The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly
Autor(a) principal: | |
---|---|
Data de Publicação: | 2014 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNIFESP |
Texto Completo: | https://repositorio.unifesp.br/handle/11600/37669 https://dx.doi.org/10.1371/journal.pone.0094774 |
Resumo: | The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are naked corals'' that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the naked coral'' hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. the initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the naked coral'' hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of Robust'' corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the naked coral'' topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. the equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data. |
id |
UFSP_cba69dae69469d566e9de9f7266ad523 |
---|---|
oai_identifier_str |
oai:repositorio.unifesp.br:11600/37669 |
network_acronym_str |
UFSP |
network_name_str |
Repositório Institucional da UNIFESP |
repository_id_str |
3465 |
spelling |
Kitahara, Marcelo Visentini [UNIFESP]Lin, Mei FangForet, SylvainHuttley, GavinMiller, David JohnChen, Chaolun AllenUniversidade Federal de São Paulo (UNIFESP)Universidade de São Paulo (USP)James Cook UnivAcad SinicaAustralian Natl UnivNatl Taiwan Univ2016-01-24T14:37:07Z2016-01-24T14:37:07Z2014-04-16Plos One. San Francisco: Public Library Science, v. 9, n. 4, 13 p., 2014.1932-6203https://repositorio.unifesp.br/handle/11600/37669https://dx.doi.org/10.1371/journal.pone.0094774WOS000336863900064.pdf10.1371/journal.pone.0094774WOS:000336863900064The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are naked corals'' that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the naked coral'' hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. the initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the naked coral'' hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of Robust'' corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the naked coral'' topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. the equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.National Science Council (NSC)Academia SinicaAustralian Research CouncilFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Dept Ciencias Mar, São Paulo, BrazilUniv São Paulo, Ctr Biol Marinha CEBIMar, São Paulo, BrazilJames Cook Univ, Sch Pharm & Mol Sci, Townsville, Qld 4811, AustraliaAcad Sinica, Biodivers Res Ctr, Taipei 115, TaiwanJames Cook Univ, ARC Ctr Excellence Coral Reef Studies, Townsville, Qld 4811, AustraliaAustralian Natl Univ, Res Sch Biol, Canberra, ACT, AustraliaAustralian Natl Univ, John Curtin Sch Med Res, Canberra, ACT 2601, AustraliaNatl Taiwan Univ, Inst Oceanog, Taipei 10764, TaiwanAcad Sinica, Taiwan Int Grad Program TIGP Biodivers, Taipei 115, TaiwanUniversidade Federal de São Paulo, Dept Ciencias Mar, São Paulo, BrazilFAPESP: 2012/21583-1Web of Science13engPublic Library SciencePlos OneThe Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophylyinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESPORIGINALWOS000336863900064.pdfapplication/pdf1143913${dspace.ui.url}/bitstream/11600/37669/1/WOS000336863900064.pdfeafcb8433c9b5e8e729ada39f1631c37MD51open accessTEXTWOS000336863900064.pdf.txtWOS000336863900064.pdf.txtExtracted texttext/plain64863${dspace.ui.url}/bitstream/11600/37669/6/WOS000336863900064.pdf.txt2663e24aecbac7892a210dc6ae58a535MD56open accessTHUMBNAILWOS000336863900064.pdf.jpgWOS000336863900064.pdf.jpgIM Thumbnailimage/jpeg7984${dspace.ui.url}/bitstream/11600/37669/8/WOS000336863900064.pdf.jpg857675715e123e62d96305d3f7dbf487MD58open access11600/376692023-06-05 19:38:43.263open accessoai:repositorio.unifesp.br:11600/37669Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestopendoar:34652023-06-05T22:38:43Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false |
dc.title.en.fl_str_mv |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
title |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
spellingShingle |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly Kitahara, Marcelo Visentini [UNIFESP] |
title_short |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
title_full |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
title_fullStr |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
title_full_unstemmed |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
title_sort |
The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly |
author |
Kitahara, Marcelo Visentini [UNIFESP] |
author_facet |
Kitahara, Marcelo Visentini [UNIFESP] Lin, Mei Fang Foret, Sylvain Huttley, Gavin Miller, David John Chen, Chaolun Allen |
author_role |
author |
author2 |
Lin, Mei Fang Foret, Sylvain Huttley, Gavin Miller, David John Chen, Chaolun Allen |
author2_role |
author author author author author |
dc.contributor.institution.none.fl_str_mv |
Universidade Federal de São Paulo (UNIFESP) Universidade de São Paulo (USP) James Cook Univ Acad Sinica Australian Natl Univ Natl Taiwan Univ |
dc.contributor.author.fl_str_mv |
Kitahara, Marcelo Visentini [UNIFESP] Lin, Mei Fang Foret, Sylvain Huttley, Gavin Miller, David John Chen, Chaolun Allen |
description |
The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are naked corals'' that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the naked coral'' hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. the initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the naked coral'' hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of Robust'' corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the naked coral'' topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. the equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data. |
publishDate |
2014 |
dc.date.issued.fl_str_mv |
2014-04-16 |
dc.date.accessioned.fl_str_mv |
2016-01-24T14:37:07Z |
dc.date.available.fl_str_mv |
2016-01-24T14:37:07Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
Plos One. San Francisco: Public Library Science, v. 9, n. 4, 13 p., 2014. |
dc.identifier.uri.fl_str_mv |
https://repositorio.unifesp.br/handle/11600/37669 https://dx.doi.org/10.1371/journal.pone.0094774 |
dc.identifier.issn.none.fl_str_mv |
1932-6203 |
dc.identifier.file.none.fl_str_mv |
WOS000336863900064.pdf |
dc.identifier.doi.none.fl_str_mv |
10.1371/journal.pone.0094774 |
dc.identifier.wos.none.fl_str_mv |
WOS:000336863900064 |
identifier_str_mv |
Plos One. San Francisco: Public Library Science, v. 9, n. 4, 13 p., 2014. 1932-6203 WOS000336863900064.pdf 10.1371/journal.pone.0094774 WOS:000336863900064 |
url |
https://repositorio.unifesp.br/handle/11600/37669 https://dx.doi.org/10.1371/journal.pone.0094774 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.none.fl_str_mv |
Plos One |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
13 |
dc.publisher.none.fl_str_mv |
Public Library Science |
publisher.none.fl_str_mv |
Public Library Science |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UNIFESP instname:Universidade Federal de São Paulo (UNIFESP) instacron:UNIFESP |
instname_str |
Universidade Federal de São Paulo (UNIFESP) |
instacron_str |
UNIFESP |
institution |
UNIFESP |
reponame_str |
Repositório Institucional da UNIFESP |
collection |
Repositório Institucional da UNIFESP |
bitstream.url.fl_str_mv |
${dspace.ui.url}/bitstream/11600/37669/1/WOS000336863900064.pdf ${dspace.ui.url}/bitstream/11600/37669/6/WOS000336863900064.pdf.txt ${dspace.ui.url}/bitstream/11600/37669/8/WOS000336863900064.pdf.jpg |
bitstream.checksum.fl_str_mv |
eafcb8433c9b5e8e729ada39f1631c37 2663e24aecbac7892a210dc6ae58a535 857675715e123e62d96305d3f7dbf487 |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP) |
repository.mail.fl_str_mv |
|
_version_ |
1802764178612551680 |