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      Polyploidization was not involved in the origin of five endemic species from southern Europe but is otherwise frequent in Euphorbia section Esula (Euphorbiaceae)

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      Botanical Journal of the Linnean Society
      Oxford University Press (OUP)

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          Abstract

          Polyploidization is a key factor in the diversification of flowering plants, but appears to be of only minor importance in the evolution of Euphorbia subgenus Esula. An exception is Euphorbia section Esula, including c. 100 species, many of which are widespread, but several have restricted distribution areas. We used ITS sequencing and relative genome size estimation to explore the evolutionary origin of E. gayi, E. graminifolia, E. tommasiniana, E. valliniana and E. variabilis, which are endemic to disjunct areas along the southern and western margins of the Alps, Corsica and Sardinia. In addition, we explored the incidence of polyploidy across different lineages of E. section Esula. Our phylogenetic results revealed several lineages with unresolved relationships that probably diverged in the Late Miocene, but only one (the Eurasian Group) underwent considerable diversification, probably due to numerous polyploidization events. Several polyploid species or mixed ploidy species in this group are distributed across large areas of Eurasia. All other lineages remained mostly diploid and species-poor, but dispersed to various continents, where most of the species have restricted distribution areas. The five focal species are diploid, but they do not share a common ancestor. Euphorbia graminifolia and E. tommasiniana belong to the Eurasian Group, whereas E. gayi, E. valliniana and E. variabilis belong to the Cosmopolitan Group and are thus not closely related to other European members of the section. Phylogenetic analyses recovered E. valliniana and E. variabilis as genetically distinct, although closely related. This, in combination with a clear morphological differentiation as revealed by morphometric analyses, supports their recognition as independent species. Our study highlights the important role polyploidization had for plant diversification as well as the effects of other factors such as vicariance in disjunct refugia, which probably led to the origin of the five endemic species from Euphorbia section Esula.

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          Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

          Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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            MRBAYES: Bayesian inference of phylogenetic trees.

            The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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              Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

              Abstract The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.
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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                Botanical Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4074
                1095-8339
                March 01 2023
                February 24 2023
                January 06 2023
                March 01 2023
                February 24 2023
                January 06 2023
                : 201
                : 3
                : 260-285
                Article
                10.1093/botlinnean/boac040
                5f28b247-1f42-495b-a681-a0d6720234cf
                © 2023

                https://academic.oup.com/pages/standard-publication-reuse-rights

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