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      Species delimitation, classical taxonomy and genome skimming: a review of the ground beetle genus Lionepha (Coleoptera: Carabidae)

      1 , 1 , 2
      Zoological Journal of the Linnean Society
      Oxford University Press (OUP)

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          Abstract

          The western North American genus Lionepha is shown to contain at least 11 species through a combination of eight-gene species delimitation analyses and morphological study. In order to confirm the names of several species, we sequence DNA of primary types of several names, including a LeConte lectotype collected in the 1850s, using next-generation sequencing. We examine chromosomes of eight species, and show that all have 12 pairs of autosomes and an X0/XX sex-chromosome system. The following species are described as new: Lionepha australerasa, L. kavanaughi, L. lindrothi and L. tuulukwa. The name Lionepha erasa is shown to belong to a relatively rare, western species ranging from Oregon through Alaska; the common, widespread species previously known as Lionepha erasa now takes the name L. probata. Bembidion chintimini, B. lindrothellus and B. lummi are synonymized with L. erasa. We provide tools to identify specimens to species, including illustrations, diagnoses and distribution maps.

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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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              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
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                August 2020
                August 03 2020
                February 26 2020
                August 2020
                August 03 2020
                February 26 2020
                : 189
                : 4
                : 1313-1358
                Affiliations
                [1 ]Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR, USA
                [2 ]Department of Biology, University of Rochester, Rochester, NY, USA
                Article
                10.1093/zoolinnean/zlz167
                961428e3-b01c-4a01-a908-268de1aa1c91
                © 2020

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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