Recent, Late Pleistocene fragmentation shaped the phylogeographic structure of the European black pine (Pinus nigra Arnold)

Fragmentation acting over geological times confers wide, biogeographical scale and genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a widespread forest tree, Pinus nigra Arnold, the European black pine, and to resolve its demographic history, we described and modelled its spatial genetic structure and gene genealogy. We then tested which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution. We used a set of different genetic markers, both neutral and potentially adaptive, and either bi-parentally or paternally only inherited, and we sampled natural populations across the entire species range. We analysed the data using both frequentist population genetic and Bayesian inference methods to calibrate realistic, demographic timed scenarios. We also considered how habitat suitability might have affected demography by correlating climate variables at different recent Pleistocene ages with genetic diversity estimates. Species with geographically fragmented distribution areas are expected to display significant among-population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure result from the Late Pleistocene or Early Holocene fragmentation of one ancestral population into six distinct genetic lineages. Gene flow among the different lineages is strong across forests and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five sub-species and name these six lineages using regionally accepted sub-species-level names.