was a paraphyletic subfamily. The present study confirmed a close relationship between the genera Capricornis and Naemorhedus while supporting their designation as separate genera and suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox) should be placed in the Caprinae. Bison, Bos, and Tragelaphus (bison & cattle and kudus and nyalas) were paraphyletic. The very close relationship between Bison and Bos suggested that Bos and Bison should be integrated into a single Bos genus. Saiga and Pantholops (the Chiru or Tibetan Antelope), unique genera which have sometimes been lumped together, were placed in different groups: Saiga within the Antilopinae and Pantholops at the base of the Caprinae. Our results also supported a new taxonomy which places the three species of Hemitragus into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr.     

Analysis of three leafminers' complete mitochondrial genomes

Liriomyza trifolii (Burgess), Liriomyza huidobrensis (Blanchard), and Liriomyza bryoniae (Kaltenbach), are three closely related and economically important leafminer pests in the world. This study examined the complete mitochondrial genomes of L. trifolii, L. huidobrensis and L. bryoniae, which were 16141 bp, 16236 bp and 16183 bp in length, respectively. All of them displayed 37 typical animal mitochondrial genes and an A + T-rich region. The genomes were highly compact with only 60–68 bp of non-coding intergenic spacer. However, considerable differences in the A + T-rich region were detected among the three species. Results of this study also showed the two ribosomal RNA genes of the three species had very limited variable sites and thus should not provide much information in the study of population genetics of these species. Data generated from three leafminers' complete mitochondrial genomes should provide valuable information in studying phylogeny of Diptera, and developing genetic markers for species identification in leafminers.     

Phylogeny and evolution of Burmanniaceae (Dioscoreales) based on nuclear and mitochondrial data

The mycoheterotrophic Burmanniaceae are one of the three families currently recognized in the order Dioscoreales. Phylogenetic inference using nucleotide sequences of the nuclear 18S rDNA region and the mitochondrial nad1 b-c intron revealed two well-supported, major lineages within the family, corresponding to the two tribes recognized in the family: Burmannieae and Thismieae. All data supported a strong relationship between Thismieae and Tacca (Dioscoreaceae) making both Burmanniaceae and Dioscoreaceae polyphyletic. The three largest Burmanniaceae genera, Burmannia, Gymnosiphon, and Thismia, are paraphyletic. The splitting of Burmanniaceae into Burmannieae and Thismieae indicates two independent origins of mycoheterotrophy and correlated loss of chlorophyll in Dioscoreales. In the genus Burmannia, in which many species still contain chlorophyll, the achlorophyllous species are nested in between the autotrophic species, suggesting many independent changes from autotrophy to heterotrophy or vice versa. A Bayesian relative rates test on the 18S rDNA data showed considerable variation in substitution rates among Burmanniaceae. The substitution rates in all Thismieae and many Burmannieae are significantly faster than in Dioscoreaceae, but there seems to be no correlation between rate increases and the loss of photosynthesis.     

One-step PCR amplification of complete arthropod mitochondrial genomes

A new PCR primer set which enables one-step amplification of complete arthropod mitochondrial genomes was designed from two conserved 16S rDNA regions for the long PCR technique. For this purpose, partial 16S rDNAs amplified with universal primers 16SA and 16SB were newly sequenced from six representative arthropods: Armadillidium vulgare and Macrobrachium nipponense (Crustacea), Anopheles sinensis (Insecta), Lithobius forficatus and Megaphyllum sp. (Myriapoda), and Limulus polyphemus (Chelicerata). The genomic locations of two new primers, HPK16Saa and HPK16Sbb, correspond to positions 13314-13345 and 12951-12984, respectively, in the Drosophila yakuba mitochondrial genome. The usefulness of the primer set was experimentally examined and confirmed with five of the representative arthropods, except for A. vulgare, which has a linearized mitochondrial genome. With this set, therefore, we could easily and rapidly amplify complete mitochondrial genomes with small amounts of arthropod DNA. Although the primers suggested here were examined only with arthropod groups, a possibility of successful application to other invertebrates is very high, since the high degree of sequence conservation is shown on the primer sites in other invertebrates. Thus, this primer set can serve various research fields, such as molecular evolution, population genetics, and molecular phylogenetics based on DNA sequences, RFLP, and gene rearrangement of mitochondrial genomes in arthropods and other invertebrates.     

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs

Prosimians (tarsiers and strepsirrhini) represent the basal lineages in primates and have a close bearing on the origin of primates. Although major lineages among anthropoidea (humans, apes and monkeys) are well represented by complete mitochondrial DNA (mtDNA) sequence data, only one complete mtDNA sequence from a representative of each of the infraorders in prosimians has been described until quite recently, and therefore we newly determined complete mtDNA sequences from 5 lemurs, 4 lorises, one tarsier and one platyrrhini. These sequences were provided to phylogenetic analyses in combination with the sequences from the 15 primates species reported to the database. The position of tarsiers among primates could not be resolved by the maximum likelihood (ML) and neighbor-joining (NJ) analyses with several data sets. As to the position of tarsiers, any of the three alternative topologies (monophyly of haplorhini, monophyly of prosimians, and tarsiers being basal in primates) was not rejected at the significance level of 5%, neither at the nucleotide nor at the amino acid level. In addition, the significant variations of C and T compositions were observed across primates species. Furthermore, we used AGY data sets for phylogenetic analyses in order to remove the effect of different C/T composition bias across species. The analyses of AGY data sets provided a medium support for the monophyly of haplorhini, which might have been screened by the variation in base composition of mtDNA across species. To estimates the speciation dates within primates, we analyzed the amino acid sequences of mt-proteins with a Bayesian method of Thorne and Kishino. Divergence dates were estimated as follows for the crown groups: about 35.4 million years ago (mya) for lorisiformes, 55.3 mya for lemuriformes, 64.5 mya for strepsirrhini, 70.1 mya for haplorhini and 76.0 mya for primates. Furthermore, we reexamined the biogeographic scenarios which have been proposed for the origin of strepsirrhini (lemuriformes and lorisiformes) and for the dispersal of the lemuriformes and lorisiformes.     

Phylogeny and evolution of the Archaea: one hundred genomes later

Little more than 30 years since the discovery of the Archaea, over one hundred archaeal genome sequences are now publicly available, of which ～40% have been released in the last two years. Their analysis provides an increasingly complex picture of archaeal phylogeny and evolution with the proposal of new major phyla, such as the Thaumarchaeota, and important information on the evolution of key central cellular features such as cell division. Insights have been gained into the events and processes in archaeal evolution, with a number of additional and unexpected links to the Eukaryotes revealed. Taken together, these results predict that many more surprises will be found as new archaeal genomes are sequenced.