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      Evolutionary and biogeographical patterns of barnacles from deep‐sea hydrothermal vents

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          Abstract

          The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep‐sea hydrothermal vent barnacles represent an excellent model for testing biogeographical hypotheses regarding the origin, dispersal and diversity of modern vent fauna. Here, we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal and diversification. Our approach was to target a suite of multiple loci in samples representing seven of the eight described genera. We also performed restriction‐site associated DNA sequencing on individuals from each species. Phylogenetic inferences and topology hypothesis tests indicate that vent barnacles have colonized deep‐sea hydrothermal vents at least twice in history. Consistent with preliminary estimates, we find a likely radiation of barnacles in vent ecosystems during the Cenozoic. Our analyses suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastwards through the Southern Hemisphere during the Neogene. The inferred time of radiation rejects the classic hypotheses of antiquity of vent taxa. The timing and the mode of origin, radiation and dispersal are consistent with recent inferences made for other deep‐sea taxa, including nonvent species, and are correlated with the occurrence of major geological events and mass extinctions. Thus, we suggest that the geological processes and dispersal mechanisms discussed here can explain the current distribution patterns of many other marine taxa and have played an important role shaping deep‐sea faunal diversity. These results also constitute the critical baseline data with which to assess potential effects of anthropogenic disturbances on deep‐sea ecosystems.

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          Evolution of genes and genomes on the Drosophila phylogeny.

          Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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            Mass extinctions in the marine fossil record.

            A new compilation of fossil data on invertebrate and vertebrate families indicates that four mass extinctions in the marine realm are statistically distinct from background extinction levels. These four occurred late in the Ordovician, Permian, Triassic, and Cretaceous periods. A fifth extinction event in the Devonian stands out from the background but is not statistically significant in these data. Background extinction rates appear to have declined since Cambrian time, which is consistent with the prediction that optimization of fitness should increase through evolutionary time.
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              Is a new and general theory of molecular systematics emerging?

              The advent and maturation of algorithms for estimating species trees-phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes-represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a "local optimum" for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term "phylogeny" for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.
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                Author and article information

                Journal
                Mol Ecol
                Mol. Ecol
                10.1111/(ISSN)1365-294X
                MEC
                Molecular Ecology
                John Wiley and Sons Inc. (Hoboken )
                0962-1083
                1365-294X
                February 2015
                20 January 2015
                : 24
                : 3 ( doiID: 10.1111/mec.2015.24.issue-3 )
                : 673-689
                Affiliations
                [ 1 ]Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139USA
                [ 2 ] Biology DepartmentWoods Hole Oceanographic Institution 266 Woods Hole Road Woods Hole MA 02543USA
                [ 3 ] Institute of BiogeosciencesJapan Agency for Marine‐Earth Science and Technology Yokosuka KanagawaJapan
                Author notes
                [*] [* ]Correspondence: Timothy M. Shank and Santiago Herrera, Fax: +1 508‐457‐2134; E‐mails: tshank@ 123456whoi.edu and sherrera@ 123456alum.mit.edu
                Article
                MEC13054
                10.1111/mec.13054
                5006861
                25602032
                86f8e474-5aa5-4a97-b2bb-058a2f3afa79
                © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 26 September 2014
                : 14 December 2014
                : 20 December 2014
                Page count
                Pages: 17
                Funding
                Funded by: Office of Ocean Exploration and Research of the National Oceanic and Atmospheric Administration
                Award ID: NA09OAR4320129
                Funded by: Auckland University, Institute of Geological and Nuclear Science
                Funded by: WHOI
                Funded by: Land Information New Zealand
                Funded by: MBIE
                Funded by: FRST
                Funded by: Division of Ocean Sciences of the National Science Foundation
                Award ID: OCE‐1131620
                Funded by: Division of Polar Programs of the National Science Foundation
                Award ID: PLR‐0739675
                Funded by: Astrobiology Science and Technology for Exploring Planets program of the National Aeronautics and Space Administration
                Award ID: NNX09AB76G
                Funded by: Academic Programs Office
                Funded by: Ocean Exploration Institute
                Funded by: Ocean Life Institute of the Woods Hole Oceanographic Institution
                Funded by: National Institute of Water and Atmospheric Research
                Funded by: New Zealand Ministry of Business, Innovation & Employment
                Award ID: CO1X0508
                Categories
                Original Article
                Original Articles
                Phylogeography
                Custom metadata
                2.0
                mec13054
                February 2015
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.9.4 mode:remove_FC converted:31.08.2016

                Ecology
                cenozoic,dispersal,hydrothermal vents,polyphyly,southern hemisphere,species delimitation,rad‐seq
                Ecology
                cenozoic, dispersal, hydrothermal vents, polyphyly, southern hemisphere, species delimitation, rad‐seq

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