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Query: UNIPROT:P06889 (Mol)
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A PCR primer from the mitochondrial COI gene is described that enhances the amplification of the COI-COII region of insect mtDNA. When used in conjunction with a primer from the COII gene identified by R. Crozier, a 1600-1700 bp segment is amplified in nine species of insects representing the orders Lepidoptera, Diptera, Coleoptera and Hymenoptera.
Insect Mol Biol 1993
PMID:An improved primer for PCR amplification of mitochondrial DNA in a variety of insect species. 908 47

We inferred the incidence of nucleotide conversions in the COI and 16S rRNA mitochondrial genes of members of the Symphyta and basal Apocrita (Hymenoptera). Character-state reconstructions in both genes suggested that conversions between A and T (AT transversions) occurred much more frequently than any other type of change, although we cannot wholly discount an underlying transition bias. Parsimony analysis of COI nucleotide characters did not recover phylogeny; e.g., neither the Tenthredinoidea nor Apocrita were recovered as monophyletic. However, analysis of COI amino acid characters did recover these relationships, as well as others based on fossil and morphological evidence. Analysis of 16S rRNA characters also recovered these relationships providing conversions between A and T were down-weighted. Analysis of the combined data sets gave relatively strong support for various relationships, suggesting that both data sets supported similar topographies. These data sets, both separately and combined, suggested that the phytophagous Siricidae were more closely related to the predominantly parasitic Apocrita than were the ectoparasitic Orussoidea. This suggests that the wasp parasitic lifestyle did not have a single origin, unless the Siricidae have more recently reverted to phytophagy. Alternatively, parasitism evolved twice independently, once in the Orussoidea and again in the Apocrita. The latter scenario is supported by the observation that the evolution of parasitism was accompanied by a tendency for the larvae to develop inside plant tissues. Adaptations that accompanied the movement of wasps into a confined, wood-boring habitat may have preadapted them to becoming ectoparasitic.
J Mol Evol 1997 Apr
PMID:Evidence for AT-transversion bias in wasp (Hymenoptera: Symphyta) mitochondrial genes and its implications for the origin of parasitism. 908 79

A set of mitochondrial COI primers has been studied by genomic PCR and many primer combinations shown to work universally well across Insecta. They are able to amplify various amplicons with different variability which enables the selection of a particular amplicon as a suitable DNA marker for a project. The potential usefulness of different amplicons is examined, with analysis on published study cases employing these regions. With respect to their variability, amplicons UEA5/UEA6, UEA7/UEA8 and UEA5/UEA8 could be useful for low- to mid-level phylogenetic analysis, i.e. from species, genus to perhaps family level depending on taxa involved. UEA5/UEA6 will be too conserved for intraspecific studies. Amplicons UEA3/UEA4 and UEA9/UEA10 would be better suited to low-level phylogenetic investigations, such a analysis of relationships among closely related species and population genetic studies. However, these guidelines should not be over-generalized for the reasons given. Amplification conditions of various primer combinations, and general problems in the use of conserved PCR primers are discussed.
Insect Mol Biol 1997 May
PMID:Assessment of the universality and utility of a set of conserved mitochondrial COI primers in insects. 909 78

The neotropical pseudoscorpion Cordylochernes scorpioides (Chernetidae: Lamprochernetinae) is currently described as a single species ranging from Central America to northern Argentina. However, interpopulation crosses have recently demonstrated that C. scorpioides actually represents a complex of cryptic species. Here we present mitochondrial COI gene sequence data from C. scorpioides individuals from Panama, Trinidad, and French Guiana which demonstrate little or no intrapopulation variability but divergence ranging from 2.6 to 13.8% between geographic populations. Phylogenetic analysis provides evidence of a major split between C. scorpioides lineages from Central and South America. Levels of interpopulation mtDNA divergence correspond well with previously established patterns of postzygotic reproductive incompatibility between geographically distinct units within the C. scorpioides complex. By contrast, multivariate morphometric analysis demonstrates that extensive sequence divergence has occurred in the absence of appreciable morphological differentiation between the populations. To provide a framework for assessing the scale of geographic divergence in C. scorpioides, Cordylochernes sequences were compared with homologous sequence from its presumed sister taxon, Lustrochernes, and from Parachernes and Semeiochernes, representatives of the second chernetid subfamily, the Chernetinae. Our preliminary, generic-level analysis suggests that COI sequence data may prove useful in resolving relationships within this problematic family.
Mol Phylogenet Evol 1997 Apr
PMID:Mitochondrial DNA sequencing reveals extreme genetic differentiation in a cryptic species complex of neotropical pseudoscorpions. 912 63

A phylogenetic tree for major lineages of iguanian lizards is estimated from 1,488 aligned base positions (858 informative) of newly reported mitochondrial DNA sequences representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Two well-supported groups are defined, the Acrodonta and the Iguanidae (sensu lato). This phylogenetic hypothesis is used to investigate evolutionary shifts in mitochondrial gene order, origin for light-strand replication, and secondary structure of tRNACys. These three characters shift together on the branch leading to acrodont lizards. Plate tectonics and the fossil record indicate that these characters changed in the Jurassic. We propose that changes to the secondary structure of tRNACys may destroy function of the origin for light-strand replication which, in turn, may facilitate shifts in gene order.
J Mol Evol 1997 Jun
PMID:Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards. 916 59

An A to G point mutation at nucleotide position 7445 in the mitochondrial DNA genome is associated with maternally-inherited sensorineural deafness in two separate human pedigrees. To determine whether this point mutation [tRNA(SER)UCN)/COI A7445G] led to sensorineural deafness by affecting cellular energy metabolism we investigated the bioenergetic function of mitochondria in lymphoblastoid cultures established from these patients. Even though essentially all of the mitochondrial DNA in these cells contained the mutation at nucleotide position 7445, there was no effect on a number of mitochondrial bioenergetic functions (mitochondrial content, membrane potential in both intact and digitonin-permeabilised cells, cellular ATP/ADP ratios and respiratory enzyme activity) when compared with control cells. The implications of these findings for both the aetiology of the sensorineural deafness associated with the A7445G mtDNA mutation, and the role of bioenergetic defects in mitochondrial DNA diseases in general are discussed.
Biochem Mol Biol Int 1997 Jul
PMID:The effect on mitochondrial function of the tRNA Ser(UCN)/COI A7445G mtDNA point mutation associated with maternally-inherited sensorineural deafness. 924 14

Vestimentiferan tube worms from deep-sea hydrothermal vents and cold-water seeps rely entirely on sulfur-oxidizing bacterial endosymbionts for nutriment. We examined host-symbiont co-evolution by comparing phylogenetic trees from symbiont 16S ribosomal DNA and host mitochondrial COI genes. The endosymbionts comprised two distinct clades, one associated with tube worms from basaltic vent habitats and the other associated with tube worms from sedimented seep-like environments. Within each symbiont clade, 16S rDNA sequences were nearly identical, suggesting that vent vestimentiferans share a single endosymbiont species that is distinct from the seep endosymbiont species. A third endosymbiont type, related to the seep species, was found in a tube worm collected from a whale carcass. Our results are consistent with a horizontal model of symbiont transmission.
Mol Mar Biol Biotechnol 1997 Sep
PMID:Molecular phylogenetics of bacterial endosymbionts and their vestimentiferan hosts. 928 65

The coffee berry borer beetle Hypothenemus hampei (Ferrari) (Curculionidae: Scolytinae) is the major insect pest of coffee and has spread to most of the coffee-growing countries of the world. This beetle also displays an unusual life cycle, with regular sibling mating. This regular inbreeding and the population bottlenecks occurring on colonization of new regions should lead to low levels of genetic diversity. We were therefore interested in determining the level of nucleotide variation in nuclear and mitochondrial genomes of this beetle worldwide. Here we show that two nuclear loci (Resistance to dieldrin and ITS2) are completely invariant, whereas some variability is maintained at a mitochondrial locus (COI), probably corresponding to a higher mutation rate in the mitochondrial genome. Phylogenetic analysis of the mitochondrial data shows only two clades of beetle haplotypes outside of Kenya, the proposed origin of the species. These data confirm that inbreeding greatly reduces nucleotide variation and suggest the recent global spread of only two inbreeding lines of this bark beetle.
Insect Mol Biol 1998 May
PMID:Lack of nucleotide variability in a beetle pest with extreme inbreeding. 953 65

Phylogenetic relationships within the Laudakia caucasia species group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation of Laudakia populations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north-south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5-10 MYBP (million years before present)]. The shortest tree suggest the later hypothesis, and statistical tests reject the other two hypothesis. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north-south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61-0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree.
Mol Phylogenet Evol 1998 Aug
PMID:Phylogenetic relationships among Agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau. 975 22

The hemlock looper, Lambdina fiscellaria (Gn.), is a recurring major forest pest that is widely distributed in North America. Three subspecies (L. f. fiscellaria, L. f. lugubrosa (Hulst) and L. f. somniaria (Hulst)) have been recognized based on larval host or adult pheromone differences, but no consistent morphological differences have been reported. To clarify their taxonomic status, we surveyed mitochondrial DNA (mtDNA) sequence and restriction site variation in two protein coding genes, cytochrome oxidase I and II (COI and COII), in populations across the range of L. fiscellaria. In addition to variation in COI and COII, we found an intergenic spacer region of 20-23 bp located between the tRNA tyrosine gene and the start of COI. Of the 141 specimens of L. fiscellaria assayed, 137 were grouped into two distinct mtDNA lineages, one of which was disproportionately associated with eastern populations and one with western populations. However, single specimens and two populations in eastern Canada had mtDNA resembling that of western populations. Three divergent and rare haplotypes had basal affinities to the two common lineages. The two major lineages of L. fiscellaria were diverged by approximately 2% from each other, as well as from the mtDNA of two outgroup species, L. athasaria (Walker) and L. pellucidaria(G. & R.). The two outgroup species had essentially the same mtDNA and may be conspecific. We interpret the pattern of mtDNA variation within L. fiscellaria as indicating genetic polymorphism within a single species without clear subspecific divisions, rather than evidence of multiple cryptic species.
Insect Mol Biol 1999 Feb
PMID:Mitochondrial DNA sequence variation among populations and host races of Lambdina fiscellaria (Gn.) (Lepidoptera: Geometridae). 992 78


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