DOI: 10.5061/dryad.866t1g1v6
title: A range-wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence

description: Aim: Knowing a species’ response to historical climate shifts
 helps understanding its perspectives under global warming. We
 infer the hitherto unresolved postglacial history of Pinus
 cembra. Using independent evidence from genetic structure and
 demographic inference of extant populations, and from palaeoecological
 findings, we derive putative refugia and re-colonisation routes.
 Location: European Alps and Carpathians. Taxa: Pinus
 cembra. Methods: We genotyped nuclear and chloroplast
 microsatellite markers in nearly 3,000 individuals from 147 locations
 across the entire natural range of P. cembra. Spatial genetic
 structure (Bayesian modelling) and demographic history (Approximate
 Bayesian Computation) were combined with palaeobotanical records (pollen,
 macrofossils) to infer putative refugial areas during the Last Glacial
 Maximum (LGM) and re-colonisation of the current range.
 Results: We found distinct spatial genetic structure, despite low
 genetic differentiation even between the two disjunct mountain ranges.
 Nuclear markers revealed five genetic clusters aligned East–West across
 the range, while chloroplast haplotype distribution suggested nine
 clusters. Spatially congruent separation at both marker types highlighted
 two main genetic lineages in the East and West of the range. Demographic
 inference supported early separation of these lineages dating back to a
 previous interstadial or interglacial c. 210,000 years
 ago. Differentiation into five biologically meaningful genetic clusters
 likely established during post-glacial re-colonisation. Main
 conclusions: Combining genetic and palaeoecological evidence
 suggests that P. cembra primarily survived the LGM in
 “cold period” refugia south of the Central European Alps and near the
 Carpathians, from where it expanded during the Late Glacial into its
 current Holocene “warm period” refugia. This colonisation history has led
 to the distinct East–West structure of five genetic clusters. The two main
 genetic lineages likely derived from ancient divergence during an
 interglacial or interstadial. The respective contact zone (Brenner line)
 matches a main biogeographic break in the European Alps also found in
 herbaceous alpine plant species.
description: All methodological approaches are described in the associated
 paper (Gugerli et al., Journal of Biogeography 2023).
description: Genotype file with individual genotypes from 11 nuclear
 microsatellites (2 lines per individual), prepared for input in the
 clustering software STRUCTURE (Pritchard et al., Genetics 2000), available
 at
 https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html: Gugerli_etal_JoB2023_nSSRs_STRUCTURE.csv Gugerli_etal_JoB2023_nSSRs_GenePop.csv   Three files with data from 4 chloroplast microsatellites, formatted for input in the clustering software BAPS (Corander et al., Genetics 2003), currently under development as an R package at https://github.com/ocbe-uio/rBAPS: Gugerli_etal_JoB2023_cpSSRs-BAPS_Pop_PopGroupsUnlinkedLoci.csv Gugerli_etal_JoB2023_cpSSRs-BAPS_Pop_names.csv Gugerli_etal_JoB2023_cpSSRs-BAPS_Pop_indices.csv   Populations file with information on sampling sites (population codes, mountain range, country, population name, geographic coordinates in WGS84 format) and sample numbers. Gugerli_etal_JoB2023_PopulationSampling.csv