DOI: 10.5061/dryad.vdncjsz5w
title: Spatial discontinuity of mountain systems and genetic structure of alpine plants: the Alps-Carpathians disjunction in a comparative phylogeographical context

description: Aim In mountain areas, geographical isolation and history of mountain
 systems are believed to be among the most important factors which
 determine population distribution and connectivity. In this study we
 address the importance of discontinuity among mountain systems for
 intraspecific genetic structure by investigating whether the geographical
 disjunction between the Alps and the Carpathians (and the related habitat
 gap) is the primary factor that shapes the genetic structure of the
 high-mountain plant populations. We compare the large-scale genetic
 structure of alpine plants from these two parts of the European Alpine
 System concerning the location of the main genetic split in the studied
 species, large-scale patterns of phylogeographical lineages and potential
 factors influencing their distribution. Location The Alps and the
 Carpathians Taxon 22 alpine/subalpine vascular plant species Methods We
 performed Bayesian population structure analysis on genome-wide genotyping
 (AFLP) data and reconstructed relationships between individuals and
 populations using the PCoA and Neighbour Joining. We also performed AMOVA
 to estimate the contribution of genetic variation among regions. Based on
 these analyses, we examined the location of primary and lower-level
 phylogeographical breaks. Results A clear primary genetic split between
 the Alps and the Carpathians was observed in three species (14% of studied
 species). In seventeen species (77%) we identified other genetic patterns
 or, in some cases, we did not observe any geographical pattern (two
 species, 9%). We found no specific pattern of biological traits that are
 correlated with genetic split between the Alps and the Carpathians.
 Conclusions The geographical gap between the Alps and the Carpathians is
 not a primary factor in shaping the genetic structure of the regional
 high-mountain flora as it aligns with a first-rank phylogeographic break
 in a minority of species. The genetic division between the Alps and the
 Carpathians appears mostly at higher K values, showing that internal
 complexity of these large mountain systems plays a no less important role.
 Several patterns of large-scale distribution of intraspecific lineages
 were detected, including connections between the Carpathians and the
 nearest Eastern Alps but also historical links of the Carpathians with
 Southern and Western Alps through latitudinally extended genetic groups.
description: Structure datasets based on AFLP markers from https://doi.org/10.5061/dryad.s4q6s with only the species occurring in the Alps and the Carpathians. Datasets for both mountain ranges were merged. In the case of two species (Gypsophila repens and Oreojuncus trifidus), we removed a few outlier individuals (4 and 14 individuals, respectively) based on PCoA, as they likely resulted from genotyping errors. Original dataset: Taberlet, Pierre; Zimmermann, Niklaus E.; Englisch, Thorsten et al. (2023). Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities [Dataset]. Dryad. https://doi.org/10.5061/dryad.s4q6s  
description: # Spatial discontinuity of mountain systems and genetic structure of
 alpine plants: the Alps-Carpathians disjunction in a comparative
 phylogeographical context
 [https://doi.org/10.5061/dryad.vdncjsz5w](https://doi.org/10.5061/dryad.vdncjsz5w) ## Description of the data and file structure Structure datasets based on AFLP markers from [https://doi.org/10.5061/dryad.s4q6s.](https://doi.org/10.5061/dryad.s4q6s) Only species occurring in the Alps and the Carpathians were retained. The original dataset contained separate structure files for both mountain ranges, thus the files were merged. In the case of two species (Gypsophila repens and Oreojuncus trifidus), we removed a few outlier individuals (4 and 14 individuals, respectively) based on PCoA, as they likely resulted from genotyping errors. ## Files The resulting dataset consists of the following files: * Arabis_alpina.str * Campanula_alpina.str * Carex_firma.str * Carex_sempervirens.str * Cerastium_uniflorum.str * Dryas_octopetala.str * Festuca_versicolor.str * Gentiana_nivalis.str * Geum_montanum.str * Geum_reptans.str * Gypsophila_repens.str * Hedysarum_hedysaroides.str * Hornungia_alpina.str * Hypochaeris_uniflora.str * Kalmia_procumbens.str * Luzula_alpinopilosa.str * Micranthes_stellaris.str * Neogaya_simplex.str * Oreojuncus_trifidus.str * Primula_minima.str * Ranunculus_alpestris.str * Soldanella_pusilla.str The file name denotes the species name. Files contain AFLP data (1/0 matrices) for each species. The first row consists of L integers (0) to indicate the recessive allele at each of the L loci in the data set. The data for each individual is stored as 2 consecutive rows, first column contains the name of the individual, second the number of the population, columns from 3 onwards contain data for each locus (one per column). Missing data is coded by -9. Original dataset: Taberlet, Pierre; Zimmermann, Niklaus E.; Englisch, Thorsten et al. (2023). Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities [Dataset]. Dryad. [https://doi.org/10.5061/dryad.s4q6s](https://doi.org/10.5061/dryad.s4q6s) The work has been published as: Janiczek, A., Suchan, T., Paul, W., IntraBioDiv Consortium and Ronikier, M. (2025), Spatial Discontinuity of Mountain Systems and Genetic Structure of Alpine Plants: The Alps–Carpathians Disjunction in a Comparative Phylogeographical Context. J Biogeogr, 52: e15122. [https://doi.org/10.1111/jbi.15122](https://doi.org/10.1111/jbi.15122)