The Complete Mitochondrial Genomes of Six Species of Tetranychus Provide Insights into the Phylogeny and Evolution of Spider Mites

Many spider mites belonging to the genus Tetranychus are of agronomical importance. With limited morphological characters, Tetranychus mites are usually identified by a combination of morphological characteristics and molecular diagnostics. To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared. The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans. The order of the mitochondrial (mt) genes is the same as that in the mt genomes of Panonychus citri and P. ulmi, but very different from that in other Acari. The J-strands of the mitochondrial genomes have high (∼84%) A+T contents, negative GC-skews and positive AT-skews. The nucleotide sequence of the cox1 gene, which is commonly used as a taxon barcode and molecular marker, is more highly conserved than the nucleotide sequences of other mitochondrial genes in these seven species. Most tRNA genes in the seven genomes lose the D-arm and/or the T-arm. The functions of these tRNAs need to be evaluated. The mitochondrial genome of T. malaysiensis differs from the other six genomes in having a slightly smaller genome size, a slight difference in codon usage, and a variable loop in place of the T-arm of some tRNAs by a variable loop. A phylogenic analysis shows that T. malaysiensis first split from other Tetranychus species and that the clade of the family Tetranychoidea occupies a basal position in the Trombidiformes. The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.     

The Complete Mitochondrial Genome of the Entomopathogenic Nematode Steinernema carpocapsae: Insights into Nematode Mitochondrial DNA Evolution and Phylogeny

We determined the complete sequence of the mitochondrial DNA of the entomopathogenic nematode Steinernema carpocapsae and analyzed its structure and composition as well as the secondary structures predicted for its tRNAs and rRNAs. Almost the complete genome has been amplified in one fragment with long PCR and sequenced using a shotgun strategy. The 13,925-bp genome contains genes for 2 rRNAs, 22 tRNAs, and 12 proteins and lacks an ORF encoding ATPase subunit 8. Four initiation codons were inferred, TTT, TTA, ATA, and ATT, most of the genes ended with TAA or TAG, and only two had a T as an incomplete stop codon. All predicted tRNAs showed the nonconventional secondary structure typical of Secernentea. Although we were able to fold the sequences of trnN, trnD, and trnC into more conventional cloverleaf structures after adding adjacent nucleotides, northern blot experiments showed that the nonstandard tRNAs are actually expressed. Phylogenetic and comparative analyses showed that the mitochondrial genome of S. carpocapsae is more closely related to the genomes of A. suum and C. elegans than to that of Strongyloides stercoralis. This finding does not support the phylogeny based on nuclear small subunit ribosomal DNA sequences previously published. This discrepancy may result from differential reproductive strategies and/or differential selective pressure acting on nuclear and mitochondrial genes. The distinctive characteristics observed among mitochondrial genomes of Secernentea may have arisen to counteract the deleterious effects of Muller’s ratchet, which is probably enhanced by the reproductive strategies and selective pressures referred to above. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Rafael Zardoya]     

Chronology of Deep Nodes in the Neotropical Primate Phylogeny: Insights from Mitochondrial Genomes

The evolution of Neotropical Primates (NP) is permeated by factors associated with the pattern of diversification and the biogeography of the major lineages. These questions can be better understood by providing a robust estimate of the chronological scenario of NP evolution, a reason why molecular dating methods have been widely applied. One aspect of especial interest is the timing of diversification of the major NP lineages (pitheciids, atelids and cebids), which may have resulted from rapid episodes of adaptive radiation, a question that requires NP divergence time estimates with accurate statistical certainty. In this study, we evaluated the primate timescale focused on the age of nodes of NP radiation. We investigated the performance of complete primate mitochondrial genomes as traditional molecular markers of primate evolution and further including original mitochondrial data from the endangered muriqui, Brachyteles arachnoides (Accession No. {"type":"entrez-nucleotide","attrs":{"text":"JX262672","term_id":"403488686","term_text":"JX262672"}}JX262672). Comparisons of the age estimates at NP nodes based on mitochondrial genomes with those obtained from a nuclear supermatrix showed similar degrees of uncertainty. Further molecular data and more informative calibration priors are required for a more precise understanding of the early NP diversification.     

New insights into an ancient insect nose: the olfactory pathway of Lepismachilis y-signata (Archaeognatha: Machilidae)

Hexapods most likely derived from an aquatic ancestor, which they shared with crustaceans. During the transition from water to land, their sensory systems had to face the new physiological demands that terrestrial conditions impose. This process also concerns the sense of smell and, more specifically, detection of volatile, air-borne chemicals. In insects, olfaction plays an important role in orientation, mating choice, and food and host finding behavior. The first integration center of odor information in the insect brain is the antennal lobe, which is targeted by the afferents from olfactory sensory neurons on the antennae. Within the antennal lobe of most pterygote insects, spherical substructures called olfactory glomeruli are present. In order to gain insights into the evolution of the structure of the central olfactory pathway in insects, we analyzed a representative of the wingless Archaeognatha or jumping bristletails, using immunocytochemistry, antennal backfills and histological section series combined with 3D reconstruction. In the deutocerebrum of Lepismachilis y-signata, we found three different neuropil regions. Two of them show a glomerular organization, but these glomeruli differ in their shape from those in all other insect groups. The connection of the glomerular neuropils to higher brain centers remains unclear and mushroom bodies are absent as reported from other archaeognathan species. We discuss the evolutionary implications of these findings.     

A Phylogeny of the Bears (Ursidae) Inferred from Complete Sequences of Three Mitochondrial Genes

Complete sequences of DNA are described for the cytochrome b, tRNA^Thrand tRNA^Progenes of mitochondria of four extant species of ursids and compared to sequences of four other species of ursids previously studied by us. Phylogenetic analyses indicate that the giant panda and the spectacled bear are the basal taxa of the ursid radiation. The ursines, a group which includes the sun bear, sloth bear, American black bear, Asiatic black bear, brown bear, and polar bear, experienced a rapid radiation during the mid Pliocene to early Pleistocene. The Asiatic black bear and American black bear are sister taxa. The brown bear and polar bear are the most recently derived of the ursines, with the polar bear originating from within a clade of brown bears during the Pleistocene. This paraphyletic association suggests that the rate of morphological evolution may be accelerated relative to that of molecular evolution when a new ecological niche is occupied. Calibration of the corrected average number of nucleotide differences per site with the fossil record indicates that transitions at third positions of codons in the ursid cytochrome b gene occur at a rate of approximately 6% per million years, which is considerably slower than comparable values reported for other species of mammal.     

Phylogeny of embiopterans (Insecta)

A cladistic analysis of embiopterans, based on 157 species (representing 70% of the known genera) and 186 morphological characters, is presented, as well as a molecular analysis for 22 taxa using genes encoding 16S, 18S and 28S rDNA and COI. Species of all known families are included, except Andesembiidae Ross (specimens of which are in a private collection). The evidence presented supports the monophyly of four of the families (Australembiidae, Oligotomidae, Teratembiidae, and Anisembiidae). Notoligotomidae is paraphyletic and included within the Afro‐neotropical family Archembiidae (which is also paraphyletic). The genera Embia, Cleomia, Macrembia, and Dihybocercus (Embiidae) form, together with Australembiidae, a group strongly supported by morphology; the position of the remaining genera of Embiidae has two quite different resolutions. Almost 80% of the genera of Anisembiidae recently described appear as either paraphyletic or polyphyletic. Contrary to the opinion of other specialists, the major groups as well as the monophyly of some families are supported by features which have been ignored in classical approaches to the systematics of Embioptera, such as the ovipositor and cephalic and leg structures, characters with an almost perfect fit.     

Phylogeny of Ptychopteroidea (Insecta: Diptera)

A phylogenetic tree is proposed for the superfamily Ptychopteroidea, reconstructed taking into account both extinct and extant taxa and based mainly on characters of wing venation.     

Phylogeny of Oestridae (Insecta: Diptera)

The phylogeny of Oestridae was analysed at the generic level using 118 characters from all developmental stages and including morphology, ontogeny, physiology and behaviour. Four major clades were given subfamilial rank with the phylogenetic relationship (Cuterebrinae (Gasterophilinae (Hypodermatinae + Oestrinae))). The subdermal parasites of the African elephant, Neocuterebra squamosa Grünberg and Ruttenia loxodontis Rodhain, had their most probable affiliation subordinate to the clade of stomach parasites, although their exact position needs further investigation. Genus Ochotonia Grunin, which is known from a single third‐instar larva only, was the probable sister group of all other Hypodermatinae. Twenty‐five oestrid genera were recognised as valid and those containing more than one species were defined through lists of autapomorphies. Cuterebra Clark was proposed as a senior synonym of Alouattamyia Townsend, Andinocuterebra Guimarães, Pseudogametes Bischof and Rogenhofera Brauer. The clade of hypodermatine ungulate parasites (Hypoderma Latreille +Pallasiomyia Rubtzov +Pavlovskiata Grunin +Przhevalskiana Grunin +Strobiloestrus Brauer) remained largely unresolved, and genus Przhevalskiana emerged without defining characters.     

湾鳄(Crocodylus porosus)线粒体基因组全序列结构分析与鳄类系统发生

该文测序了湾鳄的线粒体基因组全序列,全长为16,917bp。湾鳄mtDNA结构与其他脊椎动物相似,由22个tRNA,2个rRNA和13个蛋白质编码基因及1个非编码的控制区(D-loop)所组成。除NADH6和tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer(UCN)、tRNAGlu、tRNAPro在L-链上编码之外,其余基因均在H-链编码。基因排列顺序与已测序的鳄类一致,这显示了鳄类线粒体基因排列顺序上的保守性。但鳄类线粒体基因排列顺序与脊椎动物的典型排列方式相比,有较大的差异,尤其是tRNAPhe基因的重排、tRNASer-tRNAHis-tRNALeu基因族的排列方式等。湾鳄mtDNA和已测序的鳄类一样,缺失轻链复制起始点(OLR)。基于17种鳄mtDNA控制区保守区,采用PAUP4.0最大简约法(Maximumparsimony,MP)构建MP树,邻接法(Neighbor-joiningmethod,NJ)构建NJ树,结果显示:食鱼鳄(Gavialisgangeticus)和假食鱼鳄(Tomistomaschlegelii)聚为一支后再与鳄科(Crocodylidae)的其他物种形成姐妹群,这与基于食鱼鳄和假食鱼鳄的线粒体全序列的分析结果一致,支持将食鱼鳄并入鳄科的观点。结果还支持非洲窄吻鳄(Crocodyluscataphractus)与鳄属(Crocodylus)构成姐妹群,可以单独划分为属的观点。     

Phylogeny of the Ecnomidae (Insecta: Trichoptera)

Ecnomidae are a family of seven previously accepted extant genera having a typical Gondwanan distribution, except one genus ( Ecnomus ) being widely distributed also in the Oriental and Palearctic regions. We analysed a molecular data set of 3379 characters representing the sum of four different protein-coding genes (COI, CAD, EF-1a and POL-II). Six equally most parsimonious trees were generated from the combined data set, distributed into two distinct islands. In all maximum parsimony (MP) trees the Ecnomidae is monophyletic when the genus Zelandoptila (Psychomyiidae) is included. The sister group to Ecnomidae including Zelandoptila is Pseudoneureclipsis , previously classified in the other families. This sister-group relationship contradicts earlier findings that the Polycentropodidae are the sister group to Ecnomidae. A Bayesian analysis resulted in a monophyletic Ecnomidae when accepting inclusion of Pseudoneureclipsis , which contradicts the results from the MP analysis by leaving Zelandoptila as the sister group to Ecnomidae including Pseudoneureclipsis . In the majority rule tree from this analysis Polycentropodidae form the sister group to Ecnomidae. We were not able to obtain a monophyletic Ecnomus due to the inclusion of Psychomyillodes . We conclude that the genus Zelandoptila or Pseudoneureclipsis probably belongs to the Ecnomidae, and that Psychomyiellodes and Ecnomus are synonyms. Three additional, as yet undescribed monotypic genera from Australia and New Caledonia remain to be erected in Ecnomidae.
© The Willi Hennig Society 2009.     

Phylogeny of the Neuropterida (Insecta: Holometabola)

The Neuropterida, with about 6500 known species — living fossils in a way — at the base of the Holometabola (as a sister group of the Coleoptera), comprise Raphidioptera (about 210 species, two families), Megaloptera (about 300 species, two families) and Neuroptera (6000 species, 17 families). Megaloptera + Neuroptera is argued vs. the traditional Raphidioptera + Megaloptera. Raphidioptera are undisputedly monophyletic. Monophyly of Megaloptera is the operational hypothesis, although occasionally questioned. Sucking tubes of the larvae are the most spectacular autapomorphy of Neuroptera. The construction of larval head capsules indicates three evolutionary lines: Nevrorthiformia, and Myrmeleontiformia + Hemerobiiformia. Traditional Myrmeleontiformia is Psychopsidae + (Nemopteridae + (Nymphidae + (Myrmeleontidae + Ascalaphidae))), the present approach is (Psychopsidae + Nemopteridae) + all other Myrmeleontiformia. Hemerobiiformia are based on the ‘maxillary head’ concept. The ithonid clade Ithonidae/Rapismatidae + Polystoechothidae and the dilarid clade Dilaridae + (Mantispidae + (Rhachiberothidae + Berothidae)) are based on robust criteria. Other relationships remain unclear: Hemerobiidae + Chrysopidae (on similarity) and the ‘early offshoot’ concept of coniopterygidae (on autapomorphies) should not be perpetuated. Chysopidae + Osmylidae and (Hemerobiidae + (Coniopterygidae + Sisyridae)) + dilarid clade are discussed. Aquatic larvae, regarded as independent apomorphies of megaloptera and neuropteran Nevrorthidae and Sisyridae for a long time, are re‐interpreted as a synapomorphy of Megaloptera + Neuroptera and thus plesiomorphic within these groups. Terrestrial larvae (with cryptonephry to solve osmotic problems) are consequently apomorphic. Aquatic Sisyridae with cryptonephry of a single malpighian tubule, is conflicting, but larvae may have become secondarily aquatic, after a terrestrial intermezzo.     

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

Background

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.

Methodology/Principal Findings

We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.

Conclusion

The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.     

Phylogeny of caddisflies (Insecta, Trichoptera)

Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Previous phylogenetic hypotheses and progress on our ongoing data collection are summarized. Fragments of the large and small subunit nuclear ribosomal RNAs (D1, D3, V4–5), the nuclear elongation factor 1 alpha gene and a fragment of mitochondrial cytochrome oxidase 1 (COI) were sequenced, and molecular data were combined with previously published morphological data. Equally and differentially weighted parsimony analyses were conducted in order to present a phylogeny of Trichoptera, including 43 of 45 families. Our phylogeny closely resembles that proposed by Herbert Ross with respect to the relationships among suborders, with a monophyletic Annulipalpia at the base of the tree, and a clade consisting of Spicipalpia plus a monophyletic Integripalpia. The monophyly of Spicipalpia is weakly supported in the combined equally weighted analysis, and Spicipalpia is paraphyletic in the differentially weighted analysis. Within Integripalpia, our phylogeny recovered monophyletic Plenitentoria, Brevitentoria and Sericostomatoidea. Leptoceroidea was unresolved in the equally weighted analysis and monophyletic in the differentially weighted analysis. Within Annulipalpia, we recovered a basal but paraphyletic Philopotamoidea and a monophyletic Hydropsychoidea.     

Maximum Likelihood Analysis of the Complete Mitochondrial Genomes of Eutherians and a Reevaluation of the Phylogeny of Bats and Insectivores

The complete mitochondrial genomes of two microbats, the horseshoe bat Rhinolophus pumilus, and the Japanese pipistrelle Pipistrellus abramus, and that of an insectivore, the long-clawed shrew Sorex unguiculatus, were sequenced and analyzed phylogenetically by a maximum likelihood method in an effort to enhance our understanding of mammalian evolution. Our analysis suggested that (1) a sister relationship exists between moles and shrews, which form an eulipotyphlan clade; (2) chiropterans have a sister-relationship with eulipotyphlans; and (3) the Eulipotyphla/Chiroptera clade is closely related to fereuungulates (Cetartiodactyla, Perissodactyla and Carnivora). Divergence times on the mammalian tree were estimated from consideration of a relaxed molecular clock, the amino acid sequences of 12 concatenated mitochondrial proteins and multiple reference criteria. Moles and shrews were estimated to have diverged approximately 48 MyrBP, and bats and eulipotyphlans to have diverged 68 MyrBP. Recent phylogenetic controversy over the polyphyly of microbats, the monophyly of rodents, and the position of hedgehogs is also examined. Received: 21 December 2000 / Accepted: 16 February 2001     

The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura

Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (??0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.

     

Phylogeny of the Hymenoptera (Insecta): The state of the art

The Hymenoptera form one of the major insect orders in terms of species diversity and they are also of great ecological and economic importance, notably as pollinators and natural enemies of pests. Phylogenies provide an essential framework for systematic, comparative and evolutionary research on hymenopterans. Here, I summarise what we know about the higher-level phylogeny of the Hymenoptera based on presentations given at a recent symposium on hymenopteran phylogenetics. I identify agreement and conflict among morphological and molecular analyses and suggest important priority areas for future research.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth(Mammuthus primigenius), and the Asian(Elephas maximus) and African savanna(Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch—the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population ofM. primigenius throughout the late Pleistocene.     

The Complete Chloroplast and Mitochondrial Genomes of the Green Macroalga Ulva sp. UNA00071828 (Ulvophyceae,Chlorophyta)

Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).