Data from: Phylogenomic and ecological systematics of Melocactus (Cactaceae)
Data files
Jan 08, 2025 version files 91.39 MB
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melodat_30loci_partitions.txt
48.65 KB
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Melodat20_plastidC_partition.txt
3.95 KB
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Melodat20_plastidC_supercontig.fasta
2.42 MB
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melodat30_supercontig.fasta
42.23 MB
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Melosiste-locisupercontig_partition.txt
37.40 KB
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Melosistem-locisupercontig.fasta
44.89 MB
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Melosistem-up-to30miss_genetrees.txt
1.76 MB
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README.md
4.02 KB
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Table_S2-Assigned_substrates_melocactus_r1.csv
1.04 KB
Abstract
Melocactus (L.) Link & Otto (Cactaceae) is a widely distributed genus in the Neotropical region and has fascinated the botanical community since the 15th century due to its unique appearance. Even though this genus has been studied for centuries, its diversification, phylogenetic relationships, and species delimitation have not been evaluated using comprehensive taxon sampling and genetic data. Here, we inferred maximum likelihood and coalescent phylogenies using the Cactaceae591 genomic dataset and investigated potential environmental variables associated with Melocactus diversification. Ancestral character reconstructions were performed using edaphic and climatic data. A well-resolved Melocactus phylogeny was estimated, allowing the redefinition of informal infrageneric groups and the taxonomic rearrangement of some taxa. The ancestral character reconstructions suggest that the observed species relationships and distribution patterns in Melocactus result from the interplay of climatic and edaphic factors, highlighting a complex evolutionary history for the genus.
README: Data from: Phylogenomic and ecological systematics of Melocactus (Cactaceae)
https://doi.org/10.5061/dryad.1rn8pk14k
Description of the data and file structure
Datasets Associated with this Manuscript
DOI: https://doi.org/10.5061/dryad.1rn8pk14k
Description of the Data and File Structure
This dataset provides alignments and related files derived from the genomic analysis of Melocactus species. DNA was extracted from cactus root tissue using a 3% CTAB extraction protocol. Genomic data were generated using a target sequencing capture approach with the Cactaceae591 probe set. The raw sequencing reads were processed using fastp v.0.23.3 for quality filtering and trimming. Loci assembly was conducted with the HybPiper pipeline, enabling efficient processing of target-enriched sequence data.
Further processing of the aligned sequences included multiple alignments with MAFFT v.7.520, trimming with TrimAL v.1.4, and refining with Spruceup to improve alignment quality and remove potential errors.
The files are structured to include supermatrices, partitions, gene trees, and metadata, supporting phylogenomic and ecological analyses. The manuscript associated with this dataset provides detailed descriptions of all methods and parameters used in the data processing.
Files and variables
Supermatrices and Partition Files
File: Melosiste-locisupercontig_partition.txt
- Description: Partition file for the Melosistem-locisupercontig supermatrix (concatenated loci).
File: melodat_30loci_partitions.txt
- Description: Partition file to the melodat_30loci supermatrix (concatenated loci).
File: Melodat20_plastidC_partition.txt
- Description: Partition file for the supermatrix of plastid loci.
Files and variables
Sequence Alignments
File: Melosistem-locisupercontig.fasta
- Description: Multiple sequence alignment supermatrix (concatenated loci) of nuclear data, including up to 30% missing data (missing loci per individual).
File: melodat30_supercontig.fasta
- Description: Multiple sequence alignment supermatrix (concatenated loci) of nuclear data, including up to 30% missing data (missing loci per individual).
File: Melodat20_plastidC_supercontig.fasta
- Description: Multiple sequence alignment supermatrix (concatenated loci) of plastidial data, including up to 20% missing data (missing loci per individual).
Gene Trees and Metadata
File: Melosistem-up-to30miss_genetrees.txt
- Description: Gene trees estimated using IQ-TREE with ModelFinderPlus. These were used as input for coalescent inference performed with wASTRAL.
File: Table_S2-Assigned_substrates_melocactus_r1.csv
- Description: Dataset listing each Melocactus species included in the study and its primary substrate type. Substrate data were obtained from a literature review.
Variables in Metadata
Species
- M. violaceus violaceus, M. violaceus ritteri, M. violaceus margaritaceus, M. glaucescens, M. depressus, M. azureus, M. pachyacanthus pachyacanthus, M. levitestatus, M. ferreophilus, M. neoviridenscens, M. sergipensis, M. zehntneri, M. salvadorensis, M. concinnus, M. broadwayi, M. estevesii, M. mazelianus, M. caroli-linnaei, M. intortus, M. macracanthos, M. harlowii, M. paucispinus, M. deinacanthus, M. ernestii, M. longicarpus, M. amethystinus, M. inconcinnus, M. bahiensis, M. conoideus, M. braunii, M. oreas oreas, M. oreas cremnophilus, M. brederooianus, M. schatzlii, M. matanzanus.
Substrate Categories
- Granitic, limestone, quartz, mixed rocky, sand, sandstone, serpentine.
Access information
This dataset is publicly accessible through Dryad and derived from multiple sources. The associated manuscript provides further details on data acquisition, processing, and analysis.
Methods
Alignments provided here are derived from the following methods: DNA was obtained from cactus root tissue using a CTAB 3% extraction protocol, and genomic data were obtained through a target sequencing capture method using the Cactaceae591 probe set. Raw reads were processed using the fastp v.0.23.3, and loci assembly was carried out using the Hybpiper pipeline. After, the data were processed using MAFFT v.7.520, TrimAL v.1.4, and spruceup. Parameters and detailed information are described in the manuscript.