Reconstructing Ancestral Patterns of Colonization and Dispersal in the Hawaiian Understory Tree Genus Psychotria (Rubiaceae): A Comparison of Parsimony and Likelihood Approaches
Systematic and biogeographical relationships within the Hawaiian clade of the pantropical understory shrub genus Psychotria (Rubiaceae) were investigated using phylogenetic analysis of 18S-26S ribosomal DNA internal (ITS) and external (ETS) transcribed spacers. Phylogenetic analyses strongly suggest...
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Veröffentlicht in: | Systematic biology 2003-12, Vol.52 (6), p.820-838 |
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description | Systematic and biogeographical relationships within the Hawaiian clade of the pantropical understory shrub genus Psychotria (Rubiaceae) were investigated using phylogenetic analysis of 18S-26S ribosomal DNA internal (ITS) and external (ETS) transcribed spacers. Phylogenetic analyses strongly suggest that the Hawaiian Psychotria are monophyletic and the result of a single introduction to the Hawaiian Islands. The results of phylogenetic analyses of ITS and ETS partitions alone give slightly different topologies among basal lineages of the Hawaiian clade; however, such differences are not well supported. Relationships in the section Straussia clade in particular are not well resolved because of few nucleotide changes on internal branches, suggesting extremely rapid radiation in the lineage. Parsimony and likelihood reconstructions of ancestral geographical distributions using the topologies inferred from both parsimony and likelihood analysis of combined data and using different combinations of models and branch lengths gave highly congruent results. However, for one internal node (corresponding to the majority of the "greenwelliae" clade), parsimony reconstructions were unable to distinguish between three possible island states, whereas likelihood reconstructions resulted in clear ordering of possible states, with the island of O'ahu slightly more probable than other islands under all but one model and branch length combination considered (the Jukes-Cantor-like model with branch lengths inferred under parsimony, under which conditions Maui Nui is more probable). A pattern of colonization from oldest to youngest islands was inferred from the phylogeny, using maximum parsimony and maximum likelihood. Additionally, a much higher incidence of intraisland versus interisland speciation was inferred. |
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Phylogenetic analyses strongly suggest that the Hawaiian Psychotria are monophyletic and the result of a single introduction to the Hawaiian Islands. The results of phylogenetic analyses of ITS and ETS partitions alone give slightly different topologies among basal lineages of the Hawaiian clade; however, such differences are not well supported. Relationships in the section Straussia clade in particular are not well resolved because of few nucleotide changes on internal branches, suggesting extremely rapid radiation in the lineage. Parsimony and likelihood reconstructions of ancestral geographical distributions using the topologies inferred from both parsimony and likelihood analysis of combined data and using different combinations of models and branch lengths gave highly congruent results. However, for one internal node (corresponding to the majority of the "greenwelliae" clade), parsimony reconstructions were unable to distinguish between three possible island states, whereas likelihood reconstructions resulted in clear ordering of possible states, with the island of O'ahu slightly more probable than other islands under all but one model and branch length combination considered (the Jukes-Cantor-like model with branch lengths inferred under parsimony, under which conditions Maui Nui is more probable). A pattern of colonization from oldest to youngest islands was inferred from the phylogeny, using maximum parsimony and maximum likelihood. Additionally, a much higher incidence of intraisland versus interisland speciation was inferred.</description><identifier>ISSN: 1063-5157</identifier><identifier>EISSN: 1076-836X</identifier><identifier>DOI: 10.1080/10635150390251072</identifier><identifier>PMID: 14668119</identifier><language>eng</language><publisher>England: Taylor and Francis</publisher><subject>Archipelagos ; Base Sequence ; Biogeography ; Biological taxonomies ; Biology ; cladistics ; Demography ; DNA Primers ; DNA, Ribosomal - genetics ; Evolution ; Evolution, Molecular ; Genetics ; Geography ; Hawaii ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Parsimony ; Phylogenetics ; Phylogeny ; Psychotria ; Psychotria - genetics ; Ribosomal DNA ; Sequence Analysis, DNA ; Taxa ; Topology ; Trees</subject><ispartof>Systematic biology, 2003-12, Vol.52 (6), p.820-838</ispartof><rights>Copyright 2003 Society of Systematic Biologists</rights><rights>Copyright Society of Systematic Biologists Dec 2003</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c442t-dd150d667f19f71be97e6a0d9264aed872287e6b6e3db38e7dd6b620e7c0fe313</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/3651099$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/3651099$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,27924,27925,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/14668119$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nepokroeff, Molly</creatorcontrib><creatorcontrib>Sytsma, Kenneth J.</creatorcontrib><creatorcontrib>Wagner, Warren L.</creatorcontrib><creatorcontrib>Zimmer, Elizabeth A.</creatorcontrib><title>Reconstructing Ancestral Patterns of Colonization and Dispersal in the Hawaiian Understory Tree Genus Psychotria (Rubiaceae): A Comparison of Parsimony and Likelihood Approaches</title><title>Systematic biology</title><addtitle>Syst Biol</addtitle><description>Systematic and biogeographical relationships within the Hawaiian clade of the pantropical understory shrub genus Psychotria (Rubiaceae) were investigated using phylogenetic analysis of 18S-26S ribosomal DNA internal (ITS) and external (ETS) transcribed spacers. Phylogenetic analyses strongly suggest that the Hawaiian Psychotria are monophyletic and the result of a single introduction to the Hawaiian Islands. The results of phylogenetic analyses of ITS and ETS partitions alone give slightly different topologies among basal lineages of the Hawaiian clade; however, such differences are not well supported. Relationships in the section Straussia clade in particular are not well resolved because of few nucleotide changes on internal branches, suggesting extremely rapid radiation in the lineage. Parsimony and likelihood reconstructions of ancestral geographical distributions using the topologies inferred from both parsimony and likelihood analysis of combined data and using different combinations of models and branch lengths gave highly congruent results. However, for one internal node (corresponding to the majority of the "greenwelliae" clade), parsimony reconstructions were unable to distinguish between three possible island states, whereas likelihood reconstructions resulted in clear ordering of possible states, with the island of O'ahu slightly more probable than other islands under all but one model and branch length combination considered (the Jukes-Cantor-like model with branch lengths inferred under parsimony, under which conditions Maui Nui is more probable). A pattern of colonization from oldest to youngest islands was inferred from the phylogeny, using maximum parsimony and maximum likelihood. Additionally, a much higher incidence of intraisland versus interisland speciation was inferred.</description><subject>Archipelagos</subject><subject>Base Sequence</subject><subject>Biogeography</subject><subject>Biological taxonomies</subject><subject>Biology</subject><subject>cladistics</subject><subject>Demography</subject><subject>DNA Primers</subject><subject>DNA, Ribosomal - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Genetics</subject><subject>Geography</subject><subject>Hawaii</subject><subject>Likelihood Functions</subject><subject>Models, Genetic</subject><subject>Molecular Sequence Data</subject><subject>Parsimony</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Psychotria</subject><subject>Psychotria - genetics</subject><subject>Ribosomal DNA</subject><subject>Sequence Analysis, DNA</subject><subject>Taxa</subject><subject>Topology</subject><subject>Trees</subject><issn>1063-5157</issn><issn>1076-836X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFklGL1DAQx4t4eOfpBxBEgg9yPlSTpk0a35bVuxMWXI478K2kydTN2iY1aZH1W_kNb9ZdFPTBp8lkfjN_Mv9k2TNG3zBa07eMCl6xinJFi4pRWTzIzjCIvObi88P9WfAcAXmaPU5pSyljomKPslNWClEzps6ynzdggk9TnM3k_Bey8AYw0z1Z62mC6BMJHVmGPnj3Q08ueKK9Je9dGiEmxJwn0wbItf6undOe3HmLhSnEHbmNAOQK_JzIOu3MJkzRaXJxM7dOG9Dw-h1Z4Ohh1NElHIxCax2TG4Lf_VJZua_Qu00IlizGMQZtNpCeZCed7hM8Pcbz7O7yw-3yOl99uvq4XKxyU5bFlFuLi7FCyI6pTrIWlAShqVWFKDXYWhZFjTetAG5bXoO0FpOCgjS0A874efbqMBeFv824lGZwyUDfaw9hTo1kZaWEEv8FmSooLwVH8OVf4DbM0eMjkCmlKAu5l2UHyMSQUoSuGaMbdNw1jDZ715t_XMeeF8fBczuA_dNxtBmB5wdgu3fmd53jb6BK8Xt-e7Nz</recordid><startdate>20031201</startdate><enddate>20031201</enddate><creator>Nepokroeff, Molly</creator><creator>Sytsma, Kenneth J.</creator><creator>Wagner, Warren L.</creator><creator>Zimmer, Elizabeth A.</creator><general>Taylor and Francis</general><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8AO</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7P</scope><scope>MBDVC</scope><scope>PADUT</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>S0X</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20031201</creationdate><title>Reconstructing Ancestral Patterns of Colonization and Dispersal in the Hawaiian Understory Tree Genus Psychotria (Rubiaceae): A Comparison of Parsimony and Likelihood Approaches</title><author>Nepokroeff, Molly ; Sytsma, Kenneth J. ; Wagner, Warren L. ; Zimmer, Elizabeth A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c442t-dd150d667f19f71be97e6a0d9264aed872287e6b6e3db38e7dd6b620e7c0fe313</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Archipelagos</topic><topic>Base Sequence</topic><topic>Biogeography</topic><topic>Biological taxonomies</topic><topic>Biology</topic><topic>cladistics</topic><topic>Demography</topic><topic>DNA Primers</topic><topic>DNA, Ribosomal - genetics</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Genetics</topic><topic>Geography</topic><topic>Hawaii</topic><topic>Likelihood Functions</topic><topic>Models, Genetic</topic><topic>Molecular Sequence Data</topic><topic>Parsimony</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Psychotria</topic><topic>Psychotria - genetics</topic><topic>Ribosomal DNA</topic><topic>Sequence Analysis, DNA</topic><topic>Taxa</topic><topic>Topology</topic><topic>Trees</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nepokroeff, Molly</creatorcontrib><creatorcontrib>Sytsma, Kenneth J.</creatorcontrib><creatorcontrib>Wagner, Warren L.</creatorcontrib><creatorcontrib>Zimmer, Elizabeth A.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Research Library China</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Systematic biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nepokroeff, Molly</au><au>Sytsma, Kenneth J.</au><au>Wagner, Warren L.</au><au>Zimmer, Elizabeth A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Reconstructing Ancestral Patterns of Colonization and Dispersal in the Hawaiian Understory Tree Genus Psychotria (Rubiaceae): A Comparison of Parsimony and Likelihood Approaches</atitle><jtitle>Systematic biology</jtitle><addtitle>Syst Biol</addtitle><date>2003-12-01</date><risdate>2003</risdate><volume>52</volume><issue>6</issue><spage>820</spage><epage>838</epage><pages>820-838</pages><issn>1063-5157</issn><eissn>1076-836X</eissn><abstract>Systematic and biogeographical relationships within the Hawaiian clade of the pantropical understory shrub genus Psychotria (Rubiaceae) were investigated using phylogenetic analysis of 18S-26S ribosomal DNA internal (ITS) and external (ETS) transcribed spacers. Phylogenetic analyses strongly suggest that the Hawaiian Psychotria are monophyletic and the result of a single introduction to the Hawaiian Islands. The results of phylogenetic analyses of ITS and ETS partitions alone give slightly different topologies among basal lineages of the Hawaiian clade; however, such differences are not well supported. Relationships in the section Straussia clade in particular are not well resolved because of few nucleotide changes on internal branches, suggesting extremely rapid radiation in the lineage. Parsimony and likelihood reconstructions of ancestral geographical distributions using the topologies inferred from both parsimony and likelihood analysis of combined data and using different combinations of models and branch lengths gave highly congruent results. However, for one internal node (corresponding to the majority of the "greenwelliae" clade), parsimony reconstructions were unable to distinguish between three possible island states, whereas likelihood reconstructions resulted in clear ordering of possible states, with the island of O'ahu slightly more probable than other islands under all but one model and branch length combination considered (the Jukes-Cantor-like model with branch lengths inferred under parsimony, under which conditions Maui Nui is more probable). A pattern of colonization from oldest to youngest islands was inferred from the phylogeny, using maximum parsimony and maximum likelihood. Additionally, a much higher incidence of intraisland versus interisland speciation was inferred.</abstract><cop>England</cop><pub>Taylor and Francis</pub><pmid>14668119</pmid><doi>10.1080/10635150390251072</doi><tpages>19</tpages></addata></record> |
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subjects | Archipelagos Base Sequence Biogeography Biological taxonomies Biology cladistics Demography DNA Primers DNA, Ribosomal - genetics Evolution Evolution, Molecular Genetics Geography Hawaii Likelihood Functions Models, Genetic Molecular Sequence Data Parsimony Phylogenetics Phylogeny Psychotria Psychotria - genetics Ribosomal DNA Sequence Analysis, DNA Taxa Topology Trees |
title | Reconstructing Ancestral Patterns of Colonization and Dispersal in the Hawaiian Understory Tree Genus Psychotria (Rubiaceae): A Comparison of Parsimony and Likelihood Approaches |
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