Molecular systematics of aphids and their primary endosymbionts

Aphids constitute a monophyletic group within the order Homoptera (i.e., superfamily Aphidoidea). The Aphidoidea originated in the Jurassic about 150 my ago from some aphidiform ancestor whose origin can be traced back to about 250 my ago. They exhibit a mutualistic association with intracellular bacteria (Buchnera sp.) related to Escherichia coli. Buchnera is usually considered the aphids' primary endosymbiont. The association is obligate for both partners. The 16S rDNA-based phylogeny of Buchnera from four aphid families showed complete concordance with the morphology-based phylogeny of their aphid hosts, which pointed to a single original infection in a common ancestor of aphids some 100-250 my ago followed by cospeciation of aphids and Buchnera. This study concentrated on the molecular phylogeny of both the aphids and their primary endosymbionts of five aphid families including for the first time representatives of the family Lachnidae. We discuss results based on two Buchnera genes (16S rDNA and the beta subunit of the F-ATPase complex) and on one host mitochondrial gene (the subunit 6 of the F-ATPase complex). Although our data do not allow definitive evolutionary relationships to be established among the different aphid families, some traditionally accepted groupings are put into question from both bacterial and insect data. In particular, the Lachnidae and the Aphididae, which from morphological data are considered recently evolved sister groups, do not seem to be as closely related as is usually accepted. Finally, we discuss our results in the light of the proposed parallel evolution of aphids and their endosymbionts.     

Chromosomes of tuatara, Sphenodon, a chromosome heteromorphism and an archaic reptilian karyotype

We examined karyotypes of the endemic New Zealand reptile genus Sphenodon (tuatara) from five populations, finding a karyotype unchanged for at least one million years. Animals karyotyped were from five geographically distinct populations, representing three groups, namely S. guntheri, S. punctatus (Cook Strait group), and S. punctatus (northeastern North Island group). All five populations have a diploid chromosome number of 2n = 36, consisting of 14 pairs of macrochromosomes and four pairs of microchromosomes. Chromosomal differences were not found between the five populations nor between female and male animals, except for one animal with a structural heteromorphism. Similarity between Sphenodon and Testudine karyotypes suggests an ancestral karyotype with a macrochromosome complement of 14 pairs and the ability to accumulate variable numbers of microchromosome pairs. Our research supports molecular phylogenies of the Reptilia.     

Molecular organization and heredity of the mitochondrial genome in Basidiomycetes

Conclusion The studies on basidiomycete mitochondrial genomes provide numerous amounts of information with important repercussions on fundamental as well as aplied fields of mycology. This information is particularly interesting to furnish performant molecular markers (RFLPs) which allow a precise characterization of species and, within a species, constitute strain-specific markers.Moreover, these markers will be useful to correlate sequences of the mitochondrial genome with physiologically important and, at this time, seemingly unrelated functions.The analysis of the complex mitochondrial heredity of basidiomycetes will allow a better understanding of the transmission of mitochondria in eukaryotic life cycles and especially a characterization of the molecular mechanisms involved in mitochondria selection after plasmogamy in these somatogamic species and, certainly, in other eukaryotic cells.     

Molecular phylogenetics of 'river dolphins' and the baiji mitochondrial genome

It is well known that the classical river dolphins are not a natural group, but up to now the phylogenetic relationships among them are not very clear because different views have been referred from different studies. In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of the baiji (Lipotes vexillifer), the most endangered cetacean species, and conducted phylogenetic analyses for the classical river dolphins based on data from cetacean mitochondrial genomes available. In our analyses, the classical river dolphins split into two separate lineages, Platanista and Lipotes+(Inia+Pontoporia), having no sister relationship with each other, and the Platanista lineage is always within the odontocete clade instead of having a closer affinity to Mysticeti. The position of the Platanista is more basal, suggesting separate divergence of this lineage well before the other one. The Lipotes has a sister relationship with Inia+pontoporia, and they together formed the sister group to the Delphinoidea. This result strongly supports paraphyly of the classical river dolphins, and the nonplatanistoid river dolphins do represent a monophyletic grouping, with the Lipotidae as the sister taxa to (Iniidae+Pontoporiidae), and is well congruent with the studies based on short interspersed repetitive elements (SINEs).     

Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources

For their apparent morphological simplicity, the Platyhelminthes or “flatworms” are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade.Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a “Turbellarian-like” clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.     

Phylogeny of the M superhaplogroup inferred from complete mitochondrial genome sequence of Indian specific lineages

Background  

Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.     

Molecular characterization of a cloned dolphin mitochondrial genome

Summary DNA clones have been isolated that span the complete mitochondrial (mt) genome of the dolphin,Cephalorhynchus commersonii. Hybridization experiments with purified primate mtDNA probes have established that there is close resemblance in the general organization of the dolphin mt genome and the terrestrial mammalian mt genomes. Sequences covering 2381 bp of the dolphin mt genome from the major noncoding region, three tRNA genes, and parts of the genes encoding cytochrome b, NADH dehydrogenase subunit 3 (ND3), and 16S rRNA have been compared with corresponding regions from other mammalian genomes. There is a general tendency throughout the sequenced regions for greater similarity between dolphin and bovine mt genomes than between dolphin and rodent or human mt genomes.     

Molecular systematics of the Canidae

Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.     

Molecular systematics of theDrosophila hydei subgroup as inferred from mitochondrial DNA sequences

The phylogeny of theDrosophila hydei subgroup, which is a member of theD. repleta species group, was inferred from 1,515 base pairs of mitochondrial DNA sequence of the cytochrome oxidase subunits I, II, and III. Four of the seven species in the subgroup were examined, which are placed into two taxonomic complexes: theD. bifurca complex (D. bifurca) andD. nigrohydei) and theD. hydei complex (D. hydei and (D. eohydei). Both complexes appear to be monophyletic, although theD. bifurca complex is only weakly supported. The evolution of chromosomal change, interspecific crossability, sperm gigantism, and divergence times of the subgroup is discussed in a phylogenetic context. Correspondence to: G. Spicer     

The primary structure of the mitochondrial genome of Saccharomyces cerevisiae--a review

We have collated and compiled all the available primary structure data on the mitochondrial genome of Saccharomyces cerevisiae. Data concern 78,500 bp, namely 92% of the 'long' genomes; they are derived from several laboratory strains. Interstrain differences belong to three classes: a small number of large deletions/additions, mainly concerning introns; a large number of small (10-150 bp) deletions/additions located in the intergenic sequences; 1-3 bp deletions/additions and point mutations; the interstrain sequence divergence due to the latter, is of the order of 2% for the strains compared; this low value is, however, an overestimate because of sequence mistakes.     

Mining the mammalian genome for artiodactyl systematics

A total of 7,806 nucleotide positions derived from one mitochondrial and eight nuclear DNA segments were used to provide a robust phylogeny for members of the order Artiodactyla. Twenty-four artiodactyl and two cetacean species were included, and the horse (order Perissodactyla) was used as the outgroup. Limited rate heterogeneity was observed among the nuclear genes. The partition homogeneity tests indicated no conflicting signal among the nuclear genes fragments, so the sequence data were analyzed together and as separate loci. Analyses based on the individual nuclear DNA fragments and on 34 unique indels all produced phylogenies largely congruent with the topology from the combined data set. In sharp contrast to the nuclear DNA data, the mtDNA cytochrome b sequence data showed high levels of homoplasy, failed to produce a robust phylogeny, and were remarkably sensitive to taxon sampling. The nuclear DNA data clearly support the paraphyletic nature of the Artiodactyla. Additionally, the family Suidae is diphyletic, and the nonruminating pigs and peccaries (Suiformes) were the most basal cetartiodactyl group. The morphologically derived Ruminantia was always monophyletic; within this group, all taxa with paired bony structures on their skulls clustered together. The nuclear DNA data suggest that the Antilocaprinae account for a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa, and the Giraffidae are more primitive.     

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e. , represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau. On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister taxa of one steppe dweller and one shrub dweller is very low. These findings support the hypothesis that pikas have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution.     

Molecular systematics of the genus Neotoma

DNA sequences from the mitochondrial DNA cytochrome-b gene were used to infer the systematic relationships of 13 species of wood rats (genus Neotoma). Parsimony, likelihood, and neighbor-joining analyses produced similar topologies in most cases and produced six systematic conclusions. First, results of previous studies were supported in the recognition of N. floridana magister as distinct species (N. magister). Second, evidence was provided for the recognition of cryptic species within N. albigula (N. albigula and N. leucodon) and N. mexicana (N. mexicana, N. isthmica, and N. picta). Third, the subgenus Neotoma is composed of four species groups (floridana, lepida, mexicana, and micropus). Fourth, support was provided for placement of N. stephensi within the lepida species group. Fifth, support was provided for the recognition of Hodomys as a separate genus, sister to Xenomys. Sixth, support for the elevation of the subgenus Teonoma to generic status is discussed.     

Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents

Nuclear sequences of mitochondrial origin (numts) are common among animals and plants. The mechanism(s) by which numts transfer from the mitochondrion to the nucleus is uncertain, but their insertions may be mediated in part by chromosomal repair mechanisms. If so, then lineages where chromosomal rearrangements are common should be good models for the study of numt evolution. Arvicoline rodents are known for their karyotypic plasticity and numt pseudogenes have been discovered in this group. Here, we characterize a 4 kb numt pseudogene in the arvicoline vole Microtus rossiaemeridionalis. This sequence is among the largest numts described for a mammal lacking a completely sequenced genome. It encompasses three protein-coding and six tRNA pseudogenes that span ∼25% of the entire mammalian mitochondrial genome. It is bordered by a dinucleotide microsatellite repeat and contains four transposable elements within its sequence and flanking regions. To determine the phylogenetic distribution of this numt among the arvicolines, we characterized one of the mitochondrial pseudogenes (cytochrome b) in 21 additional arvicoline species. Average rates of nucleotide substitution in this arvicoline pseudogene are estimated as 2.3 × 10⁻⁸ substitutions/per site/per year. Furthermore, we performed comparative analyses among all species to estimate the age of this mitochondrial transfer at nearly 4 MYA, predating the origin of most arvicolines. All sequences generated in this study have been deposited within the GenBank database.