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

PremiseGlobally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula, in western North America, exhibit strong genetic structure and highly concordant divergent lineages across their ranges, as they were isolated during the Pleistocene glacial-interglacial cycles and thus accumulated genetic differentiation in their genomes. A representative plant genus of this Peninsula is Yucca, with Yucca valida having the widest range. Whereas Y. valida is a dominant species, there is an extensive distribution discontinuity between 26{degrees} N and 27{degrees} N, where no individuals have been identified, suggesting restricted gene flow. Moreover, the historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. MethodsWe examined the phylogeography of Y. valida throughout its range to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the species age. Key resultsWe assembled 4,411 SNPs from 147 plants, identifying three allopatric lineages. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age under one million years for the common ancestor of Y. valida and its sister species. ConclusionsHabitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.