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      The genomic timeline of cichlid fish diversification across continents

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          Abstract

          Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution — the timeline of their diversification — remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypothesis of cichlid and teleost evolution that we time-calibrate with 58 re-evaluated fossil constraints and a new Bayesian model accounting for fossil-assignment uncertainty. Our results support cichlid diversification long after the breakup of the supercontinent Gondwana and lay the foundation for precise temporal reconstructions of the exceptional continental cichlid adaptive radiations.

          Abstract

          Cichlids are a model for adaptive radiation, but the timing of their diversification is debated. Here the authors assemble 14 cichlid genomes, introduce a Bayesian approach to account for fossil-assignment uncertainty, and present a dated phylogenomic hypothesis of cichlid and teleost evolution.

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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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            Basic local alignment search tool.

            Stephen F Altschul, Warren Gish, Webb Miller … (1990)
            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              FLASH: fast length adjustment of short reads to improve genome assemblies.

              T. Magoc, S. L. Salzberg (2013)
              Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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                Author and article information

                Contributors
                Michael Matschiner:
                ORCID: http://orcid.org/0000-0003-4741-3884
                michaelmatschiner@mac.com
                Walter Salzburger:
                ORCID: http://orcid.org/0000-0002-9988-1674
                walter.salzburger@unibas.ch
                Journal
                Journal ID (nlm-ta): Nat Commun
                Journal ID (iso-abbrev): Nat Commun
                Title: Nature Communications
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2041-1723
                Publication date (Electronic): 18 November 2020
                Publication date PMC-release: 18 November 2020
                Publication date Collection: 2020
                Volume: 11
                Electronic Location Identifier: 5895
                Affiliations
                [1 ]GRID grid.6612.3, ISNI 0000 0004 1937 0642, Zoological Institute, , University of Basel, ; Basel, Switzerland
                [2 ]GRID grid.7400.3, ISNI 0000 0004 1937 0650, Department of Palaeontology and Museum, , University of Zurich, ; Zurich, Switzerland
                [3 ]GRID grid.5510.1, ISNI 0000 0004 1936 8921, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, , University of Oslo, ; Oslo, Norway
                [4 ]GRID grid.452935.c, ISNI 0000 0001 2216 5875, Center for Molecular Biodiversity Research (ZMB), , Zoological Research Museum Alexander Koenig, ; Bonn, Germany
                Author information
                http://orcid.org/0000-0003-4741-3884
                http://orcid.org/0000-0002-1284-3115
                http://orcid.org/0000-0003-1583-8108
                http://orcid.org/0000-0002-9988-1674
                Article
                Publisher ID: 17827
                DOI: 10.1038/s41467-020-17827-9
                PMC ID: 7674422
                PubMed ID: 33208747
                SO-VID: 041c09c8-361f-4c93-863b-78fd9a66b643
                Copyright © © The Author(s) 2020
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 26 February 2020
                Date accepted : 15 July 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/100010663, EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council);
                Award ID: 617585
                Award Recipient :
                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2020

                ScienceOpen disciplines: Uncategorized
                Keywords: phylogenetics,ichthyology
                Data availability:
                ScienceOpen disciplines: Uncategorized
                Keywords: phylogenetics, ichthyology

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