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At least 973 records · Page 54Linked to original sources
PubMed2001

Molecular phylogeny of Eastern Pacific porcelain crabs, genera Petrolisthes and Pachycheles, based on the mtDNA 16S rDNA sequence: phylogeographic and systematic implications.

Porcelain crabs, genera Petrolisthes and Pachycheles, are diverse and abundant members of the eastern Pacific near-shore decapod crustacean community. Morphology-based taxonomic analyses of these crabs have determined groupings of affiliated species, but phylogenetic relationships remain unknown. We used sequence data from the mitochondrial 16S rRNA gene of 46 species of eastern Pacific porcelain crabs to perform phylogenetic analyses by distance and parsimony methods. Our results are used to compare the taxonomic significance of morphological and molecular characters, to examine sequence divergence rates of crab 16S rRNA genes, and to analyze the phylogeographic history of these crabs. Our phylogenetic trees indicate that the genus Petrolisthes is divided into two main clades, reflecting morphological features. One clade contains primarily tropical species, and the other contains species from throughout the eastern Pacific, as well as species in the genera Allopetrolisthes and Liopetrolisthes. Phylogenetic trees of Pachycheles suggest an antitropical distribution; north and south temperate species form one clade and tropical species form a second clade. Sequence divergence rates of the 16S rRNA gene from three pairs of geminate species can be used to date divergence times, and we discuss porcelain crab phylogeographic patterns in relation to paleogeographic events.

Animals↗
PubMed2001

MtDNA sequences support monophyly of Hemispingus tanagers.

Tanagers of the genus Hemispingus comprise an array of 12 recognized species of rather dull-colored tanagers restricted to Andean forests. Four of these species are polytypic, with as many as seven subspecies recognized for H. superciliaris. Taxonomic relationships within this group, and with similar-looking Basileuterus warblers, have been confusing and not well understood. We used partial DNA sequences of the mitochondrial ND2 gene and a set of morphological characters to study their phylogenetic relationships. Our molecular dataset strongly supports the monophyly of Hemispingus (including the warbler-like species and the finch-like H. rufosuperciliaris) compared to other nine-primaried oscines (Ramphocelus, Chlorospingus, Atlapetes/Buarremon, Basileuterus) and indicates either that Atlapetes/Buarremon could be tanagers or that Chlorospingus could be finches. We propose a phylogeny containing three major clades: mostly greenish eye-browed birds (trifasciatus, atropileus, auricularis, calophrys), mostly gray warbler-like birds (superciliaris, verticalis, xanthophthalmus), and mostly ochraceous birds (rufosuperciliaris and goeringi, piurae, frontalis, melanotis). The relationships among these three clades are left unresolved. We suggest species status for H. auricularis and H. piurae. Our molecular data suggest that most of the diversity in Hemispingus tanagers predates the period of marked ecoclimatic fluctuations in the upper Pleistocene.

Animals↗
PubMedDate not supplied

Frequent site-specific mit- deletions at cryptic exon-intron junctions in the COX1 gene of yeast mtDNA.

A class of large site-specific deletions (del-B) occurs with exceptionally-high frequencies of 10(-3) in the mitochondrial COX1 gene of Mn(2+)-treated yeast cells. This work shows that del-B deletions are associated with COX1 intron aI1. All five deletion mutants studied have their upstream end at the authentic 3' splice site of this intron. The deletion ends 8.2 kb downstream in intron aI5b. This downstream deletion-end constitutes a potentially-cryptic 5' splice site for intron aI1. The coincidences of the del-B deletion-ends with authentic and cryptic RNA splice sites suggest that the group-II intron aI1, and/or the RNA maturase encoded in it, plays an active role in this exceptionally-frequent, site-specific deletion process.

Base Sequence↗
PubMed1982

The cytochrome oxidase subunit I split gene in Saccharomyces cerevisiae: genetic and physical studies of the mtDNA segment encompassing the 'cytochrome b-homologous' intron.

We have constructed a refined genetic and physical map of 38 oxi3 mutations. With the help of the rho- clones derived from 'short' and 'long' genes, pairwise crosses between mutants, estimations of their reversion frequencies and analyses of mitochondrially synthesized proteins, we have characterized and localized several mutants in the exon A4 and in the intron aI4. We present genetic and physical evidence that in the 'long' gene the exon A5 is split into at least three quite distinct exons, A5-1, A5-2 and A5-3 where numerous mutations are localized. We suggest that a novel 56 Kd polypeptide, which accumulates in some cis-dominant oxi3- mutants results from the translation of the upstream exons and the downstream aI4 intron.

Base Sequence↗
PubMed2004

Mitochondrial permeability transition triggers the release of mtDNA fragments.

Fragments of mitochondrial DNA are released from mitochondria upon opening of the mitochondrial permeability transition pore. Cyclosporin A, an inhibitor of pore opening, completely prevented the release of mitochondrial fragments. Induction of mitochondrial permeability transition and subsequent release of the fragments of mitochondrial DNA could be one cause of genomic instability in the cell.

Animals↗
PubMed2002

Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents.

This paper reports an intraorder study on the D-loop-containing region of the mitochondrial DNA in rodents. A complete multialignment of this region is not feasible with the exception of some conserved regions. The comparative analysis of 25 complete rodent sequences from 23 species plus one lagomorph has revealed that only the central domain (CD), a conserved region of about 80 bp in the extended termination-associated sequences (ETAS) domain, adjacent to the CD, the ETAS1, and conserved sequence block (CSB) 1 blocks are present in all rodent species, whereas the presence of CSB2 and CSB3 is erratic within the order. We have also found a conserved region of 90 bp located between tRNAPro and ETAS1 present in fat dormouse, squirrel, guinea pig, and rabbit. Repeated sequences are present in both the ETAS and the CSB domain, but the repeats differ in length, copy number, and base composition in different species. The potential use of the D-loop for evolutionary studies has been investigated; the presence/absence of conserved blocks and/or repeated sequences cannot be used as a reliable phylogenetic marker, since in some cases they may be shared by distantly related organisms but not by close ones, while in other ones a relationship between tree topology and presence/absence of such motifs is observed. Better results can be obtained by the use of the CD, which, however, due to its reduced size, when used for tracing a phylogenetic tree, shows some nodes with low statistical support.

Animals↗
PubMed2000

mtDNA sequence diversity of orangutans from the islands of Borneo and Sumatra.

A comparison of mitochondrial DNA sequences was undertaken for two genes among orangutans from Borneo and Sumatra. The distribution of haplotypes among 42 individuals for NADH dehydrogenease subunit 3 and 39 individuals for cytochrome B was used to infer population structure. The haplotypes among all Bornean orangutans form a cluster of closely related individuals for both genes, with two distinct haplotypes occupying different regions of the island. Sumatran haplotypes fall into three distinct, and highly diverged, groups. Strikingly, one of the Sumatran haplotypes shares sequence identity with the most widespread Bornean haplotype. This haplotype distribution is considered in the context of the highly complex geological history for the area around the Malay Archipelago. Alternating periods of geographic isolation and reunion, resulting from glacially induced land bridge formation, presented substantial opportunity for population dispersal between periodically isolated demes. We present a paleodispersal model that is consistent with genetic, geological, paleoecological, and fossil data. The disparity of sequences present in orangutan populations argues against a simple Sumatra-Borneo dichotomy. Our evidence, and that of others, suggests that the Sumatran population alone contains the remnants of at least three separate lineages.

Animals↗
PubMed2001

The Old World sparrows (genus Passer) phylogeography and their relative abundance of nuclear mtDNA pseudogenes.

The phylogenetic relationships of genus Passer (Old World sparrows) have been studied with species covering their complete world living range. Mitochondrial (mt) cyt b genes and pseudogenes have been analyzed, the latter being strikingly abundant in genus Passer compared with other studied songbirds. The significance of these Passer pseudogenes is presently unclear. The mechanisms by which mt cyt b genes become pseudogenes after nuclear translocation are discussed together with their mode of evolution, i.e., transition/transversion mitochondrial ratio is decreased in the nucleus, as is the constraint for variability at the three codon positions. However, the skewed base composition according to codon position (in 1st position the percentage is very similar for the four bases, in 2nd position there are fewer percentage of A and G and more percentage of T, and in 3rd codon position fewer percentage of G and T and is very rich in A and C) is maintained in the translocated nuclear pseudogenes. Different nuclear internal mechanisms and/or selective pressures must exist for explaining this nuclear/mitochondrial differential DNA base evolutive variability. Also, the phylogenetic usefulness of pseudogenes for defining relationships between closely related lineages is stressed. The analyses suggest that the primitive genus Passer species comes from Africa, the Cape sparrow being the oldest: P. hispaniolensis italiae is more likely conspecific to P. domesticus than to P. hispaniolensis. Also, Passer species are not included within weavers or Estrildinae or Emberizinae, as previously suggested. European and American Emberizinae sparrows are closely related to each other and seem to be the earliest species that radiated among the studied songbirds (all in the Miocene Epoch).

Cell Nucleus↗