Ancient genetic bottleneck and Plio-Pleistocene climatic changes imprinted the phylobiogeography of European Black Pine populations

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

“…We sampled natural populations across the entire range of the species. We discuss why our results differ from, or concur with, the few previous molecular studies carried out at a similar scale on this species (Nikolić and Tucić 1983;Naydenov et al 2016Naydenov et al , 2017Rafii and Dodd 2007). We also considered how habitat suitability might have affected demography by correlating climate variables at different Pleistocene ages with genetic diversity estimates under the assumption that harsher climate conditions and thus declining habitat suitability would produce demographic contractions with observable signatures in the genetic data (Conord et al 2012).…”

“…Focusing on Western Europe, they were able to identify five barriers to gene flow including, similarly to ours, between the Alps and the Calabria-Corsica group and between France and Spain. Naydenov et al (2016Naydenov et al ( , 2017 identified three genetic groups from three different geographical areas that are not contradicting our own analysis: Western Mediterranean, Balkan Peninsula and Eastern Mediterranean. However, they estimated their most recent common ancestor to be older than 10 million years and dated the most recent splits between groups in the Late Pliocene.…”

“…This low mutation rate, identical for both length polymorphism and sequence variation in cpDNA, could be one of the reasons why our results are so different. Also, our ancestral effective population size is 30 times lower than that of Naydenov et al (2016Naydenov et al ( , 2017. Finally, as our study uses a suite of different molecular markers and because an old Pliocene divergence time would certainly have left a mutational signature in organelle DNA genes, we are confident that Late Pleistocene or Holocene demographic events are the most likely explanations for the genetic patterns we observed.…”

“…The population genetic pattern of the Pinus nigra biogeographical islands of today (particularly at the southern and western edges of the species) should thus be the result of relatively recent fragmentation. However, widely contradicting divergence timings have been proposed for explaining the genetic diversity and structure of the European black pine, from very recent Holocene or Quaternary divergence (Rafii and Dodd 2007) to pre-Pleistocene divergence (Naydenov et al 2016(Naydenov et al , 2017.…”

Speciation and historical migration pattern interaction: examples from P. nigra and P. sylvestris phylogeography

“…This result is supported by not only our result here but also the simple deduction that the molecular markers have very different molecular masses, i.e., signi cant differences in base pairs (bps), and that the mutation frequency for large DNA fragments is very low and requires more generations for population structure establishment and xation, i.e., a relaxed molecular clock. For example, here, the mutation rate (µ) for NAD7-intron1 size variants was calculated to be approximately 3.6 x10 − 6 per generation (i.e., 3.5-3.7 x10 − 6 per generation at a 5% SE); in comparison, the average mutation rate (µ) for P. nigra from seven chloroplast DNA microsatellites (SSRs) with 13 regions of sequencing variation from our previous publications, Naydenov et al (2016Naydenov et al ( , 2017, was 5.6 x10 − 5 (i.e., 5.4-5.8 x10 − 5 ) per generation at a 5% SE. Comparing the mutation rates, the difference occurred based on two factors: different fragment sizes and different organelle origins (i.e., chloroplast vs. mitochondrion).…”