A new species, a new combination, and a new record of Crossotarsus Chapuis, 1865 (Coleoptera, Curculionidae, Platypodinae) from China

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Abstract

This study describes a new species, Crossotarsus beaveri Lai & Wang, sp. nov., designates a new combination, C. brevis (Browne, 1975, comb. nov. from Platypus Herbst, 1793), and notes a new record, C. emorsus Beeson, 1937, from China. Genetic data from four genes indicate that the new species and C. brevis form a clade clustered with other Crossotarsus species. Molecular phylogeny and morphological characters support their taxonomic placement.

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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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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

Robert Lanfear, Paul Frandsen, April M Wright … (2017)

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

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Author and article information

Contributors

You Li: (View ORCID Profile)

Journal

Title: ZooKeys

Abbreviated Title: ZK

Publisher: Pensoft Publishers

ISSN (Electronic): 1313-2970

ISSN (Print): 1313-2989

Publication date Created: April 06 2021

Publication date (Electronic): April 06 2021

Volume: 1028

Pages: 69-83

Article

DOI: 10.3897/zookeys.1028.61018

SO-VID: f53b9d40-c963-4a8d-bb84-286e3cc59bde

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http://creativecommons.org/licenses/by/4.0/

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A new species, a new combination, and a new record of Crossotarsus Chapuis, 1865 (Coleoptera, Curculionidae, Platypodinae) from China

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Abstract

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Pensoft Biodiversity

Most cited references 38

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

ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

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