On a taxonomic feature that has been overestimated in classification practice: an integrative taxonomic revision of Stephoblemmus Saussure, 1877 based on morphology and molecular phylogeny (Orthoptera: Grylloidea; Gryllidae; Gryllinae)

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Abstract

The hemispherical head is prevalent in Gryllinae crickets, so the rare crickets that have a unique form of head will be extremely unusual. In previous studies, this special feature can be one of the important features to distinguish and identify these crickets. But does this particular head shape truly reflect a clear-cut taxonomic relationship? The species of the genus Loxoblemmus have a typical truncate head; species of the genus Stephoblemmus have a more exaggerated truncate head, with the frontal end even extending into a lamellar. The genus Mitius is relatively unusual in that species of this genus have both globose or truncate heads. How are these species related? Does the cephalic shape perfectly reflect the natural classification of these species? Based on these questions, the study applied species definition and morphological classification to explore the intergeneric and intrageneric species relationships of the genera Mitius, Stephoblemmus, and Loxoblemmus, and derived the following main conclusions: (1) Mitius and Stephoblemmus are related and distinct from Loxoblemmus; (2) Mitius species bear two types of frons (truncated and rounded), but this feature disallows them to be classified as natural groups; (3) one genus synonym and three species synonyms are raised (Mitius Gorochov, 1985 syn. n., Mitius splendens (Shiraki, 1930) syn. n., Mitius eryuanensis Yuan, Xie & Liu, 2021 syn. n. and Mitius brevipennis Yuan, Ma & Gu, 2022 syn. n.), and seven new status combinations are proposed (Stephoblemmus blennus (Saussure, 1877) comb. n., Stephoblemmus castaneus (Chopard, 1937) comb. n., Stephoblemmus enatus Gorochov, 1994 comb. n., Stephoblemmus flavipes (Chopard, 1928) comb. n., Stephoblemmus minor (Shiraki, 1911) comb. n., Stephoblemmus minutulus (Yang & Yang, 1995) comb. n. and Stephoblemmus vaturu (Otte & Cowper, 2007) comb. n.). The studies indicated that frons shapes that appear to be significantly different might not always reflect the correct Gryllinae species relationships and a combination of more taxonomic features and taxonomic techniques is needed often to reveal the true taxonomic relationships.

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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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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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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.