Data from: Phylogenetic relationships of genera Cladocolea and Struthanthus (Loranthaceae) with emphasis on the Mexican species
Data files
Apr 05, 2024 version files 989.15 KB
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1_Alignment_trnLF_ITS_matK.fas
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10_BI_trnLF_matK_sumt.con.tre
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11_BI_trnLF_ITS_matK_sumt.con.tre
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12_ML_trnLF_ITS_matK_47.contree
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13_Trace_character.nex
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2_Alignment_ITS.fas
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3_Alignment_trnLF.fas
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4_Alignment_matK.fas
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5_Alignment_ITS_trnLF_matK_47tax.fas
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6_ML_ITS.nex.contree
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7_ML_trnLF_matK.nex.contree
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8_ML_trnLF_ITS_matK.nex.contree
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9_BI_ITS_sumt.con.tre
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README.md
Abstract
Cladocolea (Loranthaceae) is a neotropical genus currently containing 24 species. Its taxonomic history included changes in its circumscription as the transfers of some of its species to other genera of the family. Several phylogenetic studies of Loranthaceae have recognized a close relationship between Cladocolea and Struthanthus. However, both genera were poorly represented in these studies, so here we generate a phylogeny of Mexican species of Cladocolea, Struthanthus, and other genera of Psittacanthinae, using nuclear DNA sequences of the ITS region, as well as the chloroplast regions matK and trnL-F. One hundred twelve individuals were sampled and 12 GenBank sequences were included. We included 23 taxa of Cladocolea and 30 species of nine other genera of Loranthaceae. In order to estimate ancestral states and character evolution, 13 morphological characters were mapped, both vegetative and reproductive. Bayesian Inference and Maximum Likelihood analyses were performed using independent matrices and a concatenated matrix of 2842 characters. Our results show that Cladocolea and Struthanthus are both polyphyletic genera. However, the Mexican species of Cladocolea and Struthanthus with convolute or sigmoid styles form a monophyletic group. Finally, the analysis of ancestral character states indicates a trend towards a reduction of inflorescences in the Cladocolea-Struthanthus complex. New combinations and synonymies are proposed.
README: Data from: Phylogenetic relationships of genera Cladocolea and Struthanthus (Loranthaceae) with emphasis on the Mexican species
Authors: Luis G. Galván-González, Rosa Cerros-Tlatilpa, Adolfo Espejo-Serna, Victor W. Steinmann
This README file describes the data package accompanying the above publication.
Files:
1_Alignment_trnLF_ITS_matK.fas: Fasta file containing the alignment for the 115 accession Combined dataset for Cladocolea, Struthanthus and outgroups.
2_Alignment_ITS.fas: Fasta file containing the alignment for the 115 accession ITS region dataset for Cladocolea, Struthanthus and outgroups.
3_Alignment_trnLF.fas: Fasta file containing the alignment for the 115 accession trnL-F region dataset for Cladocolea, Struthanthus and outgroups.
4_Alignment_matK.fas: Fasta file containing the alignment for the 97 accession matK region dataset for Cladocolea, Struthanthus and outgroups.
5_Alignment_ITS_trnLF_matK_47tax.fas: Fasta file containing the alignment for the 47 accession Combined dataset for Cladocolea, Struthanthus and outgroups. This alignment was used to construct the maximum likelihood tree, implemented in the ancestral character reconstruction analysis.
6_ML_ITS.nex.contree: Maximum likelihood consensus tree for the ITS alignment, obtained by the UltraFast Bootstrap support test in the IQ-TREE program, with 10000 bootstrap replicates.
7_ML_trnLF_matK.nex.contree: Maximum likelihood consensus tree for the trnL-F an matK alignment, obtained by the UltraFast Bootstrap support test in the IQ-TREE program, with 10000 bootstrap replicates.
8_ML_trnLF_matK_ITS.nex.contree:Maximum likelihood consensus tree for the alignment of concatenated nucleotide and chloroplast data, obtained using the UltraFast Bootstrap support test in the IQ-TREE program, with 10000 bootstrap replicates.
9_BI_ITS_sumt.con.tre: Bayesian consensus tree for the ITS alignment, obtained with the MrBayes program, with 20 million generations and resampling of trees every thousand generations.
10_BI_trnLF_matK_sumt.con.tre: Bayesian consensus tree for trnL-F and matK alignment, obtained with the MrBayes program, with 20 million generations and resampling of trees every thousand generations.
11_BI_trnLF_ITS_matK_sumt.con.tre: Bayesian consensus treefor the alignment of concatenated nucleotide and chloroplast data, obtained with the MrBayes program, with 20 million generations and resampling of trees every thousand generations.
12_ML_trnLF_ITS_matK_47.contree: Maximum likelihood consensus tree for the alignment of 47 accessions of concatenated nucleotide and chloroplast data, obtained using the UltraFast Bootstrap support test of the IQ-TREE program, with 10000 bootstrap replicates.
13_Trace_character.nex: nexus file containing the reduced maximum likelihood tree, and the morphological data matrix for the analysis of ancestral characters in the Mesquite program.