Data from: Deep phylogenomic structure and microendemism in Baja California Ammotrechidae (Arachnida: Solifugae) reveal a mosaic of diversification
Data files
Sep 07, 2026 version files 473.72 KB
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Graham_et_al_Ammotrechid.zip
471.79 KB
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README.md
1.93 KB
Abstract
This phylogeographic study of ammotrechid camel spiders in Baja California Sur reveals extensive cryptic diversity and deep evolutionary structure across the peninsula. By integrating mitochondrial and RADseq data, the authors identified sixteen distinct lineages, most of which are highly localized. The research highlights camel spiders as sensitive indicators of landscape history and ideal models for geogenomic studies in desert biogeography.
Dataset DOI: 10.5061/dryad.6djh9w1gx
Description of the data and file structure
This dataset contains genomic restriction site-associated DNA sequencing (3RAD) data and mitochondrial sequences used to evaluate phylogenomic structure, lineage diversification, and microendemism within camel spiders (Arachnida: Solifugae: Ammotrechidae) across the Baja California peninsula.
Files and variables
All data files are archived together in the primary archive: File: Graham_et_al_Ammotrechid.zip
1. Variant and Alignment Datasets
- File Name: AMMO.snps
- File Format: Plain text (fasta format). ipyrad output
- Description: Concatenated matrix containing all identified single-nucleotide polymorphisms (SNPs) across Ammotrechidae samples generated from the ipyrad pipeline (clustering threshold = 0.95).
- File Name: AMMO_N28_MIN7_usnps_TRIM.fasta
- File Format: FASTA format (plain text).
- Description: Unlinked SNP alignment matrix (trimmed) containing one randomly sampled SNP per 3RAD locus to mitigate the effects of linkage disequilibrium in downstream population genomic and coalescent analyses.
- File Name: AMMO_COI_TRIM.fasta
- File Format: FASTA format (plain text).
- Description: Multiple sequence alignment (trimmed) of the mitochondrial Cytochrome c Oxidase Subunit I (COI) gene for all sequenced individuals, used for comparative phylogeographic and mitochondrial divergence analyses.
2. Summary and Tabular Data
- File Name: AMMO_stats.txt
- File Format: plain text (ipyrad output)
- Description: Summary metrics for each individual sequenced, detailing raw sequencing yield, filtering steps, and locus recovery from ipyrad.
Camel spiders were collected from ten localities across Baja California Sur and one locality in Baja California using light pitfall trap arrays. DNA extractions and prepared libraries for dual-indexed sequencing using the 3RAD protocol. Libraries were sequenced (2 × 150 paired-end) with Illumina HiSeq X. Raw reads were assembled using iPyrad (Eaton and Overcast 2020) with default parameters (cluster threshold = 0.95). The resulting matrix was filtered to generate SNP-only and unlinked SNP-only datasets. Phylogenetic relationships were inferred using Maximum likelihood using IQ-TREE 2 (Minh et al. 2020), with appropriate substitution models selected by ModelFinder (Kalyaanamoorthy et al. 2017) and nodal support assessed using 1,000 ultrafast bootstrap replicates (Hoang et al.,2018). We generated a dated topology using BEAST v1.10.4 (Drummond et al. 2012).