Deep Phylogenomic Structure and Microendemism in Baja California Ammotrechidae (Arachnida: Solifugae) Support a Model of Distributed Diversification

Abstract

Aim To assess phylogeographic structure, phylogenetic diversity and historical diversification processes in ammotrechid camel spiders from the Baja California Peninsula. Location Baja California Sur, Mexico. Time Period Miocene to Pleistocene. Major Taxa Studied Ammotrechid camel spiders (Solifugae: Ammotrechidae). Methods We conducted the first phylogeographic analysis of Baja California Sur ammotrechid camel spiders using mitochondrial COI sequences and genome‐wide RADseq data. Phylogenomic analyses, divergence dating, species accumulation curves and tests of admixture (F 3 statistics) were used to evaluate lineage structure, timing of diversification and patterns of connectivity. Results We uncovered deep phylogenomic structure and extensive cryptic diversity, identifying at least 16 putative lineages, many restricted to single localities. Divergence dating indicates Miocene origins with subsequent Plio–Pleistocene diversification. Although several lineages exhibit north–south structure, divergence times and spatial patterns do not support diversification driven by discrete transpeninsular seaway vicariance at major southern breaks (e.g., La Paz/Loreto). Instead, patterns support a model of distributed diversification shaped by tectonic segmentation, habitat heterogeneity, and climatic oscillation. Limited admixture among a subset of closely related lineages, suggested by incongruent tree topologies and F 3 statistics, indicates episodic secondary contact rather than long‐term connectivity. Species accumulation curves did not approach an asymptote, suggesting that much of the region's solifuge diversity remains undocumented. Main Conclusions Ammotrechid camel spiders preserve fine‐scale genomic signatures of landscape history in Baja California Sur and reveal previously undocumented levels of endemism and diversification. These results highlight Solifugae as promising but underused systems for geogenomic studies of desert biogeography.

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