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      Description of a new leaf litter toad of Leptobrachella (Anura, Megophryidae) from Hunan, China

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          Abstract

          A new leaf litter toad, Leptobrachella yongshunensis sp. nov., is described on the basis of morphological, acoustic, and molecular data in this study. The new species was distributed in Xiaoxi National Nature Reserve, Yongshun County, Xiangxi Tujia and Miao Autonomous Prefecture, Hunan Province, China. Phylogenetical analysis revealed that the new species is sister species of L. wulingensis (p-distance 0.019 in 16s rRNA gene, p-distance 0.073 in COI gene). The duration of advertisement call was 194.2 ± 6.7 ms, the mean dominant frequency of the first note was 3.885 ± 0.066 kHz, and the mean dominant frequency of the second note was 3.914 ± 0.052 kHz. The new species can be distinguished from its congers by the following morphological characters: snout-vent length (SVL) 27.2–28.9 in males, SVL 26.2–31.6 in females; black spots on flanks; toes webbing rudimentarily; narrow fringes on toes; creamy white ventral body with indistinct black speckling at margins; dorsal body with sparse large warts, dense little wart grains, and longitudinal ridges; head width greater than head length; tibiotarsal articulation reaching to anterior edge of the eye; brick-red color in the dorsal surface; upper parts of iris bright coppery in life. We still supplemented the molecular data of the COI gene of L. wulingensis for further research. The discovery of the new species not only enhances the species diversity of the Wuling Mountains, but also suggests the hidden species diversity in the area.

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

          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

            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

              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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                Author and article information

                Contributors
                Journal
                Zoosystematics and Evolution
                ZSE
                Pensoft Publishers
                1860-0743
                1435-1935
                January 16 2025
                January 16 2025
                : 101
                : 1
                : 103-117
                Article
                10.3897/zse.101.135586
                5806bac7-e979-48fd-b9fe-a241fe413bc3
                © 2025

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

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