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      Taxonomy and phylogeny of Dalytyphloplanida Willems et al., 2006 (Platyhelminthes: Rhabdocoela), with the description of a new family, a new genus, and sixteen new species from Cuba and Panama

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          Abstract

          Twenty-two marine species of Dalytyphloplanida from Cuba, Panama, and Lanzarote are presented, sixteen of which are new to science. Five known species are recorded from Cuba: Kytorhynchus microstylus, Ceratopera paragracilis, Trigonostomum armatum, T. franki, and T. vanmecheleni. Neokytorhynchus pacificus is recorded for the first time in the Atlantic (Lanzarote). For one species, a new genus is erected to be included in a new family. A new genus and thirteen new species from Cuba and three new species from Panama are described. The new species are mainly distinguished from their congeners by the specific morphology of the copulatory structures. The new taxa are discussed in the context of a new phylogenetic analysis of Dalytyphloplanida. This analysis includes sequences of 238 species, 14 of which were sequenced for the first time. The phylogenetic analysis and the detailed morphology suggest that K. microstylus may constitute a complex of cryptic species. The internal phylogenetic relationships of Trigonostomum and Promesostoma were separately analysed to include new sequence data of the mitochondrial cox1 gene. These genera are shown to consist of several diagnosable clades, concurring with the results of early morphological studies of these taxa. Morphological and molecular data support the notion that Trigonostomum sinensis is a junior synonym of T. vanmecheleni, and we therefore propose their synonymisation. A new family is erected, Schockaertiidae fam. n., to include a monophyletic clade of neodalyellids with a pharynx rosulatus and a copulatory bulb devoid of hard structures ( Schockaertia aprostatica gen. n. sp. n. and Einarella argillophyla). We propose a new classification into families of Thalassotyphloplanida, which envolves elevating the status of Adenorhynchinae to family level (Adenorhynchidae status novus). All previously recognised thalassotyphloplanid families are recovered as monophyletic (Kytorhynchidae, Byrsophlebidae, Promesostomidae, and Trigonostomidae). No support was found for the previously described subfamilies, except Paramesostominae, and we, therefore, propose to suppress these taxa.

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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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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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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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                Author and article information

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                Journal
                Organisms Diversity & Evolution
                Org Divers Evol
                Springer Science and Business Media LLC
                1439-6092
                1618-1077
                December 2023
                October 23 2023
                December 2023
                : 23
                : 4
                : 631-681
                Article
                10.1007/s13127-023-00623-w
                f832fafe-3b35-4bd1-8046-cee11013357e
                © 2023

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

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

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