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      Abyssal fauna of polymetallic nodule exploration areas, eastern Clarion-Clipperton Zone, central Pacific Ocean: Amphinomidae and Euphrosinidae (Annelida, Amphinomida)

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          Abstract

          This is a contribution in a series of taxonomic publications on benthic fauna of polymetallic nodule fields in the eastern abyssal Clarion-Clipperton Zone (CCZ). The material was collected during environmental surveys targeting exploration contract areas ‘UK-1’, ‘OMS’ and ‘NORI-D’, as well as an Area of Particular Environmental Interest, ‘APEI-6’. The annelid families Amphinomidae and Euphrosinidae are investigated here. Taxonomic data are presented for six species from 41 CCZ-collected specimens as identified by a combination of morphological and genetic approaches; of the six species, three are here described as new, one species is likely to be new but in too poor condition to be formalised and the two others likely belong to known species. Description of three new species Euphrosinella georgievae sp. nov., Euphrosinopsis ahearni sp. nov., and Euphrosinopsis halli sp. nov. increases the number of formally described new annelid species from the targeted areas to 21 and CCZ-wide to 52. Molecular data suggest that four of the species reported here are known from CCZ only, but within CCZ they have a wide distribution. In contrast, the species identified as Bathychloeia cf. sibogae Horst, 1910 was found to have a wide distribution within the Pacific based on both morphological and molecular data, using comparative material from the abyssal South Pacific. Bathychloeia cf. balloniformis Böggemann, 2009 was found to be restricted to APEI-6 based on DNA data available from CCZ specimens only, but morphological data from other locations suggest potentially a wide abyssal distribution. The genus Euphrosinopsis was previously known only from Antarctic waters, and Euphrosinella georgievae sp. nov. was recovered as a sister taxon to the Antarctic specimens of Euphrosinella cf. cirratoformis in our molecular phylogenetic analysis, strengthening the hypothesised link between the deep-sea and Antarctic benthic fauna.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          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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            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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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2022
                22 December 2022
                : 1137
                : 33-74
                Affiliations
                [1 ] Life Sciences Department, Natural History Museum, London SW7 5BD, UK Life Sciences Department, Natural History Museum London United Kingdom
                [2 ] Department of Marine Sciences, University of Gothenburg, Box 463, 40530 Gothenburg, Sweden University of Gothenburg Gothenburg Sweden
                [3 ] Gothenburg Global Biodiversity Centre, Box 463, 40530 Gothenburg, Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden
                [4 ] Australian Museum Research Institute, 1 William Street, Sydney NSW 2010, Australia Australian Museum Research Institute Sydney Australia
                [5 ] NORCE Norwegian Research Centre, Bergen, Norway NORCE Norwegian Research Centre Bergen Norway
                Author notes
                Corresponding author: Adrian G. Glover (a.glover@nhm.ac.uk)

                Academic editor: Andrew Davinack

                Author information
                https://orcid.org/0000-0002-8252-3504
                https://orcid.org/0000-0002-8351-2313
                https://orcid.org/0000-0001-8163-8724
                https://orcid.org/0000-0001-6854-2031
                https://orcid.org/0000-0002-9489-074X
                Article
                86150
                10.3897/zookeys.1137.86150
                9836652
                36760485
                f35f835a-b65a-4348-9958-26ebef145850
                Lenka Neal, Helena Wiklund, Laetitia M. Gunton, Muriel Rabone, Guadalupe Bribiesca-Contreras, Thomas G. Dahlgren, Adrian G. Glover

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 04 May 2022
                : 01 August 2022
                Categories
                Research Article
                Amphinomida
                Amphinomidae
                Annelida
                Euphrosinidae
                Polychaeta
                Biodiversity & Conservation
                Biogeography
                Systematics
                Cenozoic
                Oceans
                Pacific Ocean

                Animal science & Zoology
                amphinomida,ccz,coi,deep-sea mining,molecular phylogeny,species distribution,taxonomic novelty,18s,16s

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