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      Nearctic Dactylogyrus species (Platyhelminthes, Monogenea) parasitizing cypriniform fishes in the context of morphology and phylogeny, with descriptions of seven new species Translated title: Espèce néarctique de Dactylogyrus (Platyhelminthes, Monogenea) parasitant des poissons cypriniformes dans un contexte de morphologie et phylogénie, avec description de sept nouvelles espèces

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      1 , * , , 1 , 1 , 1
      Parasite
      EDP Sciences
      Monogenea, Dactylogyrus, North America, Leuciscidae, Catostomidae, Morphology, Phylogeny

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          Abstract

          Ribosomal DNA sequences are currently available for 32 morphologically recognized species of Dactylogyrus parasitizing Nearctic cypriniforms, but only 16 of them are assigned to nominal species. Herein, morphological data on 28 of the 32 species are provided, together with comments on their phylogenetic relationships in the context of the morphology of taxonomically important structures. Seven new species of Dactylogyrus are described from five species of leuciscids and one species of catostomids, as follows: D. aduncus n. sp. from Campostoma spadiceum, D. cloutmani n. sp. from Luxilus chrysocephalus isolepis, D. cornifrons n. sp. from Cyprinella venusta, D. fimbratus n. sp. from Rhinichthys cataractae, D. mcallisteri n. sp. from Semotilus atromaculatus, and D. chieni n. sp. and D. haneki n. sp. from Hypentelium nigricans. Four previously described species of Dactylogyrus, D. atromaculatus from S. atromaculatus, D. eos from C. neogaeus, D. parvicirrus from Notemigonus crysoleucas and D. perlus from L. c. isolepis, are redescribed and/or figured. As for the remaining 17 species, only the male copulatory organs (MCOs) taken from the respective hologenophores are illustrated. On the basis of phylogenetic analyses, two main clades of Nearctic Dactylogyrus were recognized and supported by the different morphology of the MCO. The first one included 22 strictly Nearctic species sharing the same MCO type with Dactylogyrus spp. parasitizing cyprinids likely of Asian origin. The second clade encompassed Dactylogyrus spp. with diverse MCO morphology and was placed in the sister position to Dactylogyrus spp. parasitizing European leuciscids and North-West African cyprinids.

          Translated abstract

          Des séquences d’ADN ribosomal sont actuellement disponibles pour 32 espèces morphologiquement reconnues de Dactylogyrus parasitant les cypriniformes néarctiques, mais seulement 16 d’entre elles sont attribuées à des espèces nominales. Ici, des données morphologiques sur 28 des 32 espèces sont fournies avec des commentaires sur leurs relations phylogénétiques dans le contexte de la morphologie des structures taxonomiquement importantes. Sept nouvelles espèces de Dactylogyrus sont décrites à partir de cinq espèces de leuciscidés et d’une espèce de catostomidés, comme suit : D. aduncus n. sp. de Campostoma spadiceum, D. cloutmani n. sp. de Luxilus chrysocephalus isolepis, D. cornifrons n. sp. de Cyprinella venusta, D. fimbratus n. sp. de Rhinichthys cataractae, D. mcallisteri n. sp. de Semotilus atromaculatus et D. chieni n. sp. et D. haneki n. sp. de Hypentelium nigricans. Quatre espèces de Dactylogyrus précédemment décrites, D. atromaculatus de S. atromaculatus, D. eos de C. neogaeus, D. parvicirrus de Notemigonus crysoleucas et D. perlus de L. c. isolepis, sont redécrites et/ou figurées. Comme pour les 17 espèces restantes, seuls les organes copulateurs mâles (OCM) prélevés sur les hologénophores respectifs sont illustrés. Sur la base d’analyses phylogénétiques, deux clades principaux de Dactylogyrus néarctiques ont été reconnus et soutenus par des morphologies différentes de l’OCM. Le premier comprenait 22 espèces strictement néarctiques partageant le même type d’OCM que les Dactylogyrus spp. parasitant des cyprinidés probablement d’origine asiatique. Le deuxième clade comprenait des Dactylogyrus spp. avec diverses morphologies d’OCM et était placé en position sœur des Dactylogyrus spp. parasitant les leuciscidés européens et les cyprinidés d’Afrique du Nord-Ouest.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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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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                Author and article information

                Journal
                Parasite
                Parasite
                parasite
                Parasite
                EDP Sciences
                1252-607X
                1776-1042
                2023
                17 August 2023
                : 30
                : 30
                Affiliations
                Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
                Author notes
                [* ]Corresponding author: evar@ 123456sci.muni.cz
                Author information
                http://orcid.org/0000-0003-4406-7314
                http://orcid.org/0009-0009-0738-3124
                Article
                parasite230010 10.1051/parasite/2023032
                10.1051/parasite/2023032
                10433842
                37589452
                65b4e681-efab-452b-a3f7-8881772d91a1
                © E. Řehulková et al., published by EDP Sciences, 2023

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 January 2023
                : 16 July 2023
                Page count
                Figures: 15, Tables: 1, Equations: 0, References: 88, Pages: 26
                Categories
                Research Article

                monogenea,dactylogyrus,north america,leuciscidae,catostomidae,morphology,phylogeny

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