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      Extension of the known range of the snapping shrimp Alpheus christofferseni Anker, Hurt and Knowlton, 2007 (Caridea: Alpheidae)

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          Abstract

          Abstract Alpheus christofferseni Anker, Hurt and Knowlton, 2007 was described based on four specimens from Atol das Rocas, northeastern Brazil, and one specimen from Bocas del Toro, the Caribbean coast of Panama. Here, we report the collection of two specimens from Pernambuco, Brazil (~ 8°41’S), thus increasing the knowledge on species distribution along the Brazilian coast by approximately five latitudinal degrees south of its type locality (Atol das Rocas, Rio Grande do Norte, ~ 3°51'S). We also report a substantial increase in the known bathymetric distribution from shallow intertidal to approximately 51 m. Notes on morphological variation are provided based on the new material, and the first sequence of the 16S ribosomal subunit gene for the Brazilian coast is provided and compared with congeners.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          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.
          Article 0 comments Cited 9909 times – based on 0 reviews     Review now
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Alexandros Stamatakis (2014)
            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              MUSCLE: multiple sequence alignment with high accuracy and high throughput.

              R. C. Edgar (2004)
              We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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                Author and article information

                Journal
                Journal ID (publisher-id): nau
                Title: Nauplius
                Abbreviated Title: Nauplius
                Publisher: Sociedade Brasileira de Carcinologia (Botucatu, SP, Brazil )
                ISSN (Electronic): 2358-2936
                Publication date (Print and electronic): 2023
                Volume: 31
                Electronic Location Identifier: e2023001
                Affiliations
                [2] Porto Alegre Rio Grande do Sul orgnameFederal University of Rio Grande do Sul orgdiv1Institute of Biosciences orgdiv2Department of Zoology Brazil
                [1] Recife Pernambuco orgnameFederal University of Pernambuco orgdiv1Biosciences Center orgdiv2Department of Zoology Brazil
                Article
                Publisher ID: S0104-64972023000100206 Publisher ID: S0104-6497(23)03100000206
                DOI: 10.1590/2358-2936e2023001
                SO-VID: 79ce4df1-6ac7-4bf1-bfef-e0c551d14562
                License:

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

                History
                Date received : 14 March 2022
                Date accepted : 13 September 2022
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 26, Pages: 0
                Product

                SciELO Brazil

                Categories
                Subject: Original Article

                Keywords: Bathymetric range,Brazilian diversity,Decapoda,distribution,new record
                Data availability:
                Keywords: Bathymetric range, Brazilian diversity, Decapoda, distribution, new record

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