<i>Chrysosplenium sangzhiense </i> (Saxifragaceae), a new species from Hunan, China

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Abstract

Chrysosplenium sangzhiense Hong Liu, a new species from Hunan, China, is described and illustrated. The phylogenetic analysis revealed that the new species belongs to subgen. Chrysosplenium and is closely related to C. grayanum , C. nepalense and C. sinicum . The chromosome number of the new species is 2n = 46, indicating a novel basic number x = 23 in Chrysosplenium that is different from other species. This also suggests that C. sangzhiense is probably an allopolyploid derivative of a species with x = 11 and one with x = 12. Morphologically, C. sangzhiense can be easily distinguished from C. grayanum , C. nepalense , C. sinicum and C. cavaleriei , a species not included in our phylogenetic analysis by a suite of characters relating to the sterile shoots, basal leaves, cauline leaves, flowering stem, sepals, disc, capsule and seed. A global conservation assessment is performed, and classifies C. sangzhiense as Least Concern (LC).

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Most cited references 25

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.

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

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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ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

Subha Kalyaanamoorthy, Bui Minh, Thomas Wong … (2017)

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.

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Hong Liu

Journal

Journal ID (nlm-ta): PhytoKeys

Journal ID (iso-abbrev): PhytoKeys

Journal ID (publisher-id): 3

Journal ID (index): urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD

Title: PhytoKeys

Publisher: Pensoft Publishers

ISSN (Print): 1314-2011

ISSN (Electronic): 1314-2003

Publication date Collection: 2021

Publication date (Electronic): 16 April 2021

Volume: 176

Pages: 21-32

Affiliations

[1 ] Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China Guangxi Institute of Botany, Chinese Academy of Sciences Guilin China

[2 ] College of Life Sciences & Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of Hubei Province, South-Central University for Nationalities, Wuhan 430074, Hubei Province, China South-Central University for Nationalities Wuhan China

Author notes

Corresponding author: Hong Liu ( liuhong@ 123456scuec.edu.cn )

Academic editor: A. Freire-Fierro

Author information

Long-Fei Fu https://orcid.org/0000-0001-8708-4718

Fang Wen https://orcid.org/0000-0002-3889-8835

Article

Publisher ID: 62802

DOI: 10.3897/phytokeys.176.62802

PMC ID: 8065015

PubMed ID: 33958936

SO-VID: 4a0745e5-fcc5-4491-8732-996fd1b1283d

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This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Chrysosplenium sangzhiense (Saxifragaceae), a new species from Hunan, China

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Pensoft Biodiversity

Most cited references 25

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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

ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

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