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Query: UNIPROT:P06889 (Mol)
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To investigate the utility of a region of wingless (wg) as a marker for molecular systematics, we compared wg sequences to mitochondrial COII sequences from twenty-two nymphalid butterfly taxa and one outgroup. Compositional characteristics of the two gene regions are compared, and their contributions to a cladogram inferred from the combined data set are assessed. Primarily due to its uniform base composition, wg appears to become saturated more slowly than mtDNA, although the two genes appear to be evolving at quite similar rates. We suggest that wg will be a useful source of characters for phylogenetic studies of butterflies, and perhaps other insect taxa, with divergence times up to 60 million years ago.
Insect Mol Biol 1998 Feb
PMID:Patterns of mitochondrial versus nuclear DNA sequence divergence among nymphalid butterflies: the utility of wingless as a source of characters for phylogenetic inference. 945 31

The organization of the mitochondrial maxicircle genome of Trypanosoma brucei is unique in the close packing of the mRNA genes. For many of them, the 5' and 3' ends of adjacent transcripts overlap and formation of the proper 3' or 5' end can eliminate a portion of the coding sequence of the adjacent gene. Large, polycistronic transcripts have been detected. suggesting that mechanisms for precise cleavages at both 5' and 3' gene boundaries must exist. However, no common sequences near the ends of the mRNAs that could be candidates for control regions have been detected. In addition, nothing is known about how RNA editing interacts with and affects 5' and 3' processing and/or polyadenylation. Edited precursor transcripts have been detected, indicating that editing complexes can assemble prior to transcript cleavage. Because editing often initiates near the 3' end of the mRNA, the assembly of an editing complex in this region may influence the cleavage selection process. In order to determine the extent that RNA editing and 3' end-processing interact, RNAs were analyzed to determine the extent of editing in precursor RNAs and to determine if unedited transcripts can be cleaved and polyadenylated. Two overlapping RNA junctions were analyzed; the junction between NADH dehydrogenase (ND) subunit 7 and cytochrome oxidase (CO) subunit III, and the junction between CO subunit II and maxicircle unidentified reading frame (MURF) II. For both of these RNAs, editing affects restriction endonuclease recognition sequences, allowing us to analyze editing patterns by differential restriction digests. These analyses suggest that when the gRNA is supplied in trans, RNA editing and cleavage/polyadenylation are independent events and while they may influence one another, one event is not dependent on the other. Conversely, for the COII transcript, where the gRNA is located at the 3' end of the mRNA and appears to be supplied in cis, edited precursors were not detected. This suggests a requirement for a precise intramolecular interaction for COII editing that cannot form prior to 3' end-maturation.
Mol Biochem Parasitol 1997 Dec 01
PMID:Mitochondrial mRNA 3' cleavage/polyadenylation and RNA editing in Trypanosoma brucei are independent events. 949 34

Relationships among the genus Anopheles and its many sibling species-groups are obscure despite the importance of anophelines as the vectors of human malaria. For the first time, the interrelationships and the origin of Australasian members of the subgenus Cellia are investigated by a cladistic analysis of sequence variation within the mitochondrial cytochrome oxidase subunit II gene. Estimated divergence times between many Australasian and Oriental taxa predate the mid Miocene collision of Australasia and Southeast Asia. Phylogenetic analysis suggests that two-way exchanges with Oriental mosquitoes rather than only immigration may have been a characteristic of anopheline paleobiogeography in Australasia. The Australasian fauna is mostly included in a large clade. The medically important Punctulatus Group is monophyletic and appears derived from Oriental stock. Populations within this group from as far apart as Australia and Vanuatu were in contact in the recent past (i.e., 0.35-2.44 mya), supporting dispersal rather than vicariance explanations. Some support for the monophyly of the Myzomyia, Neomyzomyia, and Pyretophorus Series was found. However, the subgenera Anopheles and Cellia and the Neocellia Series are paraphyletic, but branch support at these taxonomic levels was poor. The COII gene shows promise for questions concerning alpha taxonomy but appears to be of limited use for resolving deeper relationships within the Anopheles.
Mol Phylogenet Evol 1998 Apr
PMID:Evolution and systematics of Anopheles: insights from a molecular phylogeny of Australasian mosquitoes. 956 85

The mitochondrial DNA (mtDNA) of individuals from 79 colonies of Apis mellifera from five Canary Islands was studied using the DraI test based on the restriction of PCR products of the tRNA(leu)-COII intergenic region. Five haplotypes of the African (A) lineage and one of the west European (C) lineage were found. The haplotypes A14 and A15 are described for the first time. These haplotypes have a new P sequence named P1. The wide distribution and high frequency of haplotype A15 suggest that it is characteristic of the Canarian Archipelago. Sources of haplotype variability of honeybee mtDNA in the Canary Islands (waves of colonization from Africa, queen importations, habitat diversification) are discussed.
Mol Ecol 1998 Nov
PMID:Mitochondrial DNA variability in the Canary Islands honeybees (Apis mellifera L.). 981 7

The complete nucleotide sequence of the mitochondrial genome of the domestic dog, Canis familiaris, was determined. The length of the sequence was 16,728 bp; however, the length was not absolute due to the variation (heteroplasmy) caused by differing numbers of the repetitive motif, 5'-GTACACGT(A/G)C-3', in the control region. The genome organization, gene contents, and codon usage conformed to those of other mammalian mitochondrial genomes. Although its features were unknown, the "CTAGA" duplication event which followed the translational stop codon of the COII gene was not observed in other mammalian mitochondrial genomes. In order to determine the possible differences between mtDNAs in carnivores, two rRNA and 13 protein-coding genes from the cat, dog, and seal were compared. The combined molecular differences, in two rRNA genes as well as in the inferred amino acid sequences of the mitochondrial 13 protein-coding genes, suggested that there is a closer relationship between the dog and the seal than there is between either of these species and the cat. Based on the molecular differences of the mtDNA, the evolutionary divergence between the cat, the dog, and the seal was dated to approximately 50 +/- 4 million years ago. The degree of difference between carnivore mtDNAs varied according to the individual protein-coding gene applied, showing that the evolutionary relationships of distantly related species should be presented in an extended study based on ample sequence data like complete mtDNA molecules.
Mol Phylogenet Evol 1998 Oct
PMID:The complete nucleotide sequence of the domestic dog (Canis familiaris) mitochondrial genome. 987 32

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

Animal mitochondrial DNA genomes are generally single circular molecules, 14-20 kb in size, containing a number of functional RNAs and 13 protein-coding genes. Among these, the COI, COII and COIII genes encode three subunits of cytochrome c oxidase. We have isolated and characterized these three mitochondrial genes from the mesozoan Dicyema, a primitive multicellular animal. Surprisingly, the COI, COII and COIII genes are encoded on three small, separate circular DNA molecules (minicircles) of length 1700, 1599 and 1697 bp, respectively. We estimated the copy number of each minicircle at 100 to 1000 per cell, and have shown a mitochondrial localization of the minicircles by in situ hybridization. Furthermore, we could not detect a putative "maxicircle" DNA molecule containing any combination of the COI, COII and COIII genes using either PCR or genomic Southern hybridization. Thus, our results show a novel mitochondrial genome organization in the mesozoan animal Dicyema.
J Mol Biol 1999 Feb 26
PMID:Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema. 1002 39

In this study, we explored how the concept of the process partition may be applied to phylogenetic analysis. Sequence data were gathered from 23 species and subspecies of the swallowtail butterfly genus Papilio, as well as from two outgroup species from the genera Eurytides and Pachliopta. Sequence data consisted of 1,010 bp of the nuclear protein-coding gene elongation factor-1 alpha (EF-1 alpha) as well as the entire sequences (a total of 2,211 bp) of the mitochondrial protein-coding genes cytochrome oxidase I and cytochrome oxidase II (COI and COII). In order to examine the interaction between the nuclear and mitochondrial partitions in a combined analysis, we used a method of visualizing branch support as a function of partition weight ratios. We demonstrated how this method may be used to diagnose error at different levels of a tree in a combined maximum-parsimony analysis. Further, we assessed patterns of evolution within and between subsets of the data by implementing a multipartition maximum-likelihood model to estimate evolutionary parameters for various putative process partitions. COI third positions have an estimated average substitution rate more than 15 times that of EF-1 alpha, while COII third positions have an estimated average substitution rate more than 22 times that of EF-1 alpha. Ultimately, we found that although the mitochondrial and nuclear data were not significantly incongruent, homoplasy in the fast-evolving mitochondrial data confounded the resolution of basal relationships in the combined unweighted parsimony analysis despite the fact that there was relatively strong support for the relationships in the nuclear data. We conclude that there may be shortcomings to the methods of "total evidence" and "conditional combination" because they may fail to detect or accommodate the type of confounding bias we found in our data.
Mol Biol Evol 1999 Feb
PMID:Interaction of process partitions in phylogenetic analysis: an example from the swallowtail butterfly genus Papilio. 1002 94

Butterflies of the genus Papilio have served as the basis for numerous studies in insect physiology, genetics, and ecology. However, phylogenetic work on relationships among major lineages in the genus has been limited and inconclusive. We have sequenced 2.3 kb of DNA from the mitochondrial cytochrome oxidase I and II genes (COI and COII) for 23 Papilio taxa and two outgroups, Pachliopta neptunus and Eurytides marcellus, in order to assess the potential of these genes for use in Papilio phylogenetics and to examine patterns of gene evolution across a broad taxonomic range. Nucleotide and amino acid variation is distributed heterogeneously, both within and between genes. Structural features of the proteins are not always reliable predictors of variation. In a combined analysis, these sequences support a nearly fully resolved topology within subgenera and species groups, though higher level relationships among species groups require additional study. The most noteworthy findings are that neither Papilio alexanor nor P. xuthus belongs in the machaon group and that the subgenus Pterourus is paraphyletic with respect to the subgenus Pyrrhosticta. We leave relationships among members of the phorcas species group as a trichotomy. These two protein coding genes, particularly COI, show excellent performance in resolving relationships at the level of species and species groups among Papilionidae. We strongly endorse a similar approach for future studies aimed at these levels.
Mol Phylogenet Evol 1999 Feb
PMID:Papilio phylogeny based on mitochondrial cytochrome oxidase I and II genes. 1008 16

A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3' end of the 16S rRNA gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5' portion of ATPase subunit 6. The Porifera cluster distinctly within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII-tRNALys-ATP8-ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
J Mol Evol 1999 May
PMID:Partial sequence of a sponge mitochondrial genome reveals sequence similarity to Cnidaria in cytochrome oxidase subunit II and the large ribosomal RNA subunit. 1019 20


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