Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification
| Main Authors: | Sinn, Brandon T., Kelly, Lawrence M., Freudenstein, John V. |
|---|---|
| Format: | info dataset Journal |
| Terbitan: |
, 2016
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4936195 |
| ctrlnum |
4936195 |
|---|---|
| fullrecord |
<?xml version="1.0"?>
<dc schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"><creator>Sinn, Brandon T.</creator><creator>Kelly, Lawrence M.</creator><creator>Freudenstein, John V.</creator><date>2016-04-20</date><description>Premise of the study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyze additional molecular markers from the nuclear and plastid genomes, reevaluate the possibility of a derived loss of autonomous self-pollination, and investigate the topological effects of matrix partitioning scheme choice. Methods: We sequenced seven plastid regions and the nuclear ITS1 - ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. Key results: Topologies recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recover six monophyletic groups that we circumscribe into three subgenera and six sections. Putative fungal mimic characters serve as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, is recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. Conclusions: Our analyses do not unambiguously support a single origin for all fungal mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction.</description><description>Combined (Plastid and Nuclear) MatrixSanger sequenced plastid and nuclear loci aligned using MAFFT through Geneious 5-7 (default alignment values).Concatenated Chloro and ITS Final BEST.nexusRAxML Matrix 6 bipartitions treeMost likely tree resulting from RAxML analysis of Matrix 6, annotated with bootstrap values.RAxML_bipartitions.matrix6.treBEAST Tree from Matrix 6BI tree resulting from the analysis of Matrix 6 with BEAST.MATRIX6BeastTree.nex</description><identifier>https://zenodo.org/record/4936195</identifier><identifier>10.5061/dryad.58fp6</identifier><identifier>oai:zenodo.org:4936195</identifier><relation>doi:10.3732/ajb.1400316</relation><relation>url:https://zenodo.org/communities/dryad</relation><rights>info:eu-repo/semantics/openAccess</rights><rights>https://creativecommons.org/publicdomain/zero/1.0/legalcode</rights><subject>PartitionFinder</subject><subject>Asarum heterophyllum Ashe</subject><subject>Asarum naniflorum (H.L.Blomq.) B.T.Sinn</subject><subject>Asarum caudigerellum C.Y.Cheng & C.S.Yang</subject><subject>Asarum arifolium Michx. var. ruthii (Ashe) Barringer</subject><subject>Asarum chueyi B.T.Sinn</subject><subject>Asarum arifolium Michx. var. arifolium</subject><subject>Asarum shuttleworthii Britten & Baker var. shuttleworthii</subject><subject>Asarum megacalyx (F.Maek.) T.Sugaw.</subject><subject>Asarum splendens (F.Maek.) C.Y.Cheng & C.S.Yang</subject><subject>Asarum blumei Duch.</subject><subject>Heterotropa</subject><subject>Asarum yakusimense Masam.</subject><subject>Asarum asaroides (C.Morren et Decne.) F.Maek.</subject><subject>Asarum hartwegii S.Watson</subject><subject>Asarum lewisii Fernald</subject><subject>Saruma henryi Oliv.</subject><subject>Japonasarum</subject><subject>Asiasarum</subject><subject>Asarum canadense L</subject><subject>Asarum muramatsui Makino</subject><subject>Asarum asperum F.Maek var. asperum</subject><subject>Asarum caudatum Lindl.</subject><subject>Asarum gelasinum (F.Maek.) Hatus.</subject><subject>Asarum savatieri Franch. subsp. savatieri</subject><subject>Asarum</subject><subject>Asarum memmingeri Ashe</subject><subject>Asarum himalaicum Hook.f. & Thomson ex Klotzsch</subject><subject>Asarum rhombiformis (Gaddy) B.T.Sinn</subject><subject>Asarum kumageanum Masam.</subject><subject>Geotaenium</subject><subject>Asarum virginicum L.</subject><subject>Asarum hatsushimae F.Maek. ex Hatus. & Yamahata</subject><subject>Asarum crassum F.Maek.</subject><subject>Maximum Parsimony</subject><subject>Asarum lemmonii S.Watson</subject><subject>Asarum delavayi Franch.</subject><subject>Asarum minamitanianum Hatus.</subject><subject>Asarum forbesii Maxim.</subject><subject>Asarum fudsinoi T.Itô</subject><subject>Asarum epigynum Hayata</subject><subject>Asarum hexalobum (F.Maek.) F.Maek. var. perfectum F.Maek.</subject><subject>Asarum speciosum (R.M.Harper) Barringer</subject><subject>Asarum maximum Hemsl.</subject><subject>Asarum shuttleworthii Britten & Baker var. harperi (Gaddy) Barringer</subject><subject>Bayesian inference</subject><subject>Hexastylis</subject><subject>Asarum caulescens Maxim</subject><subject>Asarum debile Franch.</subject><subject>Asarum pulchellum Hemsl.</subject><subject>Asarum contractum (H.L.Blomq.) Barringer</subject><subject>Asarum takaoi F.Maek.</subject><subject>Asarum sieboldii Miq. var. sieboldii</subject><subject>Asarum minus Ashe</subject><title>Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification</title><type>Other:info:eu-repo/semantics/other</type><type>Other:dataset</type><recordID>4936195</recordID></dc>
|
| format |
Other:info:eu-repo/semantics/other Other Other:dataset Journal:Journal Journal |
| author |
Sinn, Brandon T. Kelly, Lawrence M. Freudenstein, John V. |
| title |
Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification |
| publishDate |
2016 |
| topic |
PartitionFinder Asarum heterophyllum Ashe Asarum naniflorum (H.L.Blomq.) B.T.Sinn Asarum caudigerellum C.Y.Cheng & C.S.Yang Asarum arifolium Michx. var. ruthii (Ashe) Barringer Asarum chueyi B.T.Sinn Asarum arifolium Michx. var. arifolium Asarum shuttleworthii Britten & Baker var. shuttleworthii Asarum megacalyx (F.Maek.) T.Sugaw Asarum splendens (F.Maek.) C.Y.Cheng & C.S.Yang Asarum blumei Duch Heterotropa Asarum yakusimense Masam Asarum asaroides (C.Morren et Decne.) F.Maek Asarum hartwegii S.Watson Asarum lewisii Fernald Saruma henryi Oliv Japonasarum Asiasarum Asarum canadense L Asarum muramatsui Makino Asarum asperum F.Maek var. asperum Asarum caudatum Lindl Asarum gelasinum (F.Maek.) Hatus Asarum savatieri Franch. subsp. savatieri Asarum Asarum memmingeri Ashe Asarum himalaicum Hook.f. & Thomson ex Klotzsch Asarum rhombiformis (Gaddy) B.T.Sinn Asarum kumageanum Masam Geotaenium Asarum virginicum L. Asarum hatsushimae F.Maek. ex Hatus. & Yamahata Asarum crassum F.Maek Maximum Parsimony Asarum lemmonii S.Watson Asarum delavayi Franch Asarum minamitanianum Hatus Asarum forbesii Maxim Asarum fudsinoi T.Itô Asarum epigynum Hayata Asarum hexalobum (F.Maek.) F.Maek. var. perfectum F.Maek Asarum speciosum (R.M.Harper) Barringer Asarum maximum Hemsl Asarum shuttleworthii Britten & Baker var. harperi (Gaddy) Barringer Bayesian inference Hexastylis Asarum caulescens Maxim Asarum debile Franch Asarum pulchellum Hemsl Asarum contractum (H.L.Blomq.) Barringer Asarum takaoi F.Maek Asarum sieboldii Miq. var. sieboldii Asarum minus Ashe |
| url |
https://zenodo.org/record/4936195 |
| contents |
Premise of the study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyze additional molecular markers from the nuclear and plastid genomes, reevaluate the possibility of a derived loss of autonomous self-pollination, and investigate the topological effects of matrix partitioning scheme choice. Methods: We sequenced seven plastid regions and the nuclear ITS1 - ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. Key results: Topologies recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recover six monophyletic groups that we circumscribe into three subgenera and six sections. Putative fungal mimic characters serve as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, is recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. Conclusions: Our analyses do not unambiguously support a single origin for all fungal mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction. Combined (Plastid and Nuclear) MatrixSanger sequenced plastid and nuclear loci aligned using MAFFT through Geneious 5-7 (default alignment values).Concatenated Chloro and ITS Final BEST.nexusRAxML Matrix 6 bipartitions treeMost likely tree resulting from RAxML analysis of Matrix 6, annotated with bootstrap values.RAxML_bipartitions.matrix6.treBEAST Tree from Matrix 6BI tree resulting from the analysis of Matrix 6 with BEAST.MATRIX6BeastTree.nex |
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IOS16997.4936195 |
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ZAIN Publications |
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7213 |
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library:special library |
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Cognizance Journal of Multidisciplinary Studies |
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5267 |
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Cognizance Journal of Multidisciplinary Studies |
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16997 |
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Multidisciplinary |
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Stockholm |
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INTERNASIONAL |
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1 |
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IOS16997 |
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2022-06-06T05:24:23Z |
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2022-06-06T05:24:23Z |
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dc |
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1734905156877680640 |
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17.610285 |