1
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Nowell RW, Rodriguez F, Hecox-Lea BJ, Mark Welch DB, Arkhipova IR, Barraclough TG, Wilson CG. Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen. Nat Commun 2024; 15:5787. [PMID: 39025839 PMCID: PMC11258130 DOI: 10.1038/s41467-024-49919-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.
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Affiliation(s)
- Reuben W Nowell
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Institute of Ecology and Evolution, University of Edinburgh; Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.
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2
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Shain DH, Rogozhina I, Fontaneto D, Nesje A, Saglam N, Bartlett J, Zawierucha K, Kielland ØN, Dunshea G, Arnason E, Rosvold J. Ice-inhabiting species of Bdelloidea Rotifera reveal a pre-Quaternary ancestry in the Arctic cryosphere. Biol Lett 2024; 20:20230546. [PMID: 38869044 DOI: 10.1098/rsbl.2023.0546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/19/2024] [Indexed: 06/14/2024] Open
Abstract
Historical climate data indicate that the Earth has passed through multiple geological periods with much warmer-than-present climates, including epochs of the Miocene (23-5.3 mya BP) with temperatures 3-4°C above present, and more recent interglacial stages of the Quaternary, for example, Marine Isotope Stage 11c (approx. 425-395 ka BP) and Middle Holocene thermal maximum (7.5-4.2 ka BP), during which continental glaciers may have melted entirely. Such warm periods would have severe consequences for ice-obligate fauna in terms of their distribution, biodiversity and population structure. To determine the impacts of these climatic events in the Nordic cryosphere, we surveyed ice habitats throughout mainland Norway and Svalbard ranging from maritime glaciers to continental ice patches (i.e. non-flowing, inland ice subjected to deep freezing overwinter), finding particularly widespread populations of ice-inhabiting bdelloid rotifers. Combined mitochondrial and nuclear DNA sequencing identified approx. 16 undescribed, species-level rotifer lineages that revealed an ancestry predating the Quaternary (> 2.58 mya). These rotifers also displayed robust freeze/thaw tolerance in laboratory experiments. Collectively, these data suggest that extensive ice refugia, comparable with stable ice patches across the contemporary Norwegian landscape, persisted in the cryosphere over geological time, and may have facilitated the long-term survival of ice-obligate Metazoa before and throughout the Quaternary.
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Affiliation(s)
- Daniel H Shain
- Biology Department, Rutgers The State University of New Jersey , Camden, NJ 08103, USA
| | - Irina Rogozhina
- Department of Geography, Norwegian University of Science and Technology , Trondheim, Norway
| | - Diego Fontaneto
- National Research Council of Italy - Water Research Institute (CNR-IRSA), Molecular Ecology Group (MEG) , Verbania, Italy
- National Biodiversity Future Center (NBFC) , Palermo, Italy
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic , Liběchov, Czech Republic
| | - Atle Nesje
- Department of Earth Science, University of Bergen , Bergen, Norway
| | - Naim Saglam
- Department of Aquaculture and Fish Diseases, Fisheries Faculty, Firat University , Elazig 23119, Turkey
| | - Jesamine Bartlett
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research , Trondheim, Norway
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University , Poznań, Poland
| | | | - Glenn Dunshea
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology , Trondheim 7491, Norway
| | - Einar Arnason
- Institute of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7 , Reykjavík, Iceland
| | - Jørgen Rosvold
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research , Trondheim, Norway
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3
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Wilson CG, Pieszko T, Nowell RW, Barraclough TG. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet 2024; 40:422-436. [PMID: 38458877 DOI: 10.1016/j.tig.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.
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Affiliation(s)
- Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Tymoteusz Pieszko
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Reuben W Nowell
- Institute of Ecology and Evolution, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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4
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Kiemel K, Gurke M, Paraskevopoulou S, Havenstein K, Weithoff G, Tiedemann R. Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species. Sci Rep 2022; 12:22626. [PMID: 36587065 PMCID: PMC9805463 DOI: 10.1038/s41598-022-27137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
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Affiliation(s)
- K. Kiemel
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - M. Gurke
- grid.422371.10000 0001 2293 9957Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany ,grid.7468.d0000 0001 2248 7639Department of Biology, Humboldt-University, Invalidenstraße 42, 10115 Berlin, Germany
| | - S. Paraskevopoulou
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Microbiology Group, Sölvegatan 35, 223 62 Lund, Sweden
| | - K. Havenstein
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - G. Weithoff
- grid.11348.3f0000 0001 0942 1117Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
| | - R. Tiedemann
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
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5
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Terwagne M, Nicolas E, Hespeels B, Herter L, Virgo J, Demazy C, Heuskin AC, Hallet B, Van Doninck K. DNA repair during nonreductional meiosis in the asexual rotifer Adineta vaga. SCIENCE ADVANCES 2022; 8:eadc8829. [PMID: 36449626 PMCID: PMC9710870 DOI: 10.1126/sciadv.adc8829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Rotifers of the class Bdelloidea are microscopic animals notorious for their long-term persistence in the apparent absence of sexual reproduction and meiotic recombination. This evolutionary paradox is often counterbalanced by invoking their ability to repair environmentally induced genome breakage. By studying the dynamics of DNA damage response in the bdelloid species Adineta vaga, we found that it occurs rapidly in the soma, producing a partially reassembled genome. By contrast, germline DNA repair is delayed to a specific time window of oogenesis during which homologous chromosomes adopt a meiotic-like juxtaposed configuration, resulting in accurate reconstitution of the genome in the offspring. Our finding that a noncanonical meiosis is the mechanism of germline DNA repair in bdelloid rotifers gives previously unidentified insights on their enigmatic long-term evolution.
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Affiliation(s)
- Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
- Research Unit of Molecular Biology and Evolution (MBE), Université Libre de Bruxelles (ULB), Brussels, 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment (ILEE), University of Namur (UNamur), Namur 5000, Belgium
| | - Ludovic Herter
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Catherine Demazy
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Cellular Biology Research Unit (URBC), University of Namur (UNamur), Namur 5000, Belgium
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Bernard Hallet
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Research Unit of Molecular Biology and Evolution (MBE), Université Libre de Bruxelles (ULB), Brussels, 1050, Belgium
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment (ILEE), University of Namur (UNamur), Namur 5000, Belgium
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6
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Stec D, Cancellario T, Fontaneto D. Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00578-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractUnderstanding the dynamics of speciation and extinction events is one of the most interesting subjects in evolutionary biology that relates to all life forms, even the smallest ones. Tardigrades are microscopic invertebrates that attracted public and scientific attention mostly due to their ability to enter into the diapause stage called cryptobiosis and in such stage resist extremely harsh environmental conditions. However, although recent research solved a considerable number of phylogenetic uncertainties and further uncovered physiological mechanisms of cryptobiosis, not much attention is given to the evolutionary forces shaping tardigrade diversity. Here, we investigated the effect of reproductive mode on diversification rates in tardigrades using three groups: macrobiotids, echiniscids and milnesids, which represent low, moderate and high levels of parthenogenesis, respectively. Our results showed a decreasing tempo of diversification events for each of the studied groups without any differences that could be ascribed to reproductive mode. We discussed the observed lack of effect in tardigrades acknowledging deficiencies in available data sets and encouraging further studies to understand whether our results can be considered reliable.
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7
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Rasouli-Dogaheh S, Komárek J, Chatchawan T, Hauer T. Thainema gen. nov. (Leptolyngbyaceae, Synechococcales): A new genus of simple trichal cyanobacteria isolated from a solar saltern environment in Thailand. PLoS One 2022; 17:e0261682. [PMID: 34995289 PMCID: PMC8741055 DOI: 10.1371/journal.pone.0261682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Simple trichal types constitute a group of cyanobacteria with an abundance of novel, often cryptic taxa. Here, we investigated material collected from wet surface-soil in a saline environment in Petchaburi Province, central Thailand. A morphological comparison of the isolated strain with similar known species, as well as its phylogenetic and species delimitation analyses based on the combined datasets of other related organisms, especially simple trichal cyanobacteria, revealed that the material of this study represented an independent taxon. Using a multifaceted method, we propose that this material represents a new genus, Thainema gen. nov., belonging to the family Leptolyngbyaceae, with the type species Thainema salinarum sp. nov. This novel taxon shares similar ecological habitats with strains previously placed in the same lineage.
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Affiliation(s)
- Somayeh Rasouli-Dogaheh
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jiří Komárek
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Thomrat Chatchawan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Tomáš Hauer
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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8
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Moreira MO, Fonseca C, Rojas D. Parthenogenesis is self-destructive for scaled reptiles. Biol Lett 2021; 17:20210006. [PMID: 33975486 PMCID: PMC8113917 DOI: 10.1098/rsbl.2021.0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
Parthenogenesis is rare in nature. With 39 described true parthenogens, scaled reptiles (Squamata) are the only vertebrates that evolved this reproductive strategy. Parthenogenesis is ecologically advantageous in the short term, but the young age and rarity of parthenogenetic species indicate it is less advantageous in the long term. This suggests parthenogenesis is self-destructive: it arises often but is lost due to increased extinction rates, high rates of reversal or both. However, this role of parthenogenesis as a self-destructive trait remains unknown. We used a phylogeny of Squamata (5388 species), tree metrics, null simulations and macroevolutionary scenarios of trait diversification to address the factors that best explain the rarity of parthenogenetic species. We show that parthenogenesis can be considered as self-destructive, with high extinction rates mainly responsible for its rarity in nature. Since these parthenogenetic species occur, this trait should be ecologically relevant in the short term.
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Affiliation(s)
- Matthew Owen Moreira
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
- ForestWISE - Collaborative Laboratory for Integrated Forest and Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
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9
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Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun 2020; 11:6421. [PMID: 33339818 PMCID: PMC7749112 DOI: 10.1038/s41467-020-19614-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.
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Affiliation(s)
- Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation.
| | - Elena A Mnatsakanova
- Department of General Ecology and Hydrobiology, Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Yan R Galimov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
| | - Tatiana V Neretina
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, 119435, Russian Federation
| | - Sergey A Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Svetlana G Ozerova
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
- Medkvadrat, Moscow, 115409, Russian Federation
| | - Arthur O Zalevsky
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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10
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Gaytán Á, Bergsten J, Canelo T, Pérez-Izquierdo C, Santoro M, Bonal R. DNA Barcoding and geographical scale effect: The problems of undersampling genetic diversity hotspots. Ecol Evol 2020; 10:10754-10772. [PMID: 33072294 PMCID: PMC7548170 DOI: 10.1002/ece3.6733] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 01/25/2023] Open
Abstract
DNA barcoding identification needs a good characterization of intraspecific genetic divergence to establish the limits between species. Yet, the number of barcodes per species is many times low and geographically restricted. A poor coverage of the species distribution range may hamper identification, especially when undersampled areas host genetically distinct lineages. If so, the genetic distance between some query sequences and reference barcodes may exceed the maximum intraspecific threshold for unequivocal species assignation. Taking a group of Quercus herbivores (moths) in Europe as model system, we found that the number of DNA barcodes from southern Europe is proportionally very low in the Barcoding of Life Data Systems. This geographical bias complicates the identification of southern query sequences, due to their high intraspecific genetic distance with respect to barcodes from higher latitudes. Pairwise intraspecific genetic divergence increased along with spatial distance, but was higher when at least one of the sampling sites was in southern Europe. Accordingly, GMYC (General Mixed Yule Coalescent) single-threshold model retrieved clusters constituted exclusively by Iberian haplotypes, some of which could correspond to cryptic species. The number of putative species retrieved was more reliable than that of multiple-threshold GMYC but very similar to results from ABGD and jMOTU. Our results support GMYC as a key resource for species delimitation within poorly inventoried biogeographic regions in Europe, where historical factors (e.g., glaciations) have promoted genetic diversity and singularity. Future European DNA barcoding initiatives should be preferentially performed along latitudinal gradients, with special focus on southern peninsulas.
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Affiliation(s)
- Álvaro Gaytán
- Department of Ecology Environment and Plant Sciences Stockholm University Stockholm Sweden.,Research Group on Genetic and Cultural Biodiversity - IREC - (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Johannes Bergsten
- Department of Zoology Swedish Museum of Natural History Stockholm Sweden
| | - Tara Canelo
- Forest Research Group INDEHESA University of Extremadura Plasencia Spain
| | | | - Maria Santoro
- Research Group on Genetic and Cultural Biodiversity - IREC - (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Raul Bonal
- Research Group on Genetic and Cultural Biodiversity - IREC - (CSIC, UCLM, JCCM) Ciudad Real Spain.,Forest Research Group INDEHESA University of Extremadura Plasencia Spain
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11
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García-Morales AE, Domínguez-Domínguez O. Cryptic species within the rotifer Lecane bulla (Rotifera: Monogononta: Lecanidae) from North America based on molecular species delimitation. REV MEX BIODIVERS 2020. [DOI: 10.22201/ib.20078706e.2020.91.3116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Leria L, Vila-Farré M, Solà E, Riutort M. Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex. BMC Evol Biol 2019; 19:130. [PMID: 31221097 PMCID: PMC6587288 DOI: 10.1186/s12862-019-1440-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/15/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Predicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller's Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the Meselson effect and Muller's Ratchet. Dugesiidae planarians show outstanding regeneration capabilities, allowing them to naturally reproduce by fission, either strictly or combined with sex (facultative). Therefore, they are an ideal model to analyze the genetic footprint of fissiparous reproduction, both when it is alternated with sex and when it is the only mode of reproduction. RESULTS In the present study, we generate and analyze intraindividual cloned data of a nuclear and a mitochondrial gene of sexual, fissiparous and facultative wild populations of the species Dugesia subtentaculata. We find that most individuals, independently of their reproductive strategy, are mosaics. However, the intraindividual haplotype and nucleotide diversity of fissiparous and facultative individuals is significantly higher than in sexual individuals, with no signs of Muller's Ratchet. Finally, we also find that this high intraindividual genetic diversity of fissiparous and facultative individuals is composed by different combinations of ancestral and derived haplotypes of the species. CONCLUSIONS The intraindividual analyses of genetic diversity point out that fissiparous reproduction leaves a very special genetic footprint in individuals, characterized by mosaicism combined with the Meselson effect (named in the present study as the mosaic Meselson effect). Interestingly, the different intraindividual combinations of ancestral and derivate genetic diversity indicate that haplotypes generated during periods of fissiparous reproduction can be also transmitted to the progeny through sexual events, resulting in offspring showing a wide range of genetic diversity and putatively allowing purifying selection to act at both intraindividual and individual level. Further investigations, using Dugesia planarians as model organisms, would be of great value to delve into this new model of genetic evolution by the combination of fission and sex.
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Affiliation(s)
- Laia Leria
- Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia Spain
| | - Miquel Vila-Farré
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Eduard Solà
- Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia Spain
| | - Marta Riutort
- Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia Spain
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Kaczmarek Ł, Roszkowska M, Fontaneto D, Jezierska M, Pietrzak B, Wieczorek R, Poprawa I, Kosicki JZ, Karachitos A, Kmita H. Staying young and fit? Ontogenetic and phylogenetic consequences of animal anhydrobiosis. J Zool (1987) 2019. [DOI: 10.1111/jzo.12677] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ł. Kaczmarek
- Department of Animal Taxonomy and Ecology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - M. Roszkowska
- Department of Animal Taxonomy and Ecology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - D. Fontaneto
- National Research Council Water Research Institute (CNR‐IRSA) Verbania Italy
| | - M. Jezierska
- Department of Animal Histology and Embryology University of Silesia in Katowice Katowice Poland
| | - B. Pietrzak
- Department of Hydrobiology Faculty of Biology Biological and Chemical Research Centre University of Warsaw Warszawa Poland
| | - R. Wieczorek
- Faculty of Chemistry University of Warsaw Warsaw Poland
| | - I. Poprawa
- Department of Animal Histology and Embryology University of Silesia in Katowice Katowice Poland
| | - J. Z. Kosicki
- Department of Avian Biology and Ecology Faculty of Biology Adam Mickiewicz University Poznan Poznań Poland
| | - A. Karachitos
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - H. Kmita
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
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Hagen F, Lumbsch HT, Arsic Arsenijevic V, Badali H, Bertout S, Billmyre RB, Bragulat MR, Cabañes FJ, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom MF, Cornely OA, Crous PW, Cuétara MS, Diaz MR, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert PF, Ferrer Rodríguez C, Fraser JA, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi MT, Khan Z, Khayhan K, Kolecka A, Kurtzman CP, Lagrou K, Liao W, Linares C, Meis JF, Nielsen K, Nyazika TK, Pan W, Pekmezovic M, Polacheck I, Posteraro B, de Queiroz Telles F, Romeo O, Sánchez M, Sampaio A, Sanguinetti M, Sriburee P, Sugita T, Taj-Aldeen SJ, Takashima M, Taylor JW, Theelen B, Tomazin R, Verweij PE, Wahyuningsih R, Wang P, Boekhout T. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. mSphere 2017; 2:e00238-17. [PMID: 28875175 PMCID: PMC5577652 DOI: 10.1128/msphere.00238-17] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.
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Affiliation(s)
- Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | | | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Sebastien Bertout
- Unité Mixte Internationale Recherches Translationnelles sur l’Infection à VIH et les Maladies Infectieuses, Laboratoire de Parasitologie et Mycologie Médicale, UFR Pharmacie, Université Montpellier, Montpellier, France
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - M. Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F. Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mauricio Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Oliver A. Cornely
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
- Center for Clinical Trials, University Hospital Cologne, Cologne, Germany
| | - Pedro W. Crous
- Phytopathology Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Maria S. Cuétara
- Department of Microbiology, Hospital Severo Ochoa, Madrid, Spain
| | - Mara R. Diaz
- University of Miami, NSF NIEHS Oceans and Human Health Center, Miami, Florida, USA
- Rosentiel School of Marine and Atmospheric Science, Division of Marine Biology and Fisheries, University of Miami, Miami, Florida, USA
| | | | - Hamed Fakhim
- Department of Medical Parasitology and Mycology/Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
- Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Patricia F. Herkert
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | | | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Josep Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Alexander Idnurm
- School of BioSciences, BioSciences 2, University of Melbourne, Melbourne, Australia
| | | | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Katrien Lagrou
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Carlos Linares
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tinashe K. Nyazika
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Malawi-Liverpool-Wellcome Trust, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Tropical Medicine, Liverpool, United Kingdom
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Flavio de Queiroz Telles
- Department of Communitarian Health, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- IRCCS Centro Neurolesi Bonino-Pulejo, Messina, Italy
| | - Manuel Sánchez
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Ana Sampaio
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, Vila Real, Portugal
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Pojana Sriburee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan
| | - Saad J. Taj-Aldeen
- Mycology Unit, Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Bart Theelen
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paul E. Verweij
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, School of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Ping Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Teun Boekhout
- Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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16
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Gonzalez BC, Martínez A, Borda E, Iliffe TM, Fontaneto D, Worsaae K. Genetic spatial structure of an anchialine cave annelid indicates connectivity within - but not between - islands of the Great Bahama Bank. Mol Phylogenet Evol 2017; 109:259-270. [DOI: 10.1016/j.ympev.2017.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 12/30/2016] [Accepted: 01/04/2017] [Indexed: 12/18/2022]
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Koenders A, Schön I, Halse S, Martens K. Valve shape is not linked to genetic species in theEucypris virens(Ostracoda, Crustacea) species complex. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Annette Koenders
- Centre for Ecosystem Management; Edith Cowan University; 270 Joondalup Dv Joondalup WA 6027 Australia
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature; Freshwater Biology; Vautierstraat 29 B-1000 Brussels Belgium
- Research Group Zoology; University of Hasselt; Agoralaan Building D B-3590 Diepenbeek Belgium
| | - Stuart Halse
- Bennelongia Environmental Consultants; 5 Bishop Street Jolimont WA 6014 Australia
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature; Freshwater Biology; Vautierstraat 29 B-1000 Brussels Belgium
- Department of Biology; University of Ghent; K.L. Ledeganckstraat 35 B-9000 Gent Belgium
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Shain DH, Halldórsdóttir K, Pálsson F, Aðalgeirsdóttir G, Gunnarsson A, Jónsson Þ, Lang SA, Pálsson HS, Steinþórssson S, Arnason E. Colonization of maritime glacier ice by bdelloid Rotifera. Mol Phylogenet Evol 2016; 98:280-7. [DOI: 10.1016/j.ympev.2016.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/22/2016] [Accepted: 02/22/2016] [Indexed: 11/26/2022]
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Debortoli N, Li X, Eyres I, Fontaneto D, Hespeels B, Tang CQ, Flot JF, Van Doninck K. Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex. Curr Biol 2016; 26:723-32. [PMID: 26948882 DOI: 10.1016/j.cub.2016.01.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/27/2015] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
Although strict asexuality is supposed to be an evolutionary dead end, morphological, cytogenetic, and genomic data suggest that bdelloid rotifers, a clade of microscopic animals, have persisted and diversified for more than 60 Myr in an ameiotic fashion. Moreover, the genome of bdelloids of the genus Adineta comprises 8%-10% of genes of putative non-metazoan origin, indicating that horizontal gene transfers are frequent within this group and suggesting that this mechanism may also promote genetic exchanges among bdelloids as well. To test this hypothesis, we used five independent sequence markers to study the genetic diversity of 576 Adineta vaga individuals from a park in Belgium. Haplowebs and GMYC analyses revealed the existence of six species among our sampled A. vaga individuals, with strong evidence of both intra- and interspecific recombination. Comparison of genomic regions of three allele-sharing individuals further revealed signatures of genetic exchanges scattered among regions evolving asexually. Our findings suggest that bdelloids evolve asexually but exchange DNA horizontally both within and between species.
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Affiliation(s)
- Nicolas Debortoli
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Xiang Li
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Isobel Eyres
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Diego Fontaneto
- Institute of Ecosystem Study, National Research Council, Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Cuong Q Tang
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jean-François Flot
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium.
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
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Eyres I, Boschetti C, Crisp A, Smith TP, Fontaneto D, Tunnacliffe A, Barraclough TG. Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. BMC Biol 2015; 13:90. [PMID: 26537913 PMCID: PMC4632278 DOI: 10.1186/s12915-015-0202-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/20/2015] [Indexed: 11/26/2022] Open
Abstract
Background Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer in multicellular eukaryotes. Bdelloid rotifers are microscopic animals that contain a higher proportion of horizontally transferred, non-metazoan genes in their genomes than typical of animals. It has been hypothesized that bdelloids incorporate foreign DNA when they repair their chromosomes following double-strand breaks caused by desiccation. HGT might thereby contribute to species divergence and adaptation, as in prokaryotes. If so, we expect that species should differ in their complement of foreign genes, rather than sharing the same set of foreign genes inherited from a common ancestor. Furthermore, there should be more foreign genes in species that desiccate more frequently. We tested these hypotheses by surveying HGT in four congeneric species of bdelloids from different habitats: two from permanent aquatic habitats and two from temporary aquatic habitats that desiccate regularly. Results Transcriptomes of all four species contain many genes with a closer match to non-metazoan genes than to metazoan genes. Whole genome sequencing of one species confirmed the presence of these foreign genes in the genome. Nearly half of foreign genes are shared between all four species and an outgroup from another family, but many hundreds are unique to particular species, which indicates that HGT is ongoing. Using a dated phylogeny, we estimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years. Consistent with the desiccation hypothesis, the level of HGT is higher in the species that experience regular desiccation events than those that do not. However, HGT still contributed hundreds of foreign genes to the species from permanently aquatic habitats. Foreign genes were mainly enzymes with various annotated functions that include catabolism of complex polysaccharides and stress responses. We found evidence of differential loss of ancestral foreign genes previously associated with desiccation protection in the two non-desiccating species. Conclusions Nearly half of foreign genes were acquired before the divergence of bdelloid families over 60 Mya. Nonetheless, HGT is ongoing in bdelloids and has contributed to putative functional differences among species. Variation among our study species is consistent with the hypothesis that desiccating habitats promote HGT. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0202-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isobel Eyres
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Alastair Crisp
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Thomas P Smith
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.
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Vogt G, Falckenhayn C, Schrimpf A, Schmid K, Hanna K, Panteleit J, Helm M, Schulz R, Lyko F. The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals. Biol Open 2015; 4:1583-94. [PMID: 26519519 PMCID: PMC4728364 DOI: 10.1242/bio.014241] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
The parthenogenetic all-female marbled crayfish is a novel research model and potent invader of freshwater ecosystems. It is a triploid descendant of the sexually reproducing slough crayfish, Procambarus fallax, but its taxonomic status has remained unsettled. By cross-breeding experiments and parentage analysis we show here that marbled crayfish and P. fallax are reproductively separated. Both crayfish copulate readily, suggesting that the reproductive barrier is set at the cytogenetic rather than the behavioural level. Analysis of complete mitochondrial genomes of marbled crayfish from laboratory lineages and wild populations demonstrates genetic identity and indicates a single origin. Flow cytometric comparison of DNA contents of haemocytes and analysis of nuclear microsatellite loci confirm triploidy and suggest autopolyploidisation as its cause. Global DNA methylation is significantly reduced in marbled crayfish implying the involvement of molecular epigenetic mechanisms in its origination. Morphologically, both crayfish are very similar but growth and fecundity are considerably larger in marbled crayfish, making it a different animal with superior fitness. These data and the high probability of a divergent future evolution of the marbled crayfish and P. fallax clusters suggest that marbled crayfish should be considered as an independent asexual species. Our findings also establish the P. fallax-marbled crayfish pair as a novel paradigm for rare chromosomal speciation by autopolyploidy and parthenogenesis in animals and for saltational evolution in general.
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Affiliation(s)
- Günter Vogt
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Cassandra Falckenhayn
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Anne Schrimpf
- Institute for Environmental Sciences, University of Koblenz-Landau, Forststrasse 7, 76829 Landau, Germany
| | - Katharina Schmid
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Jörn Panteleit
- Institute for Environmental Sciences, University of Koblenz-Landau, Forststrasse 7, 76829 Landau, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Ralf Schulz
- Institute for Environmental Sciences, University of Koblenz-Landau, Forststrasse 7, 76829 Landau, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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Rovira L, Trobajo R, Sato S, Ibáñez C, Mann DG. Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua. J Eukaryot Microbiol 2015; 62:815-32. [DOI: 10.1111/jeu.12240] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Laia Rovira
- Aquatic Ecosystems; Institute for Food and Agricultural Research and Technology (IRTA); St. Carles de la Ràpita 43540 Catalonia Spain
| | - Rosa Trobajo
- Aquatic Ecosystems; Institute for Food and Agricultural Research and Technology (IRTA); St. Carles de la Ràpita 43540 Catalonia Spain
| | - Shinya Sato
- Laboratory of Marine Bioscience; Fukui Prefectural Univeristy; 1-1 Gauken-Cho Obama City Fukui 917-0003 Japan
| | - Carles Ibáñez
- Aquatic Ecosystems; Institute for Food and Agricultural Research and Technology (IRTA); St. Carles de la Ràpita 43540 Catalonia Spain
| | - David G. Mann
- Aquatic Ecosystems; Institute for Food and Agricultural Research and Technology (IRTA); St. Carles de la Ràpita 43540 Catalonia Spain
- Royal Botanic Garden Edinburgh; Edinburgh EH3 5LR United Kingdom
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Fontaneto D, Barraclough TG. Do Species Exist in Asexuals? Theory and Evidence from Bdelloid Rotifers. Integr Comp Biol 2015; 55:253-63. [PMID: 25912362 DOI: 10.1093/icb/icv024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The possibility for independently evolving entities to form and persist in the absence of sexual recombination in eukaryotes has been questioned; nevertheless, there are organisms that are known to be asexual and that have apparently diversified into multiple species as recognized by taxonomists. These organisms have therefore been identified as an evolutionary paradox. We explore three alternative hypotheses attempting to solve the apparent paradox, focusing on bdelloid rotifers, the most studied group of organisms in which all species are considered asexual: (1) they may have some hidden form of sex; (2) species do not represent biological entities but simply convenient names; and (3) sex may not be a necessary requirement for speciation. We provide ample evidence against the first two hypotheses, reporting several studies supporting (1) bdelloids asexuality from different approaches, and (2) the existence of species from genetics, jaw morphology, ecology, and physiology. Thus, we (3) explore the role of sex in speciation comparing bdelloid and monogonont rotifers, and conclude with some caveats that could still change our understanding of bdelloid species.
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Affiliation(s)
- Diego Fontaneto
- *National Research Council, Institute of Ecosystem Study, Largo Tonolli 50, 28922 Verbania Pallanza, Italy;
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Tang CQ, Humphreys AM, Fontaneto D, Barraclough TG, Paradis E. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data. Methods Ecol Evol 2014; 5:1086-1094. [PMID: 25821577 PMCID: PMC4374709 DOI: 10.1111/2041-210x.12246] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/13/2014] [Indexed: 11/27/2022]
Abstract
Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes.
Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods.
The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification.
Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.
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Affiliation(s)
- Cuong Q Tang
- Department of Life Sciences, Imperial College London Ascot, Berkshire, SL5 7PY, UK
| | - Aelys M Humphreys
- Department of Life Sciences, Imperial College London Ascot, Berkshire, SL5 7PY, UK ; Department of Ecology, Environment and Plant Sciences, Stockholm University 10691, Stockholm, Sweden
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study 28922, Verbania Pallanza, Italy
| | | | - Emmanuel Paradis
- Department of Life Sciences, Imperial College London Ascot, Berkshire, SL5 7PY, UK
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