doi: 10.1093/oxfordjournals.molbev.a025947pmid: N/A
Article PDF first page preview Close This content is only available as a PDF.
doi: 10.1093/oxfordjournals.molbev.a025948pmid: N/A
Article PDF first page preview Close This content is only available as a PDF.
doi: mbe;15/5/499pmid: N/A
The complete mitochondrial genome of the fat dormouse, Glis glis, has been sequenced (16,602 bp). A total of 23 complete mitochondrial mammalian genomes have been taken into account for phylogenetic reconstruction. Phylogenetic analyses were performed with parsimony, distance (stationary Markov model), and maximum-likelihood methods. In all cases, data strongly support the paraphyly of rodents, with dormouse and guinea pig in a different clade from rat and mouse, reaching bootstrap values of 95%. Rodent monophyly and the existence of Glires (Rodentia and Lagomorpha) are weakly supported, with maximum bootstrap values of 11% and 8.6%, respectively. This result agrees with the analyses of isochore patterns in the nuclear genome and the B2 and B2-like retroposons, which show a close relationship between dormice and guinea pigs rather than between dormice and rats and mice. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1998) 15 (5): 499-505. » Abstract Free Full Text (PDF) Free Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Reyes, A. Articles by Saccone, C. Search for related content PubMed PubMed citation Articles by Reyes, A. Articles by Pesole, G. Articles by Saccone, C. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue December 2015 32 (12) Alert me to new issues Editors Sudhir Kumar (Editor-in-Chief) View full Board of Editors For Authors Submit Online Now Editorial Process Manuscript Transfers Manuscript Types General Author Guidelines Supplementary Information Conflict of Interest Open Access Page Charges Copyright Public Preprint Policy Pre-Submission Inquiries Sign up for Alerts Email ToC Email Advance Access CiteTrack XML RSS feed Impact factor: 9.105 5-Yr impact factor: 11.667 Published on behalf of Society for Molecular Biology and Evolution Open access options for authors - visit Oxford Open This journal enables compliance with the NIH Public Access Policy Rights & Permissions Dispatch date of the next issue We are mobile – find out more This journal is a member of the Committee on Publication Ethics (COPE) Corporate Services Advertising sales Classified Advertising Reprints Supplements
doi: 10.1093/oxfordjournals.molbev.a025949pmid: 9580978
Abstract The complete mitochondrial genome of the fat dormouse, Glis glis, has been sequenced (16,602 bp). A total of 23 complete mitochondrial mammalian genomes have been taken into account for phylogenetic reconstruction. Phylogenetic analyses were performed with parsimony, distance (stationary Markov model), and maximum-likelihood methods. In all cases, data strongly support the paraphyly of rodents, with dormouse and guinea pig in a different clade from rat and mouse, reaching bootstrap values of 95%. Rodent monophyly and the existence of Glires (Rodentia and Lagomorpha) are weakly supported, with maximum bootstrap values of 11% and 8.6%, respectively. This result agrees with the analyses of isochore patterns in the nuclear genome and the B2 and B2-like retroposons, which show a close relationship between dormice and guinea pigs rather than between dormice and rats and mice.
Zardoya, R;Cao, Y;Hasegawa, M;Meyer, A
doi: 10.1093/oxfordjournals.molbev.a025950pmid: 10766578
Abstract The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.
R Zardoya, Y Cao, M Hasegawa, A Meyer
doi: mbe;15/5/506pmid: N/A
The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1998) 15 (5): 506-517. » Abstract Free Full Text (PDF) Free Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Zardoya, R. Articles by Meyer, A. Search for related content PubMed PubMed citation Articles by Zardoya, R. Articles by Cao, Y. Articles by Hasegawa, M. Articles by Meyer, A. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue December 2015 32 (12) Alert me to new issues Editors Sudhir Kumar (Editor-in-Chief) View full Board of Editors For Authors Submit Online Now Editorial Process Manuscript Transfers Manuscript Types General Author Guidelines Supplementary Information Conflict of Interest Open Access Page Charges Copyright Public Preprint Policy Pre-Submission Inquiries Sign up for Alerts Email ToC Email Advance Access CiteTrack XML RSS feed Impact factor: 9.105 5-Yr impact factor: 11.667 Published on behalf of Society for Molecular Biology and Evolution Open access options for authors - visit Oxford Open This journal enables compliance with the NIH Public Access Policy Rights & Permissions Dispatch date of the next issue We are mobile – find out more This journal is a member of the Committee on Publication Ethics (COPE) Corporate Services Advertising sales Classified Advertising Reprints Supplements
doi: 10.1093/oxfordjournals.molbev.a025951pmid: 9580980
Abstract A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may have appeared first in the nervous system. Moreover, we suggest that the alpha 1 subunits in the muscle system originated from the common ancestor of alpha 2, alpha 3, alpha 4, alpha 5, alpha 6, and beta 3 in the nervous system, whereas the beta 1, gamma, delta, and epsilon subunits in the muscle system shared a common ancestor with the beta 2 and beta 4 subunits in the nervous system. Using the ratio (f) of the number of nonsynonymous substitutions to that of synonymous substitutions, we predicted the functional importance of subunits. We found that the alpha 1 and alpha 7 subunits had the lowest f values in the muscle and nervous systems, respectively, indicating that very strong functional constraints work on these subunits. This is consistent with the fact that the alpha 1 subunit has sites binding to the ligand, and the alpha 7-containing receptor regulates the release of the transmitter. Moreover, the window analysis of the f values showed that strong functional constraints work on the so-called M2 region in all five types of muscle subunits. Thus, the window analysis of the f values is useful for evaluating the degree of functional constraints in not only the entire gene region, but also the within-gene subregion.
doi: mbe;15/5/518pmid: N/A
A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may have appeared first in the nervous system. Moreover, we suggest that the alpha 1 subunits in the muscle system originated from the common ancestor of alpha 2, alpha 3, alpha 4, alpha 5, alpha 6, and beta 3 in the nervous system, whereas the beta 1, gamma, delta, and epsilon subunits in the muscle system shared a common ancestor with the beta 2 and beta 4 subunits in the nervous system. Using the ratio (f) of the number of nonsynonymous substitutions to that of synonymous substitutions, we predicted the functional importance of subunits. We found that the alpha 1 and alpha 7 subunits had the lowest f values in the muscle and nervous systems, respectively, indicating that very strong functional constraints work on these subunits. This is consistent with the fact that the alpha 1 subunit has sites binding to the ligand, and the alpha 7-containing receptor regulates the release of the transmitter. Moreover, the window analysis of the f values showed that strong functional constraints work on the so-called M2 region in all five types of muscle subunits. Thus, the window analysis of the f values is useful for evaluating the degree of functional constraints in not only the entire gene region, but also the within-gene subregion. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1998) 15 (5): 518-527. » Abstract Free Full Text (PDF) Free Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Tsunoyama, K. Articles by Gojobori, T. Search for related content PubMed PubMed citation Articles by Tsunoyama, K. Articles by Gojobori, T. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue December 2015 32 (12) Alert me to new issues Editors Sudhir Kumar (Editor-in-Chief) View full Board of Editors For Authors Submit Online Now Editorial Process Manuscript Transfers Manuscript Types General Author Guidelines Supplementary Information Conflict of Interest Open Access Page Charges Copyright Public Preprint Policy Pre-Submission Inquiries Sign up for Alerts Email ToC Email Advance Access CiteTrack XML RSS feed Impact factor: 9.105 5-Yr impact factor: 11.667 Published on behalf of Society for Molecular Biology and Evolution Open access options for authors - visit Oxford Open This journal enables compliance with the NIH Public Access Policy Rights & Permissions Dispatch date of the next issue We are mobile – find out more This journal is a member of the Committee on Publication Ethics (COPE) Corporate Services Advertising sales Classified Advertising Reprints Supplements
Barbeyron, T;Gerard, A;Potin, P;Henrissat, B;Kloareg, B
doi: 10.1093/oxfordjournals.molbev.a025952pmid: 9580981
Abstract We report here cloning from the marine gliding bacterium Cytophaga drobachiensis of kappa-carrageenase, a glycoside hydrolase involved in the degradation of kappa-carrageenan. Structural features in the nucleotide sequence are pointed out, including the presence of an octameric omega sequence similar to the ribosome-binding sites of various eukaryotes and prokaryotes. The cgkA gene codes for a protein of 545 aa, with a signal peptide of 35 aa and a 229-aa-long posttranslationaly processed C-terminal domain. The enzyme displays the overall folding and catalytic domain characteristics of family 16 of glycoside hydrolases, which comprises other beta-1,4-alpha-1,3-D/L-galactan hydrolases, beta-1,3-D-glucan hydrolases (laminarinases), beta-1,4-1,3-D-glucan hydrolases (lichenases), and beta-1,4-D-xyloglucan endotransglycosylases. In order to address the origin and evolution of CgkA, a comprehensive phylogenetic tree of family 16 was built using parsimony analysis. Family-16 glycoside hydrolases cluster according to their substrate specificity, regardless of their phylogenetic distribution over eubacteria and eukaryotes. Such a topology suggests that the general homology between laminarinases, agarases, kappa-carrageenases, lichenases, and xyloglucan endotransglycosylases has arisen through gene duplication, likely from an ancestral protein with laminarinase activity.
T Barbeyron, A Gerard, P Potin, B Henrissat, B Kloareg
doi: mbe;15/5/528pmid: N/A
We report here cloning from the marine gliding bacterium Cytophaga drobachiensis of kappa-carrageenase, a glycoside hydrolase involved in the degradation of kappa-carrageenan. Structural features in the nucleotide sequence are pointed out, including the presence of an octameric omega sequence similar to the ribosome-binding sites of various eukaryotes and prokaryotes. The cgkA gene codes for a protein of 545 aa, with a signal peptide of 35 aa and a 229-aa-long posttranslationaly processed C-terminal domain. The enzyme displays the overall folding and catalytic domain characteristics of family 16 of glycoside hydrolases, which comprises other beta-1,4-alpha-1,3-D/L-galactan hydrolases, beta-1,3-D-glucan hydrolases (laminarinases), beta-1,4-1,3-D-glucan hydrolases (lichenases), and beta-1,4-D-xyloglucan endotransglycosylases. In order to address the origin and evolution of CgkA, a comprehensive phylogenetic tree of family 16 was built using parsimony analysis. Family-16 glycoside hydrolases cluster according to their substrate specificity, regardless of their phylogenetic distribution over eubacteria and eukaryotes. Such a topology suggests that the general homology between laminarinases, agarases, kappa-carrageenases, lichenases, and xyloglucan endotransglycosylases has arisen through gene duplication, likely from an ancestral protein with laminarinase activity. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1998) 15 (5): 528-537. » Abstract Free Full Text (PDF) Free Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Barbeyron, T. Articles by Kloareg, B. Search for related content PubMed PubMed citation Articles by Barbeyron, T. Articles by Gerard, A. Articles by Potin, P. Articles by Henrissat, B. Articles by Kloareg, B. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue December 2015 32 (12) Alert me to new issues Editors Sudhir Kumar (Editor-in-Chief) View full Board of Editors For Authors Submit Online Now Editorial Process Manuscript Transfers Manuscript Types General Author Guidelines Supplementary Information Conflict of Interest Open Access Page Charges Copyright Public Preprint Policy Pre-Submission Inquiries Sign up for Alerts Email ToC Email Advance Access CiteTrack XML RSS feed Impact factor: 9.105 5-Yr impact factor: 11.667 Published on behalf of Society for Molecular Biology and Evolution Open access options for authors - visit Oxford Open This journal enables compliance with the NIH Public Access Policy Rights & Permissions Dispatch date of the next issue We are mobile – find out more This journal is a member of the Committee on Publication Ethics (COPE) Corporate Services Advertising sales Classified Advertising Reprints Supplements
Showing 1 to 10 of 30 Articles