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      Integrative taxonomy of the model liverwort Riella helicophylla (Riellaceae, Sphaerocarpales) reveals its extreme rarity and an overlooked widespread new species, R. macrocarpa

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          Abstract

          Riella (Riellaceae) is a genus of rare, ephemeral, aquatic liverworts that includes some taxa specialized in growing submerged in brackish, seasonal water ponds and lagoons. One of these species, Riella helicophylla is the type of the genus. Apart from being of conservation concern, it has been used as a model organism for cytological and physiological processes. The species was described from Algeria in the mid‐nineteenth century and was not found elsewhere for almost a century, when it was discovered in central Spain. Nonetheless, those new populations were considered morphologically different and served to describe a new variety (var. macrocarpa), and a form (f. latealata) of the latter. The number of population records increased considerably in the following decades, especially in the late twentieth century; at the same time, it was discovered in several countries throughout the Mediterranean basin. Those reports, however, did not account for its infraspecific distinction. As part of a broader study of the genus, in this work, we have revisited the taxonomy of R. helicophylla based on an integrative approach considering morphological and molecular DNA sequence data. Our broadly sampled study revealed that R. helicophylla includes two morphotypes corresponding with the previously recognized varieties of this species. These varieties differ consistently in a number of morphological gametophytic and spore traits. Riella helicophylla was resolved as paraphyletic in phylogenies based on nuclear and plastid DNA sequences. The accessions clustered in two monophyletic clades in concert with morphology, supporting their recognition at the species level. Accordingly, a new combination is proposed, R. macrocarpa, which includes the neglected R. helicophylla var. macrocarpa and R. helicophylla var. macrocarpa f. latealata. Lectotypes are designated for the two latter taxa and for R. helicophylla. The two species are fully described and illustrated, and an updated identification key of the Mediterranean species is included. Updated information on the conservation status of both species is provided.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            Is Open Access

            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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              Is Open Access

              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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                Contributors
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                Journal
                TAXON
                TAXON
                Wiley
                0040-0262
                1996-8175
                June 2022
                February 18 2022
                June 2022
                : 71
                : 3
                : 506-530
                Affiliations
                [1 ] Departamento de Botánica y Geología, Facultad de Ciencias Biológicas Universitat de València Avda. Dr. Moliner 50 46100 Burjassot (Valencia) Spain
                [2 ] University of Belgrade, Faculty of Biology Institute of Botany and Botanical Garden Takovska 43 11000 Belgrade Serbia
                [3 ] Museo de Ciencias Naturales de Álava Siervas de Jesús 24 01001 Vitoria (Álava) Spain
                Article
                10.1002/tax.12682
                c1203881-63b3-4230-99e3-8eb1f4d8c46e
                © 2022

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