DOI: 10.5061/dryad.1rn8pk14k
title: Data from: Phylogenomic and ecological systematics of Melocactus (Cactaceae)

description: 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.
description: 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.
description: # Data from: Phylogenomic and ecological systematics of Melocactus
 (Cactaceae)
 [https://doi.org/10.5061/dryad.1rn8pk14k](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](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.