Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Title:
Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales
Authors:
Walker, Joseph F.; Yang, Ya; Moore, Michael J.; Mikenas, Jessica; Timoneda, Alfonso; Brockington, Samuel F.; Smith, Stephen A.
Abstract:
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68-83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.
Citation:
Walker, Joseph F., Ya Yang, Michael J. Moore, et al. 2017. "Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales." American Journal of Botany 104(6): 858-867.
Publisher:
Botanical Society of America
DATE ISSUED:
2017-06-20
Department:
Biology
Type:
Article
PUBLISHED VERSION:
10.3732/ajb.1700083
Additional Links:
http://www.amjbot.org/lookup/doi/10.3732/ajb.1700083
PERMANENT LINK:
http://hdl.handle.net/11282/620507

Full metadata record

DC FieldValue Language
dc.contributor.authorWalker, Joseph F.en
dc.contributor.authorYang, Yaen
dc.contributor.authorMoore, Michael J.en
dc.contributor.authorMikenas, Jessicaen
dc.contributor.authorTimoneda, Alfonsoen
dc.contributor.authorBrockington, Samuel F.en
dc.contributor.authorSmith, Stephen A.en
dc.date.accessioned2017-09-13T15:29:44Z-
dc.date.available2017-09-13T15:29:44Z-
dc.date.issued2017-06-20-
dc.identifier.citationWalker, Joseph F., Ya Yang, Michael J. Moore, et al. 2017. "Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales." American Journal of Botany 104(6): 858-867.en
dc.identifier.issn0002-9122-
dc.identifier.urihttp://hdl.handle.net/11282/620507-
dc.description.abstractPREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68-83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.en
dc.language.isoen_USen
dc.publisherBotanical Society of Americaen
dc.identifier.doi10.3732/ajb.1700083-
dc.relation.urlhttp://www.amjbot.org/lookup/doi/10.3732/ajb.1700083en
dc.subject.departmentBiologyen_US
dc.titleWidespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllalesen_US
dc.typeArticleen
dc.identifier.journalAmerican Journal of Botanyen
dc.subject.keywordCaryophyllalesen_US
dc.subject.keywordGene tree conflicten_US
dc.subject.keywordPaleopolyploidyen_US
dc.subject.keywordPhylogenomicsen_US
dc.subject.keywordPlant carnivoryen_US
dc.identifier.volume104en_US
dc.identifier.issue6en_US
dc.identifier.startpage858en_US
dc.rightsArchived with thanks to American Journal of Botanyen
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