Molecular Biology and Evolution

Tan, I H;Blomster, J;Hansen, G;Leskinen, E;Maggs, C A;Mann, D G;Sluiman, H J;Stanhope, M J

doi: 10.1093/oxfordjournals.molbev.a026190pmid: 10474897

Ulva and Enteromorpha are two of the most common, ubiquitous, and environmentally important genera of green seaweeds. They are widely regarded as easily distinguishable because of their dramatically different morphologies: Ulva species are flat, lettucelike blades two cell layers thick, and Enteromorpha species form hollow liquid- or gas-filled tubes one cell thick, which may also be highly branched. We present molecular phylogenetic analyses of nuclear ribosomal RNA ITS sequences from 39 samples representing 21 purported species within these two genera. The results clearly indicate that the two genera are not respectively monophyletic and that the characteristic Ulva and Enteromorpha morphologies have arisen independently several times throughout the evolutionary diversification of the group. The analyses demonstrate that this radical change in gross morphology can also happen within clades exhibiting sequence divergence typical of conspecific assemblages of this group. We suggest that this morphological flexibility is the result of some form of developmental switch that results in either blades or tubes, but that this putative switch must be activated relatively infrequently, since there is evidence that some lineages have retained their form for significant periods. This discovery suggests a possible new model system for study of the molecular mechanisms involved in the interplay between environmental stimuli and plant development.

I H Tan, J Blomster, G Hansen, E Leskinen, C A Maggs, D G Mann, H J Sluiman, M J Stanhope

doi: mbe;16/8/1011pmid: N/A

Ulva and Enteromorpha are two of the most common, ubiquitous, and environmentally important genera of green seaweeds. They are widely regarded as easily distinguishable because of their dramatically different morphologies: Ulva species are flat, lettucelike blades two cell layers thick, and Enteromorpha species form hollow liquid- or gas-filled tubes one cell thick, which may also be highly branched. We present molecular phylogenetic analyses of nuclear ribosomal RNA ITS sequences from 39 samples representing 21 purported species within these two genera. The results clearly indicate that the two genera are not respectively monophyletic and that the characteristic Ulva and Enteromorpha morphologies have arisen independently several times throughout the evolutionary diversification of the group. The analyses demonstrate that this radical change in gross morphology can also happen within clades exhibiting sequence divergence typical of conspecific assemblages of this group. We suggest that this morphological flexibility is the result of some form of developmental switch that results in either blades or tubes, but that this putative switch must be activated relatively infrequently, since there is evidence that some lineages have retained their form for significant periods. This discovery suggests a possible new model system for study of the molecular mechanisms involved in the interplay between environmental stimuli and plant development. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1999) 16 (8): 1011-1018. » 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 Tan, I. H. Articles by Stanhope, M. J. Search for related content PubMed PubMed citation Articles by Tan, I. H. Articles by Blomster, J. Articles by Hansen, G. Articles by Leskinen, E. Articles by Maggs, C. A. Articles by Mann, D. G. Articles by Sluiman, H. J. Articles by Stanhope, M. J. 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

M P Keller, B A Seifried, P F Chance

doi: mbe;16/8/1019pmid: N/A

The CMT1A-REP repeat consists of two copies of a 24-kb sequence on human chromosome 17p11.2-12 that flank a 1.5-Mb region containing a dosage-sensitive gene, peripheral nerve protein-22 (PMP22). Unequal meiotic crossover mediated by misalignment of proximal and distal copies of the CMT1A-REP in humans leads to a 1.5-Mb duplication or deletion associated with two common peripheral nerve diseases, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP). Previous molecular hybridization studies with CMT1A-REP sequences suggested that two copies of the repeat are also found in the chimpanzee, raising the possibility that this unique repeat arose during primate evolution. To further characterize the structure and evolutionary synthesis of the CMT1A-REP repeat, fluorescent in situ hybridization (FISH) analysis and heterologous PCR-based assays were carried out for a series of primates. Genomic DNA was analyzed with primers selected to differentially amplify the centromeric and telomeric ends of the human proximal and distal CMT1A-REP elements and an associated mariner (MLE) sequence. All primate species examined (common chimpanzee, pygmy chimpanzee, gorilla, orangutan, gibbon, baboon, rhesus monkey, green monkey, owl monkey, and galago) tested positive for a copy of the distal element. In addition to humans, only the chimpanzee was found to have a copy of the proximal CMT1A-REP element. All but one primate species (galago) tested positive for the MLE located within the CMT1A-REP sequence. These observations confirm the hypothesis that the distal CMT1A-REP element is the ancestral sequence which was duplicated during primate evolution, provide support for a human-chimpanzee clade, and suggest that insertion of the MLE into the CMT1A-REP sequence occurred in the ancestor of anthropoid primates. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1999) 16 (8): 1019-1026. » 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 Keller, M. P. Articles by Chance, P. F. Search for related content PubMed PubMed citation Articles by Keller, M. P. Articles by Seifried, B. A. Articles by Chance, P. F. 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

Keller, M P;Seifried, B A;Chance, P F

doi: 10.1093/oxfordjournals.molbev.a026191pmid: 10474898

The CMT1A-REP repeat consists of two copies of a 24-kb sequence on human chromosome 17p11.2-12 that flank a 1.5-Mb region containing a dosage-sensitive gene, peripheral nerve protein-22 (PMP22). Unequal meiotic crossover mediated by misalignment of proximal and distal copies of the CMT1A-REP in humans leads to a 1.5-Mb duplication or deletion associated with two common peripheral nerve diseases, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP). Previous molecular hybridization studies with CMT1A-REP sequences suggested that two copies of the repeat are also found in the chimpanzee, raising the possibility that this unique repeat arose during primate evolution. To further characterize the structure and evolutionary synthesis of the CMT1A-REP repeat, fluorescent in situ hybridization (FISH) analysis and heterologous PCR-based assays were carried out for a series of primates. Genomic DNA was analyzed with primers selected to differentially amplify the centromeric and telomeric ends of the human proximal and distal CMT1A-REP elements and an associated mariner (MLE) sequence. All primate species examined (common chimpanzee, pygmy chimpanzee, gorilla, orangutan, gibbon, baboon, rhesus monkey, green monkey, owl monkey, and galago) tested positive for a copy of the distal element. In addition to humans, only the chimpanzee was found to have a copy of the proximal CMT1A-REP element. All but one primate species (galago) tested positive for the MLE located within the CMT1A-REP sequence. These observations confirm the hypothesis that the distal CMT1A-REP element is the ancestral sequence which was duplicated during primate evolution, provide support for a human-chimpanzee clade, and suggest that insertion of the MLE into the CMT1A-REP sequence occurred in the ancestor of anthropoid primates.

T Nishiyama, M Kato

doi: mbe;16/8/1027pmid: N/A

The basal relationship of bryophytes and tracheophytes is problematic in land plant phylogeny. In addition to cladistic analyses of morphological data, molecular phylogenetic analyses of the nuclear small-subunit ribosomal RNA gene and the plastic gene rbcL have been performed, but no confident conclusions have been reached. Using the maximum-likelihood (ML) method, we analyzed 4,563 bp of aligned sequences from plastid protein-coding genes and 1,680 bp from the nuclear 18S rRNA gene. In the ML tree of deduced amino acid sequences of the plastid genes, hornworts were basal among the land plants, while mosses and liverworts each formed a clade and were sister to each other. Total-evidence evaluation of rRNA data and plastid protein-coding genes by TOTALML had an almost identical result. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1999) 16 (8): 1027-1036. » 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 Nishiyama, T. Articles by Kato, M. Search for related content PubMed PubMed citation Articles by Nishiyama, T. Articles by Kato, M. 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

Nishiyama, T;Kato, M

doi: 10.1093/oxfordjournals.molbev.a026192pmid: 10474899

The basal relationship of bryophytes and tracheophytes is problematic in land plant phylogeny. In addition to cladistic analyses of morphological data, molecular phylogenetic analyses of the nuclear small-subunit ribosomal RNA gene and the plastic gene rbcL have been performed, but no confident conclusions have been reached. Using the maximum-likelihood (ML) method, we analyzed 4,563 bp of aligned sequences from plastid protein-coding genes and 1,680 bp from the nuclear 18S rRNA gene. In the ML tree of deduced amino acid sequences of the plastid genes, hornworts were basal among the land plants, while mosses and liverworts each formed a clade and were sister to each other. Total-evidence evaluation of rRNA data and plastid protein-coding genes by TOTALML had an almost identical result.

A L Lawton-Rauh, E S Buckler, M D Purugganan

doi: mbe;16/8/1037pmid: N/A

The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congeneric species Arabidopsis lyrata. Analysis of these loci between these two Arabidopsis species, as well as three other more distantly related taxa, reveal contrasting dynamics of molecular evolution between these paralogous floral regulatory genes. Among the four loci, the CAL locus evolves at a significantly faster rate, which may be associated with the evolution of genetic redundancy between CAL and AP1. Moreover, there are significant differences in the distribution of replacement and synonymous substitutions between the functional gene domains of different floral homeotic loci. These results indicate that divergence in developmental function among paralogous members of regulatory gene families is accompanied by changes in rate and pattern of sequence evolution among loci. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1999) 16 (8): 1037-1045. » 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 Lawton-Rauh, A. L. Articles by Purugganan, M. D. Search for related content PubMed PubMed citation Articles by Lawton-Rauh, A. L. Articles by Buckler, E. S. Articles by Purugganan, M. D. 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

Lawton-Rauh, A L;4th, E S Buckler,;Purugganan, M D

doi: 10.1093/oxfordjournals.molbev.a026193pmid: 10474900

The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congeneric species Arabidopsis lyrata. Analysis of these loci between these two Arabidopsis species, as well as three other more distantly related taxa, reveal contrasting dynamics of molecular evolution between these paralogous floral regulatory genes. Among the four loci, the CAL locus evolves at a significantly faster rate, which may be associated with the evolution of genetic redundancy between CAL and AP1. Moreover, there are significant differences in the distribution of replacement and synonymous substitutions between the functional gene domains of different floral homeotic loci. These results indicate that divergence in developmental function among paralogous members of regulatory gene families is accompanied by changes in rate and pattern of sequence evolution among loci.

M Shimamura, H Abe, M Nikaido, K Ohshima, N Okada

doi: mbe;16/8/1046pmid: N/A

Several novel (sub)families of SINEs were isolated from the genomes of cetaceans and artiodactyls, and their sequences were determined. From comparisons of diagnostic nucleotides among the short interspersed repetitive elements (SINEs) in these (sub)families, we were able to draw the following conclusions. (1) After the divergence of the suborder Tylopoda (camels), the CHRS family of SINEs was newly created from tRNA(Glu) in a common ancestor of the lineages of the Suina (pigs and peccaries), Ruminantia (cows and deer), and Cetacea (whales and dolphins). (2) After divergence of the Suina lineage, the CHR-1 SINE and the CHR-2 SINE were generated successively in a common ancestor of ruminants, hippopotamuses, and cetaceans. (3) In the Ruminantia lineage, the Bov-tA SINE was generated by recombination between the CHR-2 SINE and Bov-A. (4) In the Suina lineage, the CHRS-S SINE was generated from the CHRS SINE. (5) In this latter lineage, the PRE-1 family of SINEs was created by insertion of part of the gene for tRNA(Arg) into the 5' region of the CHRS-S family. The distribution of a particular family of SINEs among species of artiodactyls and cetaceans confirmed the most recent conclusion for paraphyly of the order Artiodactyla. The present study also revealed that a newly created tRNA(Glu)-derived family of SINEs was subjected both to recombination with different units and to duplication of an internal sequence within a SINE unit to generate, during evolution, a huge superfamily of tRNA(Glu)-related families of SINEs that are now found in the genomes of artiodactyls and cetaceans. « Previous | Next Article » Table of Contents This Article Mol Biol Evol (1999) 16 (8): 1046-1060. » 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 Shimamura, M. Articles by Okada, N. Search for related content PubMed PubMed citation Articles by Shimamura, M. Articles by Abe, H. Articles by Nikaido, M. Articles by Ohshima, K. Articles by Okada, N. 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

Shimamura, M;Abe, H;Nikaido, M;Ohshima, K;Okada, N

doi: 10.1093/oxfordjournals.molbev.a026194pmid: 10474901

Several novel (sub)families of SINEs were isolated from the genomes of cetaceans and artiodactyls, and their sequences were determined. From comparisons of diagnostic nucleotides among the short interspersed repetitive elements (SINEs) in these (sub)families, we were able to draw the following conclusions. (1) After the divergence of the suborder Tylopoda (camels), the CHRS family of SINEs was newly created from tRNA(Glu) in a common ancestor of the lineages of the Suina (pigs and peccaries), Ruminantia (cows and deer), and Cetacea (whales and dolphins). (2) After divergence of the Suina lineage, the CHR-1 SINE and the CHR-2 SINE were generated successively in a common ancestor of ruminants, hippopotamuses, and cetaceans. (3) In the Ruminantia lineage, the Bov-tA SINE was generated by recombination between the CHR-2 SINE and Bov-A. (4) In the Suina lineage, the CHRS-S SINE was generated from the CHRS SINE. (5) In this latter lineage, the PRE-1 family of SINEs was created by insertion of part of the gene for tRNA(Arg) into the 5' region of the CHRS-S family. The distribution of a particular family of SINEs among species of artiodactyls and cetaceans confirmed the most recent conclusion for paraphyly of the order Artiodactyla. The present study also revealed that a newly created tRNA(Glu)-derived family of SINEs was subjected both to recombination with different units and to duplication of an internal sequence within a SINE unit to generate, during evolution, a huge superfamily of tRNA(Glu)-related families of SINEs that are now found in the genomes of artiodactyls and cetaceans.