The Namaini, a new weevil tribe with six new genera from South Africa (Coleoptera: Curculionidae: Entiminae)

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Abstract

Based on a phylogenetic analysis of a large number of mainly undescribed edaphic Entiminae from South Africa, a new tribe of entimine weevils is described, which includes six new genera. Taxa included in Namaini trib. nov. are clustered into seven clades that are used to delimit the following genera: Nama, type genus of the tribe, plus the new genera Cederbergia gen. nov., Cervellaea gen. nov., Namaquania gen. nov., Pentamerica gen. nov., Springbokia gen. nov. and Yamalaka gen. nov. A key to the genera is given and four new species are described.

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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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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)

We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.

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Bayes Factors

Robert E. Kass, Adrian E. Raftery (1995)

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Author and article information

Journal

Title: Zoological Journal of the Linnean Society

Publisher: Oxford University Press (OUP)

ISSN (Print): 0024-4082

ISSN (Electronic): 1096-3642

Publication date Created: January 06 2021

Publication date (Electronic): January 06 2021

Affiliations

[1 ]Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina, Torino, Italy

[2 ]Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Department of Forest Protection and Entomology, Kamýcká, Praha 6-Suchdol, Czech Republic

[3 ]Institute for Plant Protection and Environment, Banatska, Zemun, Serbia

[4 ]Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini, Grugliasco (TO), Italy