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A new phylogeny of Rumex (Polygonaceae) adds evolutionary context to the diversity of reproductive systems present in the genus

Citation

Grant, Kirstie et al. (2022), A new phylogeny of Rumex (Polygonaceae) adds evolutionary context to the diversity of reproductive systems present in the genus, Dryad, Dataset, https://doi.org/10.5061/dryad.69p8cz8zs

Abstract

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.

Methods

  • 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.

Usage Notes

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.

Funding

National Science Foundation, Award: 1601031