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      The puzzling occurrence of the upside-down jellyfish Cassiopea (Cnidaria: Scyphozoa) along the Brazilian coast: a result of several invasion events?

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          Abstract

          ABSTRACT The massive occurrence of jellyfish in several areas of the world is reported annually, but most of the data come from the northern hemisphere and often refer to a restricted group of species that are not in the genus Cassiopea. This study records a massive, clonal and non-native population of Cassiopea and discusses the possible scenarios that resulted in the invasion of the Brazilian coast by these organisms. The results indicate that this jellyfish might have invaded the Brazilian coast multiple times.

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

          Kazutaka Katoh, Daron Standley (2013)
          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

            Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
            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

              Subha Kalyaanamoorthy, Bui Minh, Thomas Wong … (2017)
              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

                Journal
                Journal ID (publisher-id): zool
                Title: Zoologia (Curitiba)
                Abbreviated Title: Zoologia (Curitiba)
                Publisher: Sociedade Brasileira de Zoologia (Curitiba, PR, Brazil )
                ISSN (Print): 1984-4670
                ISSN (Electronic): 1984-4689
                Publication date (Print and electronic): 2020
                Volume: 37
                Electronic Location Identifier: e50834
                Affiliations
                [2] São Paulo São Paulo orgnameUniversidade de São Paulo orgdiv1Instituto de Biociências orgdiv2Departamento de Zoologia Brazil
                [1] Assis orgnameUniversidade Estadual Paulista orgdiv1Departamento de Ciências Biológicas orgdiv2Laboratório de Evolução e Diversidade Aquática Brazil
                [3] Maceió AL orgnameInstituto do Meio Ambiente de Alagoas Brazil
                [5] Penedo orgnameUniversidade Federal de Alagoas orgdiv1Unidade Educacional de Penedo orgdiv2Laboratório de Ictiologia e Conservação Brazil
                [6] São Sebastião orgnameUniversidade de São Paulo orgdiv1Centro de Biologia Marinha Brazil
                [4] Maceió Alagoas orgnameInstituto Biota de Conservação Brazil
                Article
                Publisher ID: S1984-46702020000100324 Publisher ID: S1984-4670(20)03700000324
                DOI: 10.3897/zoologia.37.e50834
                SO-VID: 95d22d39-62dc-4c08-943b-fe7e8db3aed5
                License:

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                Date accepted : 11 September 2020
                Date received : 05 February 2020
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 39, Pages: 0
                Product

                SciELO Brazil

                Categories
                Subject: Research Article

                Keywords: jellyfish bloom,Invasive species,non-native species,medusa
                Data availability:
                Keywords: jellyfish bloom, Invasive species, non-native species, medusa

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