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      Long neglected diversity in the Accursed Mountains (western Balkan Peninsula): Ranunculus bertisceus is a genetically and morphologically divergent new species

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          Abstract

          Southern European mountain ranges have long been recognized as important hotspots of genetic diversity and areas of high endemism. Reflecting the geographical complexity of these mountain ranges, many European high-mountain species exhibit disjunctions on a variety of geographical scales. One of the long-neglected, poorly investigated and unresolved taxonomic problems concerns Apennine and Balkan members of Ranunculus section Leucoranunculus. According to the most recent taxonomic treatment, this section includes Ranunculus crenatus, distributed predominantly in siliceous massifs of the Carpathians and the Balkan Peninsula, but with a highly disjunct partial distribution area in the eastern Alps, and Ranunculus magellensis, which is usually considered a calcicolous endemic of the central Apennines. However, R. magellensis has also been suggested to occur in the carbonate ranges of the Albanian Alps, which would render this species amphi-Adriatic. We used complementary molecular methods (sequences of the nuclear ribosomal ITS region and of plastid DNA and amplified fragment length polymorphisms), relative genome size measurements and morphometric analyses to elucidate the relationships in Ranunculus section Leucoranunculus. Specifically, we asked if it comprises only a single, widespread and morphologically variable species or several narrowly distributed species with constant morphology. The results of our study showed that populations growing on limestone in the Albanian Alps in northern Albania and southern Montenegro are divergent and should be recognized as a new species, Ranunculus bertisceus Kuzmanović, D.Lakušić, Frajman & Schönsw., sp. nov. These populations differ not only from R. crenatus s.s., which grows on silicates, but also from the calcicolous Apennine endemic R. magellensis. The eastern Alpine populations of R. crenatus, which occur very locally in the Niedere Tauern area, originate from immigration from the Bosnian mountains.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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            ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

            After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.
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              Bayesian Phylogenetics with BEAUti and the BEAST 1.7

              Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
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                Author and article information

                Contributors
                (View ORCID Profile)
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                Journal
                Botanical Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4074
                1095-8339
                July 01 2021
                June 21 2021
                March 23 2021
                July 01 2021
                June 21 2021
                March 23 2021
                : 196
                : 3
                : 384-406
                Affiliations
                [1 ]Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Takovska 43, Belgrade, Serbia
                [2 ]Department of Botany, University of Innsbruck, Sternwartestraße 15, Innsbruck, Austria
                [3 ]School of Biosciences and Veterinary Medicine, University of Camerino, San Colombo - Via Prov., Km 4.2, Barisciano, L’Aquila, Italy
                Article
                10.1093/botlinnean/boab001
                08ef2b50-69cd-4d68-8553-51f43e6d2f10
                © 2021

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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