Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

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).     

Phylogeny of early land plants: insights from genes and genomes

A large body of evidence from molecular systematic studies has confirmed the charophytic origin of land plants, and clarified monophyly of many lineages in charophytes and land plants. These studies have also identified liverworts as the earliest land plants, and the lycopods as the extant sister group to all other vascular plants. Two traditionally defined groups-bryophytes and pteridophytes-are now recognized as early grades of land plant evolution. However, several problems that complicate the use of sequence data in reconstructing plant phylogeny have become apparent; reconstruction of an accurate land plant phylogeny will require analysis of sequences of multiple genes and genomic structural characters of all three genomes.     

Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences

To set the stage for historical analyses of the ecology and behavior of tree swallows and their allies (genus Tachycineta), we reconstructed the phylogeny of the nine Tachycineta species by comparing DNA sequences of six mitochondrial genes: Cytochrome b (990 base pairs), the second subunit of nicotinamide adenine dinucleotide dehydrogenase (839 base pairs), cytochrome oxidase II (85 base pairs), ATPase 8 (158 base pairs), tRNA-lysine (73 base pairs), and tRNA-methionine (25 base pairs). The phylogeny consisted of two main clades: South and Central American species ((T. stolzmanni, T. albilinea, T. albiventris), (T. leucorrhoa, T. meyeni)), and North American and Caribbean species (T. bicolor, (T. thalassina, T. euchrysea, T. cyaneoviridis)). The genetic distances among the species suggested that Tachycineta is a relatively old group compared to other New World swallow genera. One interesting biogeographic discovery was the close relationship between Caribbean and western North American taxa. This historical connection occurs in other groups of swallows and swifts as well. To reconstruct the phylogeny, we employed Bayesian as well as traditional maximum-likelihood methods. The Bayesian approach provided probability values for trees produced from the different genes and gene combinations, as well as probabilities of branches within those trees. We compared Bayesian and maximum-likelihood bootstrap branch support and found that all branches with Bayesian probabilities > or = 95% received bootstrap support >70%.     

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta

Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.     

Mitogenomic phylogeny of Trochoidea (Gastropoda: Vetigastropoda): New insights from increased complete genomes

Increased mitochondrial (mt) genomes can provide more sets of genome‐level characteristics for resolving deeper phylogeny. Limited information with respect to the Trochoidea mitochondrial genome organization is available; besides, monophyly and internal relationships of the superfamily still remain a matter of discussion. To resolve the monophyly and internal phylogenetic controversies of Trochoidea and expand our understanding for mt genomic characteristic evolution among Trochoidea, the phylogenetic trees were reconstructed using 13 newly sequenced complete mt genomes and 35 genomes from GenBank, and both the maximum likelihood and Bayesian inference analyses were highly supported. Vetigastropoda phylogenetic analyses recovered the monophyly of Trochoidea. Trochoidea phylogenetic analyses and genetic distances supported the non‐monophyly of Tegulidae and Tegula, indicating that the taxonomic status of several genera (Rochia, Tectus and Cittarium) should be revised and Tegula, Omphalius and Chlorostoma should be placed as a same genus. The close affinity between Tectus virgatus and Rochia was also revealed. Three‐nucleotide insertion in nad1, nine‐nucleotide insertion and six‐nucleotide deletion in nad5 are detected in Tegulidae, Tectus and Rochia, respectively. Gene orders within Trochoidea are stable, with gene rearrangements exclusive to tRNA genes observed. Homoplasious convergences because of trnT rearrangement display translocation in Turbinidae and reversion in Trochidae and Calliostomatida. For trnE and trnG, we identify 11 arrangement types, suggesting that the gene rearrangement history needs to be further evaluated. Our study emphasizes the importance of mt genomes in resolving phylogenetic relationships within Trochoidea. In addition, the mt genomic characters would contribute new insights into the classification of Trochoidea.     

Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences

The phylogeny of swallows was reconstructed by comparing segments of three genes, nuclear beta-fibrinogen intron 7 (betafib7), mitochondrial cytochrome b (cytb), and mitochondrial ND2, in a variety of combinations using maximum likelihood and Bayesian methods. betafib7 was sequenced for 47 species, cytb for 74 species, and ND2 for 61 species to yield comparisons among 75 of the 84 currently recognized swallow species. The family Hirundinidae was confirmed to consist of two clades, Pseudochelidoninae (river martins) and Hirundininae (typical swallows). The Hirundininae is further divided into mud nesters (Hirundo sensu lato), core martins (Phedina, Riparia, and New World endemic genera), and basal relicts (Psalidoprocne, Cheramoeca, and Pseudhirundo). We did not resolve the hierarchy among these three hirundinine groups, but discovered many relationships within them. Mud-nesting genera have the following relationships: (Hirundo sensu stricto, Ptyonoprogne), (Delichon, (Petrochelidon, Cecropis)). Core martins have the following topology: (Phedina, Riparia cincta), (Riparia sensu stricto, Tachycineta, ((Stelgidopteryx, Progne), (Neotropical endemic genera))). Interspecific relationships among the Neotropical endemics were resolved completely; Atticora and Notiochelidon are paraphyletic, and all Neotropical endemics probably should be lumped into one or two genera. The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings (Psalidoprocne) are their likely sister group.     

Baboon phylogeny as inferred from complete mitochondrial genomes

Baboons (genus Papio) are an interesting phylogeographical primate model for the evolution of savanna species during the Pleistocene. Earlier studies, based on partial mitochondrial sequence information, revealed seven major haplogroups indicating multiple para‐ and polyphylies among the six baboon species. The most basal splits among baboon lineages remained unresolved and the credibility intervals for divergence time estimates were rather large. Assuming that genetic variation within the two studied mitochondrial loci so far was insufficient to infer the apparently rapid early radiation of baboons we used complete mitochondrial sequence information of ten specimens, representing all major baboon lineages, to reconstruct a baboon phylogeny and to re‐estimate divergence times. Our data confirmed the earlier tree topology including the para‐ and polyphyletic relationships of most baboon species; divergence time estimates are slightly younger and credibility intervals narrowed substantially, thus making the estimates more precise. However, the most basal relationships could not be resolved and it remains open whether (1) the most southern population of baboons diverged first or (2) a major split occurred between southern and northern clades. Our study shows that complete mitochondrial genome sequences are more effective to reconstruct robust phylogenies and to narrow down estimated divergence time intervals than only short portions of the mitochondrial genome, although there are also limitations in resolving phylogenetic relationships. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Afrotherian phylogeny as inferred from complete mitochondrial genomes

Afrotheria is a huge assemblage of various mammals encompassing six orders that were once classified as distantly related groups. This superordinal relationship may have resulted from the break-up of Gondowanaland followed by the isolation of the African continent between 105 and 40 million years ago. Although the monophyly of Afrotheria is well supported by recent molecular studies, the interrelationships within afrotherian mammals remain unclarified. In this study, we determined the sequence of the complete mitochondrial genomes of hyrax, golden mole, and elephant shrew. These sequences were compared with those of other eutherians to analyze the phylogenetic relationships among afrotherians and, in particular, those among paenungulates. Our mitochondrial genome analysis supports the monophyly of Tethytheria.     

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 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.     

Automated sequencing of complete mitochondrial genomes from laser-capture microdissected samples

Mitochondrial DNA mutations have been related to both aging and a variety of diseases such as cancer. Due to the relatively small size of the genome (16 kb) and with the use of automated DNA sequencing, the entire genome can be sequenced from clinical specimens in days. We present a reliable approach to complete mitochondrial genome sequencing from laser-capture microdissected human clinical cancer specimens that overcome the inherent limitations of relatively small tissue samples and partial DNA degradation, which are unavoidable when laser-capture microdissection is used to attain pure populations of cells from heterogeneous tissues obtained from surgical procedures. The acquisition of sufficient template combined with a standard set of 18 pairs of PCR primers allows for the efficient amplification of the genome. Subsequent single-stranded amplification is performed using 36 sequencing primers, and samples are run on an ABI PRISM 3100 Genetic Analyzer. The use of this procedure should allow even investigators with little experience sequencing from clinical specimens success in complete mitochondrial genome sequencing.     

Horizontal gene transfer among microbial genomes: new insights from complete genome analysis

The determination and analysis of complete genome sequences has led to the suggestion that horizontal gene transfer may be much more extensive than previously appreciated. Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling.     

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

Saccharolobus (formerly Sulfolobus) shibatae B12, isolated from a hot spring in Beppu, Japan in 1982, is one of the first hyperthermophilic and acidophilic archaeal species to be discovered. It serves as a natural host to the extensively studied spindle-shaped virus SSV1, a prototype of the Fuselloviridae family. Two additional Sa. shibatae strains, BEU9 and S38A, sensitive to viruses of the families Lipothrixviridae and Portogloboviridae, respectively, have been isolated more recently. However, none of the strains has been fully sequenced, limiting their utility for studies on archaeal biology and virus–host interactions. Here, we present the complete genome sequences of all three Sa. shibatae strains and explore the rich diversity of their integrated mobile genetic elements (MGE), including transposable insertion sequences, integrative and conjugative elements, plasmids, and viruses, some of which were also detected in the extrachromosomal form. Analysis of related MGEs in other Sulfolobales species and patterns of CRISPR spacer targeting revealed a complex network of MGE distributions, involving horizontal spread and relatively frequent host switching by MGEs over large phylogenetic distances, involving species of the genera Saccharolobus, Sulfurisphaera and Acidianus. Furthermore, we characterize a remarkable case of a virus-to-plasmid transition, whereby a fusellovirus has lost the genes encoding for the capsid proteins, while retaining the replication module, effectively becoming a plasmid.     

Progress in the complete mitochondrial genomes of the Acari

蜱螨亚纲包括蜱类和螨类,是节肢动物中物种多样性最高的类群之一.本文综述了当前已测序的28种蜱螨线粒体基因组的研究成果.概括起来,蜱螨线粒体基因组具有以下特点:(1)大小变异显著,其中柑橘全爪螨Panonychus citri线粒体基因组在目前已测节肢动物中最小(13077 bp);(2)一般碱基组成偏向A和T,但6种蜱螨具有相反的GC-偏斜(正值);(3)基因组的碱基组成及A+T富集区的位置、长度和拷贝数等变异显著,其中4种叶螨的A+T含量最高,其A+T富集区在目前已测节肢动物中最短(44 -57 bp);(4)基因高度重排,特别是真螨总目的种类,但重排与高分类阶元无相关性;(5)真螨总目部分螨类的tRNA基因极度缩短,不能形成经典的三叶草二级结构.作者建议要进一步测定更多蜱螨的线粒体基因组,验证蜱螨非典型tRNA基因的生物学功能性,分析蜱螨线粒体基因组的分子进化机制,开展蜱螨线粒体转录组研究等.     

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.