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      Vision using multiple distinct rod opsins in deep-sea fishes

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          Abstract

          Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim-light, vertebrates generally rely upon a single rod opsin (RH1) for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Amongst these, the silver spinyfin ( Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (2 cone, 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blue-shifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.

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          geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.

          Matthew Pennell, Jonathan M Eastman, Graham Slater … (2014)
          Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.
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            Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates.

            Michael Alfaro, Francesco Santini, Chad Brock … (2009)
            The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85% of all species as well as 3 slowdowns that have produced "living fossils." In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.
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              Phylogenetic classification of bony fishes

              Ricardo Betancur-R., Edward O. Wiley, Gloria Arratia … (2017)
              Background Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson’s volumes of Fishes of the World and W. Eschmeyer’s Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny (www.deepfin.org). We here update the first version of that classification by incorporating the most recent phylogenetic results. Results The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. Conclusions This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0958-3) contains supplementary material, which is available to authorized users.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 0404511
                Journal ID (pubmed-jr-id): 7473
                Journal ID (nlm-ta): Science
                Journal ID (iso-abbrev): Science
                Title: Science (New York, N.Y.)
                ISSN (Print): 0036-8075
                ISSN (Electronic): 1095-9203
                Publication date Nihms-submitted: 10 July 2019
                Publication date (Print): 10 May 2019
                Publication date PMC-release: 10 November 2019
                Volume: 364
                Issue: 6440
                Pages: 588-592
                Affiliations
                [1 ]Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
                [2 ]Department of Zoology, Charles University, Prague, Czech Republic.
                [3 ]Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
                [4 ]Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
                [5 ]Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland.
                [6 ]UWA Oceans Institute, The University of Western Australia, Perth, Australia.
                [7 ]School of Biological Sciences, The University of Western Australia, Perth, Australia.
                [8 ]Lions Eye Institute, The University of Western Australia, Perth, Australia.
                [9 ]Oceans Graduate School, The University of Western Australia, Perth, Australia.
                [10 ]Center for Modeling Complex Interactions, University of Idaho, Moscow, USA
                [11 ]Department of Biological Sciences, University of Idaho, Moscow, USA.
                [12 ]Eawag, Swiss Federal Institute for Aquatic Science and Technology, Centre of Ecology, Evolution & Biogeochemistry, Department of Fish Ecology & Evolution, Kastanienbaum, Switzerland.
                [13 ]Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
                [14 ]Thünen Institute of Fisheries Ecology, Bremerhaven, Germany.
                [15 ]Department of Biology, University of Maryland, College Park, USA.
                Author notes
                [*]

                These authors contributed equally to this work.

                Author Contributions: Z.M., F.C., J.M., and W.S. conceived the study; Mi.M., Ma.M., R.H., K.S.J., S.J. and W.S. planned and led the genome sequencing and provided samples; Z.M., F.C., F.d.B., J.M., and W.S. carried out transcriptome sequencing. Z.M. and F.C. carried out the opsin gene analyses. F.C. and S.M.S. performed the PGLS analyses. Mi.M., Ma.M., O.K.T., and S.J., carried out the genome assemblies and annotations. Mi.M. carried out phylogenetic analyses. K.L.C. performed the regulatory region analyses and visual modelling. W.I.L.D. and J.K.M. carried out the in vitro regeneration and spectral prediction analyses. J.S.P. performed the atomistic molecular simulations, and J.S.P., C.J.B., and D.L.S. generated, analyzed and interpreted the predictive model. All authors gave comments on the manuscript and approved the final version.

                Article
                Accession ID: PMC6628886 Pmcid ID: PMC6628886 Pmc-uid ID: 6628886 Manuscript ID: nihpa1033619
                DOI: 10.1126/science.aav4632
                PMC ID: 6628886
                PubMed ID: 31073066
                SO-VID: b3cfea91-2a35-4cf2-994a-6f94fba1640b
                History
                Categories
                Subject: Article

                Keywords: adaptations,teleosts,gene duplication,convergent evolution,sensory systems
                Data availability:
                Keywords: adaptations, teleosts, gene duplication, convergent evolution, sensory systems

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