DOI: 10.5061/dryad.69p8cz8zs
title: A new phylogeny of Rumex (Polygonaceae) adds evolutionary context to the diversity of reproductive systems present in the genus

description: Rumex is a unique member of the Polygonaceae family of plants. A source of
 intrigue for Rumex lies in the diversity of the reproductive systems
 associated with this genus. Four previously circumscribed subgenera and
 some two-hundred species comprise the collective Rumex genus. These
 species exhibit monoecious, dioecious, synoecious (hermaphroditic), and
 polygamous reproductive systems. Moreover, some of the dioecious species
 contain heteromorphic sex chromosomes, a phenomenon that is very rare in
 angiosperms. Apart from these confirmed morphological and
 phytogeographical distinctions, two of the four described subgenera, Rumex
 subg. Acetosa and Rumex subg. Acetosella, are distinctive in their sex
 chromosome systems. For this study, we used three chloroplast markers,
 rbcL, trnH-psbA, trnL-F, and dense taxon sampling, to reconstruct the most
 comprehensive molecular phylogeny of Rumex to date. The reconstructed
 phylogeny for this work resolves six major clades and one large grade in
 Rumex subg. Rumex. In addition, the species with known dioecious
 reproductive systems are resolved within a broader clade termed “the
 dioecious clade”. These results suggest that the species with divergent
 reproductive systems are more closely related to each other than to other
 species comprising the rest of the Rumex genus. Furthermore, some species
 with known synoecious reproductive systems are resolved in a single clade
 which is also nested within “the dioecious clade”. These results imply a
 possible reversal occurring over time which suggests the highly plastic
 nature of the reproductive systems in Rumex species.
description: These data were generated in order to study the
 evolution (phylogeny) of the plant genus Rumex (Polygonaceae).
 The data are composed of chloroplast DNA sequences.
 These sequences were generated using DNA primers and PCR,
 followed by Sanger Sequencing. These data re not
 related to human subjects.
description: From README file:
 Grant_etal_Rumex_psbA_Alignment_NEX.txt
 Description: DNA sequences for 109 individuals of the chloroplast
 spacer region psbA-trnH. The sequences have been aligned using MUSCLE and
 are presented in NEXUS file format. The anatomy of the taxon names is as
 follows. Each taxon name begins with a "T" followed by a
 three-digit number and an underscore (T###_). These are numbers associated
 with the accession database of the Burke Lab. They also serve to
 distinguish samples of the same taxon. Following these database numbers
 are the taxon names in the format "GenusSpecies", with the genus
 and species name each starting with a capitol letter. In cases where a
 sequence was not generated by us, but downloaded from GenBank, the name is
 presented as "Genus_species_GB", where "GB" indicates
 "GenBank".
 Grant_etal_Rumex_rbcL_Alignment_NEX.txt
 Description: DNA sequences for 109 individuals of the chloroplast
 region rbcL. The sequences have been aligned using MUSCLE and are
 presented in NEXUS file format. The anatomy of the taxon names is as
 follows. Each taxon name begins with a "T" followed by a
 three-digit number and an underscore (T###_). These are numbers associated
 with the accession database of the Burke Lab. They also serve to
 distinguish samples of the same taxon. Following these database numbers
 are the taxon names in the format "GenusSpecies", with the genus
 and species names each starting with a capitol letter. In cases where a
 sequence was not generated by us, but downloaded from GenBank, the name is
 presented as "Genus_species_GB", where "GB" indicates
 "GenBank".
 Grant_etal_Rumex_trnL_Alignment_NEX.txt
 Description: DNA sequences for 109 individuals of the chloroplast
 spacer region trnL-trnF. The sequences have been aligned using MUSCLE and
 are presented in NEXUS file format. The anatomy of the taxon names is as
 follows. Each taxon name begins with a "T" followed by a
 three-digit number and an underscore (T###_). These are numbers associated
 with the accession database of the Burke Lab. They also serve to
 distinguish samples of the same taxon. Following these database numbers
 are the taxon names in the format "GenusSpecies", with the genus
 and species each starting with a capitol letter. In cases where a sequence
 was not generated by us, but downloaded from GenBank, the name is
 presented as "Genus_species_GB", where "GB" indicates
 "GenBank".
 Grant_etal_Rumex_Concat_Alignment_NEX.txt
 Description: DNA sequences for 109 individuals. The sequence is a
 concatenation of the rbcL, psbA-trnH, and trnL-trnF regions (in that
 order). The sequences have been aligned using MUSCLE and are presented in
 NEXUS file format. The anatomy of the taxon names is as follows. Each
 taxon name begins with a "T" followed by a three-digit number
 and an underscore (T###_). These are numbers associated with the accession
 database of the Burke Lab. They also serve to distinguish samples of the
 same taxon. Following these database numbers are the taxon names in the
 format "GenusSpecies", with the genus and species each starting
 with a capitol letter. In cases where a sequence was not generated by us,
 but downloaded from GenBank, the name is presented as
 "Genus_species_GB", where "GB" indicates
 "GenBank".
 Grant_etal_Rumex_ModelTestNG_Infile_FASTA.fasta
 Description: DNA sequences for 109 individuals. The sequence is a
 concatenation of the rbcL, psbA-trnH, and trnL-trnF regions (in that
 order). The sequences have been aligned using MUSCLE and are presented in
 FASTA format. The taxon names are the “T###” Burke Lab accession numbers
 referenced above. In cases where a sequence was downloaded from GenBank
 and does not have an accession number, it is given as an obvious
 abbreviation of the species epithet followed by "GB" (GenBank).
 This is the infile used for the ModelTestNG analysis. 
 Grant_etal_Rumex_Garli_Infile_NEX.txt
 Description: DNA sequences for 109 individuals. The sequence is a
 concatenation of the rbcL, psbA-trnH, and trnL-trnF regions (in that
 order). The sequences have been aligned using MUSCLE and are presented in
 NEXUS file format. The anatomy of the taxon names is as follows. Each
 taxon name begins with a "T" followed by a three-digit number
 and an underscore (T###_). These are numbers associated with the accession
 database of the Burke Lab. They also serve to distinguish samples of the
 same taxon. Following these database numbers are the taxon names in the
 format "GenusSpecies", with the genus and species each starting
 with a capitol letter. In cases where a sequence was not generated by us,
 but downloaded from GenBank, the name is presented as
 "Genus_species_GB", where "GB" indicates
 "GenBank". This is the infile used for the GARLI
 analysis.
 Grant_etal_Rumex_MrBayes_Infile_NEX.txt
 Description: Description: DNA sequences for 109 individuals. The
 sequence is a concatenation of the rbcL, psbA-trnH, and trnL-trnF regions
 (in that order). The sequences have been aligned using MUSCLE and are
 presented in NEXUS file format. The taxon names are the T### Burke Lab
 accession numbers referenced above. In cases where a sequence was
 downloaded from GenBank and does not have an accession number, it is given
 as an obvious abbreviation of the species epithet followed by
 "GB" (GenBank). This is the infile used for the GARLI
 analysis.