Phylogenomic data of the Neotropical rainforest genus Zygia (Mimoseae, Fabaceae) used for phylogenetic inference
Data files
May 05, 2026 version files 619.79 MB
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all_loci_all_acc.zip
24.56 MB
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all_loci_one_acc_per_sp.zip
16.52 MB
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concatenated_all_loci_trimmed.fasta
299.06 MB
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concatenated_without_paralogs_trimmed.fasta
279.65 MB
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README.md
2.38 KB
Abstract
This data was used to infer phylogeny of the Neotropical rainforest genus Zygia (Fabaceae) and includes species of Zygia and other closely related legume genera. Data includes loci alignments of nuclear DNA data obtained from hybrid capture after assembly with Hybpiper. One zip-file contains loci alignments including all accessions (134 taxa), one zip-file contains loci alignments including one accession/species (79 taxa). Two concatenated datasets, including all accessions, are also provided. One concatenated dataset includes all loci, and for the other concatenated dataset, putatively paralogous loci and loci with >50% missing data or missing taxa are excluded.
All loci alignments, including all accessions (in total 134 taxa) and all loci alignments including one accession/species (in total 79 taxa) obtained after Hybpiper, and concatenated datasets of these loci.
Dataset DOI: 10.5061/dryad.1c59zw4bm
Description of the data and file structure
Data from 1315 nuclear loci were sequenced from 134 accessions, representing 47 species of Zygia (Fabaceae), as well as four species of the closely related genus Macrosamanea, the poorly known Marmaroxylon magdalenae, endemic to the Magdalena Valley in Colombia, and Marmaroxylon eperuetorum. The data was analyzed using species tree reconstruction based on the multispecies coalescent model and maximum likelihood analyses of concatenated datasets. Different approaches to handling putatively paralogous genes, missing data, and missing taxa were tested. Moreover, raw data from previous studies, 12 accessions of Zygia and 28 accessions of other mimosoid legumes, was downloaded from ENA projects PRJEB8722 and PRJEB52227 and included in these datasets.
Files and variables
File: all_loci_all_acc.zip
Description: All loci, including all accessions (in total 134 taxa) obtained from assembly in Hybpiper.
File: all_loci_one_acc_per_sp.zip
Description: All loci, including one accession/species (in total 79 taxa) obtained from assembly in Hybpiper.
File: concatenated_all_loci_trimmed.fasta
Description: All locus alignments, including all accessions concatenated into one supermatrix.
File: concatenated_without_paralogs_trimmed.fasta
Description: Concatenated dataset of the locus alignments excluding putatively paralogous loci and loci with >50% missing data or missing taxa.
Code/software
Aliview or any text editor can be used to view these FASTA files.
Access information
Other publicly accessible locations of the data:
- Raw data (raw reads) is available from ENA: ebi.ac.uk/ena, project PRJEB108520
Data was derived from the following sources:
- Raw data of 12 accessions of Zygia and 28 accessions of other mimosoid legumes was downloaded from ENA projects PRJEB8722 and PRJEB52227 and included in these datasets.