Divergence within diversity in the endemic, long-lived conifer Pinus greggii from the Sierra Madre Oriental, Mexico

Background: Mexico’s physiography has been recognized as a driver of Pinus diversification. This study analyzes phylogeographical patterns of the two varieties of P. greggii to cast light on genomic differentiation in allopatry. Questions: What is the role of geographic barriers in the diversification and genomic differentiation of a highland conifer? Studied species: Pinus greggii Engelm. ex Parl. Study site and dates: Sierra Madre Oriental, Mexico, 2015-2017. Methods: We used 481 nuclear SNPs and 73 non-coding plastome regions to evaluate genetic diversity and structure. Population relationships and demography were estimated using maximum likelihood and coalescent methods under an isolation with migration model and interpreted considering ecological niche modeling under present, Last Glacial Maximum and Last Interglacial conditions. Results: Admixture analyses based on nuclear data show that there are two region-specific clusters and one shared cluster, and that 47 % of SNPs are shared between varieties. Our data support a fragmentation event at the onset of the Last Interglacial (126k-148k BP), resulting in a smaller effective population size in the south. Cryptic breaks, and ecological niche models agree with secondary contact during glacial periods. Divergence has been accompanied by population equilibrium as shown by non-significant Tajima’s D in plastome sequences. Conclusions: Our results support that lineage divergence in Pinus is accompanied by the accumulation of genome-wide differences, while gene flow produced asymmetrical patterns of allele sharing. Our study highlights the effectiveness of mountain-valley systems in isolating populations and points to the need to establish conservation measures for southern P. greggii populations.