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DOI: 10.1101/2023.05.22.541794

Divergent lineages in a young species: the case of Datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula

J. A.Aleman M. C. Arteaga J. Gasca-Pineda R. Bello-Bedoy
Globally, barriers triggered by geological and climatic events have produced temporary and permanent environmental breaks, habitat fragmentation, and species divergence. Notably, diverse plant species from the Baja California Peninsula, in western North America, exhibit strong genetic structure and vicariant lineages along their range. A representative taxon of the Peninsula is the genus Yucca, with Yucca valida having the most extensive range. Although its presence is dominant, there is an extensive distribution discontinuity between 26{degrees} N and 27{degrees} N, where any populations have been identified, suggesting restricted gene flow among its populations; moreover, the potential distribution models indicate a substantial reduction in their range during the Last Interglacial. We examined the phylogeographic patterns of Y. valida across the species' range, expecting to find vicariant lineages. Using nextRAD sequencing, we recovered 4,411 SNPs on 147 plants from 20 locations, identifying three allopatric lineages. The simulation of historical scenarios supported the simultaneous divergence of these lineages. Finally, we retrieved whole-chloroplast-genome sequences and estimated an age below a million years old for the MRCA of Y. valida and its sister species, Y. capensis. Our results indicate that the origin of the nuclear lineages can be the consequence of habitat loss during historical climatic changes.