Evolutionary history of an Irano-Turanian cushion-forming legume ( <i>Onobrychis cornuta</i>)

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Abstract

The Irano-Turanian region is one of the largest floristic regions in the world and harbors a high percentage of endemics, including cushion-like and dwarf-shrubby taxa. Onobrychis cornuta is an important cushion-forming element of the subalpine/alpine flora of the Irano-Turanian floristic region. To specify the genetic diversity among the populations of this species (including individuals of O. elymaitica), we employed nrDNA ITS and two noncoding regions of plastid DNA ( rpl32- trnL _(UAG) and trnT _(UGU)- trnL _(UAA)). The most striking feature of O. cornuta assemblages was the unexpectedly high nucleotide diversity in both the nDNA and cpDNA dataset. In the analyses of nuclear and plastid regions, 25 ribotypes and 42 haplotypes were found among 77 and 59 accessions, respectively, from Iran, Turkey, and Afghanistan. Network analysis of the datasets demonstrated geographic differentiation within the species. Phylogenetic analyses of all dataset retrieved O. cornuta as a non-monophyletic species due to the inclusion of O. elymaitica, comprising four distinct lineages. In addition, our analyses showed cytonuclear discordance between both nuclear and plastid topologies regarding the position of some O. cornuta individuals. The underlying causes of this inconsistency remain unclear. However, we speculate that chloroplast capture, incomplete lineage sorting, and introgression were the main reasons for this event. Furthermore, molecular dating analysis indicated that O. cornuta originated in the early Pliocene (around 4.8 Mya) and started to diversify throughout the Pliocene and in particular the Pleistocene. Moreover, O. elymaitica was reduced to a subspecific rank within the species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12870-024-04895-y.

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Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

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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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut, Alexei J. Drummond, Dong Xie … (2018)

Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.

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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh, John Rozewicki, Kazunori Yamada (2017)

Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

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Author and article information

Contributors

Shahrokh Kazempour-Osaloo: skosaloo@modares.ac.ir

Journal

Journal ID (nlm-ta): BMC Plant Biol

Journal ID (iso-abbrev): BMC Plant Biol

Title: BMC Plant Biology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2229

Publication date (Electronic): 20 March 2024

Publication date PMC-release: 20 March 2024

Publication date Collection: 2024

Volume: 24

Electronic Location Identifier: 204

Affiliations

[1 ]Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, ( https://ror.org/03mwgfy56) Tehran, Iran 14115-154

[2 ]Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), ( https://ror.org/05d627n32) P.O. Box 13185-116, Tehran, Iran

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Publisher ID: 4895

DOI: 10.1186/s12870-024-04895-y

PMC ID: 10953250

PubMed ID: 38509474

SO-VID: d45efb88-a5b5-4bd2-9703-866df0b1e76c

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 21 October 2023

Date accepted : 10 March 2024

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ScienceOpen disciplines: Plant science & Botany

Keywords: onobrychis cornuta,o. elymaitica,haplotype diversity,irano-turanian,legume

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ScienceOpen disciplines: Plant science & Botany

Keywords: onobrychis cornuta, o. elymaitica, haplotype diversity, irano-turanian, legume

Evolutionary history of an Irano-Turanian cushion-forming legume ( Onobrychis cornuta)

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Plant MYBs

Most cited references 76

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

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

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