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  • 1.
    Garcia-Porta, Joan
    et al.
    CREAF, Cerdanyola Del Valles 08193, Spain;Univ Hull, Dept Biol & Marine Sci, Cottingham Rd, Kingston Upon Hull HU6 7RX, Yorks, England;Washington Univ, Dept Biol, St Louis, MO 63130 USA.
    Irisarri, Iker
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kirchner, Martin
    Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Invalidenstr 43, D-10115 Berlin, Germany.
    Rodriguez, Ariel
    Hannover Sch Vet Med, Inst Zool, Bunteweg 17, D-30559 Hannover, Germany.
    Kirchhof, Sebastian
    Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Invalidenstr 43, D-10115 Berlin, Germany.
    Brown, Jason L.
    Southern Illinois Univ, Dept Zool, Carbondale, IL 62901 USA.
    MacLeod, Amy
    Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Invalidenstr 43, D-10115 Berlin, Germany.
    Turner, Alexander P.
    Univ Hull, Sch Engn & Comp Sci, Cottingham Rd, Kingston Upon Hull HU6 7RX, Yorks, England.
    Ahmadzadeh, Faraham
    Shahid Beheshti Univ, Environm Sci Res Inst, Dept Biodivers & Ecosyst Management, GC, Tehran, Iran.
    Albaladejo, Gonzalo
    CSIC, IPNA, Tenerife 38206, Canary Islands, Spain.
    Crnobrnja-Isailovic, Jelka
    Univ Nis, Fac Sci & Math, Dept Biol & Ecol, Visegradska 33, Nish 18000, Serbia.
    De la Riva, Ignacio
    Univ Belgrade, Inst Biol Res S Stankovic, Despota Stefana 142, Belgrade 11000, Serbia.
    Fawzi, Adnane
    CSIC, Museo Nacl Ciencias Nat, Dept Biodivers & Evolutionary Biol, C Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    Galan, Pedro
    Cadi Ayyad Univ, Biodivers & Ecosyst Dynam Lab, Fac Sci, Marrakech, Morocco.
    Gocmen, Bayram
    Univ A Coruna, GIBE, Fac Ciencias, Dept Biol, La Coruna 15071, Spain.
    Harris, D. James
    Ege Univ, Fac Sci, Biol Dept, Zool Sect, TR-35100 Izmir, Turkey.
    Jimenez-Robles, Octavio
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO InBIO, Campus Agr Vairao, P-4485661 Vairao, Portugal.
    Joger, Ulrich
    Australian Natl Univ, Res Sch Biol, Dept Ecol & Evolut, Canberra, ACT, Australia.
    Glavas, Olga Jovanovic
    Staatliches Nat Hist Museum, Braunschweig, Germany.
    Karis, Mert
    Univ Osijek, Dept Biol, Cara Hadrijana 8A, Osijek, Croatia.
    Koziel, Giannina
    Nevsehir Haci Bektas Veli Univ, Acigol Vocat High Sch Tech Sci, Dept Chem & Chem Proc Technol, TR-50300 Nevsehir, Turkey.
    Kunzel, Sven
    Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Lyra, Mariana
    Max Planck Inst Evolutionary Biol, Plon, Germany.
    Miles, Donald
    UNESP Univ Estadual Paulista, Inst Biociencias, Dept Zool, Rio Claro, Brazil.
    Nogales, Manuel
    CSIC, IPNA, Tenerife 38206, Canary Islands, Spain.
    Oguz, Mehmet Anil
    Ege Univ, Fac Sci, Biol Dept, Zool Sect, TR-35100 Izmir, Turkey.
    Pafilis, Panayiotis
    Ohio Univ, Dept Biol Sci, Athens, OH 45701 USA.
    Rancilhac, Lois
    Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Rodriguez, Noemi
    CSIC, IPNA, Tenerife 38206, Canary Islands, Spain.
    Rodriguez Concepcion, Benza
    CSIC, IPNA, Tenerife 38206, Canary Islands, Spain.
    Sanchez, Eugenia
    Salvi, Daniele
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO InBIO, Campus Agr Vairao, P-4485661 Vairao, Portugal;Univ Athens, Dept Biol, Sect Zool & Marine Biol, Athens 15784, Greece.
    Slimani, Tahar
    Cadi Ayyad Univ, Biodivers & Ecosyst Dynam Lab, Fac Sci, Marrakech, Morocco.
    S'khifa, Abderrahim
    Cadi Ayyad Univ, Biodivers & Ecosyst Dynam Lab, Fac Sci, Marrakech, Morocco.
    Qashqaei, Ali Turk
    Shahid Beheshti Univ, Environm Sci Res Inst, Dept Biodivers & Ecosyst Management, GC, Tehran, Iran.
    Zagar, Anamarija
    Univ Aquila, Dept Hlth Life & Environm Sci, I-67100 Laquila, Italy.
    Lemmon, Alan
    Natl Inst Biol NIB, Dept Organisms & Ecosyst Res, Vecna Pot 111, Ljubljana 1000, Slovenia.
    Lemmon, Emily Moriarty
    Florida State Univ, Dirac Sci Lib, Dept Sci Comp, Tallahassee, FL 32306 USA.
    Carretero, Miguel Angel
    Carranza, Salvador
    Florida State Univ, Dept Biol Sci, Tallahassee, FL 32306 USA.
    Philippe, Herve
    Univ Pompeu Fabra, CSIC, Inst Evolutionary Biol, Passeig Maritim Barceloneta 37-49, Barcelona 08003, Spain.
    Sinervo, Barry
    Ctr Biodivers Theory & Modelling, UMR CNRS 5321, Stn Theoret & Expt Ecol, F-09200 Moulis, France;Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, 130 McAllister Way,Coastal Biol Bldg, Santa Cruz, CA 95064 USA.
    Muller, Johannes
    Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Invalidenstr 43, D-10115 Berlin, Germany.
    Vences, Miguel
    Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany;Washington Univ, Dept Biol, St Louis, MO 63130 USA.
    Valero, Katharina C. Wollenberg
    Univ Calif Santa Cruz, Inst Study Ecol & Evolutionary Climate Impacts, 130 McAllister Way,Coastal Biol Bldg, Santa Cruz, CA 95064 USA;Washington Univ, Dept Biol, St Louis, MO 63130 USA.
    Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 4077Article in journal (Refereed)
    Abstract [en]

    Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genomewide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.

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    FULLTEXT01
  • 2.
    Irisarri, Iker
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Baurain, Denis
    Univ Liege, InBioS Eukaryot Phylogen, Dept Life Sci & PhytoSYST, B-4000 Liege, Belgium.
    Brinkmann, Henner
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Delsuc, Frédéric
    Univ Montpellier, Inst Sci Evolut, UMR 5554, CNRS,IRD,EPHE, F-34095 Montpellier, France.
    Sire, Jean-Yves
    Sorbonne Univ, Inst Biol Paris Seine, UMR7138, F-75005 Paris, France.
    Kupfer, Alexander
    Stuttgart State Museum Nat Hist, Dept Zool, D-70191 Stuttgart, Germany.
    Petersen, Jörn
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Jarek, Michael
    Helmholtz Ctr Infect Res, Dept Genome Analyt, D-38124 Braunschweig, Germany.
    Meyer, Axel
    Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Vences, Miguel
    Braunschweig Univ Technol, Zool Inst, D-38106 Braunschweig, Germany.
    Philippe, Hervé
    Ctr Biodivers Theory & Modelling, UMR CNRS 5321, Stn Theoret & Expt Ecol, F-09200 Moulis, France; Univ Montreal, Dept Biochim, Montreal, PQ H3C 3J7, Canada.
    Phylotranscriptomic consolidation of the jawed vertebrate timetree2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 9, p. 1370-1378Article in journal (Refereed)
    Abstract [en]

    Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accu- rate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

  • 3.
    Irisarri, Iker
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. CSIC, Museo Nacl Ciencias Nat, Dept Biodivers & Evolutionary Biol, C Jose Gutierrez Abascal 2, E-28006 Madrid, Spain.
    Uribe, Juan E.
    CSIC, Museo Nacl Ciencias Nat, Dept Biodivers & Evolutionary Biol, C Jose Gutierrez Abascal 2, E-28006 Madrid, Spain;Natl Museum Nat Hist, Smithsonian Inst, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA.
    Eernisse, Douglas J.
    Calif State Univ Fullerton, Dept Biol Sci, 800 N State Coll Blvd, Fullerton, CA 92831 USA.
    Zardoya, Rafael
    CSIC, Museo Nacl Ciencias Nat, Dept Biodivers & Evolutionary Biol, C Jose Gutierrez Abascal 2, E-28006 Madrid, Spain.
    A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)2020In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 20, no 1, article id 22Article in journal (Refereed)
    Abstract [en]

    Background

    Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages.

    Results

    Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses.

    Conclusions

    In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.

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    FULLTEXT01
  • 4.
    Uribe, Juan E.
    et al.
    CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain;Smithonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA;Univ Magdalena, Grp Evoluc Sistemat & Ecol Mol, Carrera 32,Numero 22, Santa Marta, Magdalena, Colombia.
    Irisarri, Iker
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    Templado, Jose
    CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    Zardoya, Rafael
    CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    New patellogastropod mitogenomes help counteracting long-branch attraction in the deep phylogeny of gastropod mollusks2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 133, p. 12-23Article in journal (Refereed)
    Abstract [en]

    Long-branch attraction (LBA) is a well-known artifact in phylogenetic reconstruction. Sparse taxon sampling and extreme heterogeneity of evolutionary rates among lineages generate propitious situations for LBA, even defying probabilistic methods of phylogenetic inference. A clear example illustrating LBA challenges is the difficulty of reconstructing the deep gastropod phylogeny, particularly using mitochondrial (mt) genomes. Previous studies consistently obtained unorthodox phylogenetic relationships due to the LBA between the mitogenomes of patellogastropods (true limpets, represented only by Lottia digitalis), heterobranchs, and outgroup taxa. Here, we use the reconstruction of the gastropod mitogenomic phylogeny as a case exercise to test the effect of key methodological approaches proposed to counteract LBA, including the selection of slow-evolving representatives, the use of different outgroups, the application of site-heterogeneous evolutionary models, and the removal of fast-evolving sites. In this regard, we sequenced three new patellogastropod mt genomes, which displayed shorter branches than the one of Lottia as well as gene organizations more similar to that of the hypothetical gastropod ancestor. Phylogenetic analyses incorporating the mt genomes of Patella ferruginea, Patella vulgata, and Cellana radiata allowed eliminating the artificial clustering of Patellogastropoda and Heterobranchia that had prevailed in previous studies. Furthermore, the use of site-heterogeneous models with certain combinations of lineages within the outgroup allowed eliminating also the LBA between Heterobranchia and the outgroup, and recovering Apogastropoda (i.e., Caenogastropoda + Heterobranchia). Hence, for the first time, we were able to obtain a mitogenomic phylogeny of gastropods that is congruent with both morphological and nuclear datasets.

  • 5.
    Whelan, Simon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Irisarri, Iker
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences2018In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 22, p. 3929-3930Article in journal (Refereed)
    Abstract [en]

    A Summary: Phylogenomic datasets invariably contain undetected stretches of non-homologous characters due to poor-quality sequences or erroneous gene models. The large-scale multi-gene nature of these datasets renders impractical or impossible detailed manual curation of sequences, but few tools exist that can automate this task. To address this issue, we developed a new method that takes as input a set of unaligned homologous sequences and uses an explicit probabilistic approach to identify and mask regions with non-homologous adjacent characters. These regions are defined as sharing no statistical support for homology with any other sequence in the set, which can result from e.g. sequencing errors or gene prediction errors creating frameshifts. Our methodology is implemented in the program PREQUAL, which is a fast and accurate tool for high-throughput filtering of sequences. The program is primarily aimed at amino acid sequences, although it can handle protein coding DNA sequences as well. It is fully customizable to allow fine-tuning of the filtering sensitivity.

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