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Query: UNIPROT:P06889 (Mol)
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The 3231-nucleotide-pair (ntp) sequence of one end of one of the two linear mitochondrial (mt) DNA molecules of Hydra attenuata (phylum Cnidaria, class Hydrozoa, order Anthomedusae) has been determined. This segment contains complete genes for tRNA(f-Met), l-rRNA, tRNA(Trp), subunit 2 of cytochrome c oxidase (COII), subunit 8 of ATP synthetase (ATPase8), and the 5' 136 ntp of ATPase6. These genes are arranged in the order given and are transcribed from the same strand of the molecule. As in two other cnidarians, the hexacorallian anthozoan Metridium senile and the octocorallian anthozoan Sarcophyton glaucum, the mt-genetic code of H. attenuata is near standard. The only modification appears to be that TGA specifies tryptophan rather than termination. Also as in M. senile and S. glaucum, the encoded H. attenuata mt-tRNA(f-Met) has primary and secondary structural features resembling those of Escherichia coli initiator tRNA(t-Met). As the encoded mt-tRNA(Trp) cannot be folded into a totally orthodox secondary structure, two alternative forms are suggested. The encoded H. attenuata mt-l-rRNA is 1738 nt, which is 451 nt shorter than the M. senile mt-l-rRNA. Comparisons of secondary structure models of these two mt-l-rRNAs indicate that most of the size difference results from loss of nucleotides in the H. attenuata molecule at a minimum of 46 locations, which includes elimination of six distinct helical elements.
J Mol Evol 2000 Oct
PMID:Mitochondrial DNA of Hydra attenuata (Cnidaria): a sequence that includes an end of one linear molecule and the genes for l-rRNA, tRNA(f-Met), tRNA(Trp), COII, and ATPase8. 1104 Feb 92

We describe polymerase chain reaction (PCR) primers for gut analysis of aphid predators. The primers amplify aphid mitochondrial COII fragments ranging in size from 77 to 386 bp. Using these primers, we were able to distinguish six species of US Great Plains cereal aphids, including two congeners, Rhopalosiphum maidis (Fitch) and R. padi (L.), and to detect them in extracts of coccinellid and chrysopid predators. We devised a protocol for deriving half-lives of detectability for the DNA of a single aphid consumed by predators maintained under simulated field dietary and temperature conditions. Using this protocol and primers that amplify a 198-bp fragment, we determined statistically different half-lives of detectability for a single R. maidis of 3.95 h in Chrysoperla plorabunda (Fitch) and 8. 78 h in Hippodamia convergens Guerin. The detectability half-life for a 339-bp R. maidis fragment was statistically longer in C. plorabunda but not in H. convergens. The sensitivity of the assay for the 198-bp fragment is 10-7 aphid equivalents. For species-specific predator gut analysis, PCR is superior to monoclonal antibody technology, giving comparable detectability half-lives with lower expense, much shorter development times, and greater certainty of a successful outcome.
Mol Ecol 2000 Nov
PMID:Identifying key cereal aphid predators by molecular gut analysis. 1109 24

We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.
Mol Phylogenet Evol 2000 Dec
PMID:Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. 1113 98

The complete nucleotide sequence of the mitochondrial genome of the crinoid Florometra serratissima has been determined. It is a circular DNA molecule, 16,005 bp in length, containing the genes for 13 proteins, small and large ribosomal RNAs, and 22 transfer RNAs (tRNAs). Three regions of unassigned sequence (UAS) greater than 73 bp have been located. The largest, UAS I, is 432 bp long and exhibits sequence similarity to the putative mitochondrial control regions seen in other animals. UAS II (77 bp) and UAS III (73 bp) are located between the 5' ends of coding sequences and may play roles as bidirectional promoters. Analyses of nucleotide composition revealed that the major peptide-encoding strand is high in T and low in C. This bias is reflected in a specific pattern of codon usage. Molecular phylogenetic analyses based on cytochrome c oxidase (COI, COII, and COIII) amino acid and nucleotide sequences did not resolve all the relationships between echinoderm classes. The overall animal mitochondrial gene content has been maintained in the crinoid, but there is extensive rearrangement with respect to both the echinoid and the asteroid mtDNA gene maps. Florometra serratissima has a novel genome organization in a segment containing most of the tRNA genes, large and small rRNA genes, and the NADH dehydrogenase subunit 1 and 2 genes. Potential pathways and mechanisms for gene rearrangements between mitochondrial gene maps of echinoderm classes and vertebrates are discussed as indicators of early deuterostome phylogeny.
Mol Biol Evol 2001 Jan
PMID:A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima. 1114 Nov 93

The genetic structure of Apis mellifera populations from the Canary Islands has been assessed by mitochondrial (restriction fragment length polymorphisms of the intergenic transfer RNAleu-COII region) and nuclear (microsatellites) studies. These populations show a low level of genetic variation in terms of average number of alleles and degree of heterozygosity. Significant differences in the distribution of alleles were found in both data sets, confirming the genetic differentiation among some of the islands but not within them. Two mitochondrial haplotypes characteristic of the Canary Islands are found at high frequencies, although populations are introgressed by imported honeybees of eastern European C lineage. This introgression is rather high on Tenerife and El Hierro and low on Gran Canaria and La Gomera, whereas on La Palma it has not been recorded. The finding of microsatellite alleles characteristic of the eastern European lineage corroborates the genetic introgression. Phylogenetic analyses indicate that the Canarian honeybees are differentiated from other lineages and provide genetic evidence of their African origin.
Mol Ecol 2001 Jul
PMID:Genetic structure and distinctness of Apis mellifera L. populations from the Canary Islands. 1147 40

Bivalves of the families Mytilidae and Unionidae show a unique mode of mitochondrial DNA inheritance called doubly uniparental inheritance. In addition to receiving the maternally transmitted mtDNA lineage, males receive a separate mtDNA genome from their fathers. This system is sometimes compromised, in that female genomes are occasionally recruited into the male cycle of inheritance. These masculinization events are common in the Mytilidae but have not been reported in the Unionidae. In order to estimate the age of the male and the female lineages in the Unionidae and to look for evidence of masculinization, we sequenced the junction between the cytochrome c oxidase II gene and the cytochrome c oxidase I gene. The unionid male and female lineages diverged approximately 450 MYA. There is no evidence for masculinization during this period, suggesting that there are taxon-specific differences in the rate of masculinization. Coincidentally, a 200-codon extension of the COII gene is present in the male genome of the Unionidae and may be responsible for the absence of masculinization.
Mol Biol Evol 2002 Aug
PMID:Ancient sex-specific extension of the cytochrome c oxidase II gene in bivalves and the fidelity of doubly-uniparental inheritance. 1214 Feb 44

The winter pine processionary moth has become an important pine pest in the last century, as a consequence of the spread of pine cultivation in the Mediterranean region. The pattern of genetic differentiation of this group, that includes two sibling species (Thaumetopoea pityocampa and Th. wilkinsoni), has been studied in nine populations using amplified fragment length polymorphism (AFLP) and single strand conformation polymorphism-sequence analysis (SSCP) of the mitochondrial cytochrome oxidase 1 (COI) and cytochrome oxydase 2 (COII). Results indicate the existence of strong genetic differentiation between the two species that became separated before the Quaternary ice ages. Moreover data indicate that Th. pityocampa has a strong geographical structure, particularly evident at the nuclear level, where all pairwise phiST resulted to be highly significant and individuals from the same population resulted to be strongly clustered when an individual tree was reconstructed. The estimates of the absolute number of migrants between populations (Nm), obtained from mitochondrial and nuclear DNA markers, suggest that gene flow is low and that a gender-related dispersal could occur in this species. The males appear to disperse more than females, contributing to the genetic diversity of populations on a relatively wide range, reducing the risks of inbreeding and the genetic loss associated with bottlenecks occurring in isolated populations.
Mol Ecol 2002 Nov
PMID:Genetic differentiation in the winter pine processionary moth (Thaumetopoea pityocampa--wilkinsoni complex), inferred by AFLP and mitochondrial DNA markers. 1240 53

Recent adaptive radiations provide excellent model systems for understanding speciation, but rapid diversification can cause problems for phylogenetic inference. Here we use gene genealogies to investigate the phylogeny of recent speciation in the heliconiine butterflies. We sequenced three gene regions, intron 3 ( approximately 550 bp) of sex-linked triose-phosphate isomerase (Tpi), intron 3 ( approximately 450 bp) of autosomal mannose-phosphate isomerase (Mpi), and 1,603 bp of mitochondrial cytochrome oxidase subunits I and II (COI and COII), for 37 individuals from 25 species of Heliconius and related genera. The nuclear intron sequences evolved at rates similar to those of mitochondrial coding sequences, but the phylogenetic utility of introns was restricted to closely related geographic populations and species due to high levels of indel variation. For two sister species pairs, Heliconius erato-Heliconius himera and Heliconius melpomene-Heliconius cydno, there was highly significant discordance between the three genes. At mtDNA and Tpi, the hypotheses of reciprocal monophyly and paraphyly of at least one species with respect to its sister could not be distinguished. In contrast alleles sampled from the third locus, Mpi, showed polyphyletic relationships between both species pairs. In all cases, recent coalescence of mtDNA lineages within species suggests that polyphyly of nuclear genes is not unexpected. In addition, very similar alleles were shared between melpomene and cydno, implying recent gene flow. Our finding of discordant genealogies between genes is consistent with models of adaptive speciation with ongoing gene flow and highlights the need for multiple locus comparisons to resolve phylogeny among closely related species.
Mol Biol Evol 2002 Dec
PMID:Phylogenetic discordance at the species boundary: comparative gene genealogies among rapidly radiating Heliconius butterflies. 1244 9

Single strand conformation polymorphisms (SSCPs) provide a convenient and inexpensive method of surveying mitochondrial genetic variation in large samples. We investigated how much variation should be incorporated into such surveys by scoring SSCP variation at eight mitochondrial loci in each of four sub-Saharan African and four North American house fly (Diptera: Muscidae.) populations. Hierarchical analysis of diversity was performed on haplotype frequencies at each locus and on haplotype frequencies formed by combining haplotypes from two, three, four, five and eight loci. Composite haplotypes at two loci were as informative about population structure as those composed of a greater number of loci. Increasing the number of loci increased diversity estimates within, but not between, populations. Mean composite haplotype diversities (16S2 and COII) were 0.49 +/- 0.09 among the African populations and 0.32 +/- 0.08 among the North American populations. Only two of 16 haplotypes were shared between continents. Nei's genetic differentiation statistic between populations in continents GPC was 0.30 +/- 0.06 and mean genetic differentiation between continents GCT was 0.39 +/- 0.06. We conclude that there has been little detectable gene flow between North America and sub-Saharan Africa.
Insect Mol Biol 2003 Apr
PMID:Mitochondrial diversity evaluated by the single strand conformation polymorphism method in African and North American house flies (Musca domestica L.). 1265 31

We investigated mitochondrial COII gene sequences of Japanese wood-feeding cockroaches (Salganea spp. and Panesthia angustipennis) in detail to investigate their biogeography. The transition (TI) numbers between each genus north and south of the Tokara Strait, which is a border of the Oriental and the Palaearctic faunal regions, were almost same, but the transversion (TV) numbers were much lower in Panesthia compared with Salganea. These tendencies suggest that multiple substitutions of TIs occurred between certain pairs of Salganea taxa and that the genera must have entered to the north of the Tokara Strait at different times. Phylogenetic relationships and estimated divergence times using TVs divergences suggest that Salganea species and Panesthia taxa north and south of the Tokara Strait were diverged from each other during the latter half of the Miocene and from the late Pliocene to the early Pleistocene, respectively. These two periods are nearly consistent with the two land expanding times in the Ryukyu Islands supported by the recent palaeogeographical hypotheses.
Mol Phylogenet Evol 2003 Apr
PMID:Biogeography of Japanese wood-feeding cockroaches genus Salganea and Panesthia (Blaberidae: Panesthiinae). 1267 80


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