An integrative approach distinguishes three new species of Abyssochrysoidea (Mollusca: Caenogastropoda) associated with organic falls of the deep south-west Atlantic

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Abstract

Two new species of Rubyspira and one of Cordesia (Gastropoda: Abyssochrysoidea) are described morphologically and genetically, based on specimens collected from whale bones and wood parcels artificially implanted in the deep south-west Atlantic Ocean, at c. 1500 and 3300 m depths. Rubyspira pescaprae sp. nov. and R. elongata sp. nov. occur preferentially on whale bones. Cordesia atlantica sp. nov. is dominant on wood parcels. Distribution of Cordesia was hitherto only associated with hydrocarbon seeps off West Africa. Stable isotopes and gut content analyses were carried out to check possible trophic pathways. Both Rubyspira species are bone eaters, while Cordesia atlantica seems to rely on a wider range of food sources, including juveniles of wood-specialized xylophagid bivalves. Morphological and genetic evidence suggest that Rubyspira and Cordesia are more closely related to Abyssochrysos than to any other Abyssochrysoidea snails. In the present study, Cordesia is considered part of the family Abyssochrysidae based on molecular and morphological evidence, such as the presence of a penis and pallial tentacles arrangement.

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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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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

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

Matthew Kearse, Richard Moir, Amy Wilson … (2012)

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

Maurício Shimabukuro: (View ORCID Profile)

Journal

Title: Zoological Journal of the Linnean Society

Publisher: Oxford University Press (OUP)

ISSN (Print): 0024-4082

ISSN (Electronic): 1096-3642

Publication date Created: March 01 2021

Publication date Created: February 13 2021

Publication date Created: July 23 2020

Publication date Other: March 01 2021

Publication date (Print): February 13 2021

Publication date (Electronic): July 23 2020

Volume: 191

Issue: 3

Pages: 748-771

Affiliations

[1 ]Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, São Paulo-SP, Brazil

[2 ]Instituto de Biologia, Universidade de Campinas, Campinas-SP, Brazil

[3 ]Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER), Centre Bretagne, REM/EEP/LEP, Plouzané, France

Article

DOI: 10.1093/zoolinnean/zlaa059

SO-VID: b22c7b45-cf54-4627-8069-75ee9ffeee5c

License:

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

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