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      A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae)

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          Abstract

          Silene ciliata Pourr. (Caryophyllaceae) is a species with a highly disjunct distribution which inhabits the alpine mountains of the Mediterranean Basin. We investigated the phylogeny and phylogeography of the species to (a) clarify the long-suggested division of S. ciliata into two subspecies, (b) evaluate its phylogenetic origin and (c) assess whether the species’ diversification patterns were affected by the Mediterranean relief. For this purpose, we collected DNA from 25 populations of the species that inhabit the mountains of Portugal, Spain, France, Italy, former Yugoslav Republic of Macedonia, Bulgaria and Greece and studied the plastid regions rbcL, rps16 and trnL. Major intraspecific variation was supported by all analyses, while the possibility of the existence of more varieties or subspecies was not favoured. Plastid DNA (cpDNA) evidence was in accordance with the division of S. ciliata into the two subspecies, one spreading west (Iberian Peninsula and Central Massif) and the other east of the Alps region (Italian and Balkan Peninsula). This study proposes that the species’ geographically disconnected distribution has probably derived from vicariance processes and from the Alps acting as a barrier to the species’ dispersal. The monophyletic origin of the species is highly supported. cpDNA patterns were shown independent of the chromosome evolution in the populations and could have resulted from a combination of geographic factors providing links and barriers, climatic adversities and evolutionary processes that took place during Quaternary glaciations.

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          Positional effect of single bulge nucleotide on PNA(peptide nucleic acid)/DNA hybrid stability

          We report positional effect of bulge nucleotide on PNA/DNA hybrid stability. CD spectra showed that PNA/DNA hybrids required at least seven base pairings at a stem region to form a bulged structure. On the other hand, DNA/DNA could form bulged structure when there are only four base pairings adjacent to the bulge nucleotide. We discuss why PNA requests such a many base pairings to form bulged structure from a nearest neighbor standpoint.
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            Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

            Background During the most recent decade many Bayesian statistical models and software for answering questions related to the genetic structure underlying population samples have appeared in the scientific literature. Most of these methods utilize molecular markers for the inferences, while some are also capable of handling DNA sequence data. In a number of earlier works, we have introduced an array of statistical methods for population genetic inference that are implemented in the software BAPS. However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions. Results We discuss the necessity of enhancing the statistical approaches to face the challenges posed by the ever-increasing amounts of molecular data generated by scientists over a wide range of research areas and introduce an array of new statistical tools implemented in the most recent version of BAPS. With these methods it is possible, e.g., to fit genetic mixture models using user-specified numbers of clusters and to estimate levels of admixture under a genetic linkage model. Also, alleles representing a different ancestry compared to the average observed genomic positions can be tracked for the sampled individuals, and a priori specified hypotheses about genetic population structure can be directly compared using Bayes' theorem. In general, we have improved further the computational characteristics of the algorithms behind the methods implemented in BAPS facilitating the analyses of large and complex datasets. In particular, analysis of a single dataset can now be spread over multiple computers using a script interface to the software. Conclusion The Bayesian modelling methods introduced in this article represent an array of enhanced tools for learning the genetic structure of populations. Their implementations in the BAPS software are designed to meet the increasing need for analyzing large-scale population genetics data. The software is freely downloadable for Windows, Linux and Mac OS X systems at .
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              Glacial refugia influence plant diversity patterns in the Mediterranean Basin

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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Francisco, USA )
                2167-8359
                20 August 2015
                2015
                : 3
                : e1193
                Affiliations
                [1 ]Department of Biotechnology, Agricultural University of Athens , Athens, Greece
                [2 ]Area de Biodiversidad y Conservación, Universidad Rey Juan Carlos , Móstoles, Madrid, Spain
                Article
                1193
                10.7717/peerj.1193
                4548490
                db011a5e-202c-40ae-8110-1697d1fc7186
                © 2015 Kyrkou et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 11 March 2015
                : 26 July 2015
                Funding
                Funded by: AdAptA
                Award ID: CGL2012-33528
                Funded by: ERASMUS mobility grant
                This work was supported by the AdAptA project (CGL2012-33528) of the Spanish Ministry of Economy and Competitiveness and an ERASMUS mobility grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biogeography
                Evolutionary Studies
                Genetics
                Plant Science
                Taxonomy

                silene ciliata,mediterranean basin,cpdna markers,pleistocene glaciations,phylogeography,phylogeny,alpine plant,subspecies,silene genus

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