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Kiemel K, Weithoff G, Tiedemann R. DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity. Mol Ecol 2023; 32:6190-6209. [PMID: 35869804 DOI: 10.1111/mec.16627] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2023]
Abstract
Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.
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Affiliation(s)
- Katrin Kiemel
- Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Guntram Weithoff
- Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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2
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Maturana CS, Biersma EM, Díaz A, González-Wevar C, Contador T, Convey P, Jackson JA, Poulin E. Survivors and colonizers: Contrasting biogeographic histories reconciled in the Antarctic freshwater copepod Boeckella poppei. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1012852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Two main hypotheses have been proposed to explain the contemporary distribution of Antarctic terrestrial biota. We assess whether the current distribution of maritime Antarctic populations of the freshwater copepod Boeckella poppei is the result of (1) a post-Last Glacial Maximum (LGM) colonization, or whether (2) the species survived in regional glacial refugia throughout the LGM and earlier glaciations. Using 438 specimens from 34 different sampling sites across Southern South America, South Georgia, South Orkney Islands, South Shetland Islands, and the Antarctic Peninsula, we analyzed mitochondrial and nuclear sequences to uncover patterns of genetic diversity and population structure. We also performed median-joining haplotype network, phylogenetic reconstruction, and divergence time analyses. Finally, we evaluated past demographic changes and historical scenarios using the Approximate Bayesian Computation (ABC) method. Our data support the existence of two clades with different and contrasting biogeographic histories. The first clade has been present in maritime Antarctica since at least the mid-Pleistocene, with the South Orkney Islands the most likely refugial area. The second clade has a broader distribution including southern South America, South Georgia, South Shetland Islands, and the Antarctic Peninsula. The ABC method identified long-distance dispersal (LDD) colonization event(s) from southern South America to South Georgia and the maritime Antarctic after the LGM deglaciation, supporting more recent colonization of Antarctic locations. The current Antarctic and sub-Antarctic distribution of B. poppei is likely derived from two independent biogeographic events. The combination of both (1) post-LGM colonization from southern South America and (2) longer-term persistence in in situ regional refugia throughout glacial periods challenges current understanding of the biogeographic history of Antarctic freshwater biota. Re-colonization of ice-impacted Antarctic areas would have occurred following a LDD and Establishment model, pointing to the existence of possible post-dispersal barriers, despite widely assumed high passive dispersal capacity in freshwater invertebrates.
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3
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Leigh DM, Peranić K, Prospero S, Cornejo C, Ćurković-Perica M, Kupper Q, Nuskern L, Rigling D, Ježić M. Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections. Virus Evol 2021; 7:veab101. [PMID: 35299787 PMCID: PMC8923234 DOI: 10.1093/ve/veab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
Intra-host dynamics are a core component of virus evolution but most intra-host data come from a narrow range of hosts or experimental infections. Gaining broader information on the intra-host diversity and dynamics of naturally occurring virus infections is essential to our understanding of evolution across the virosphere. Here we used PacBio long-read HiFi sequencing to characterize the intra-host populations of natural infections of the RNA mycovirus Cryphonectria hypovirus 1 (CHV1). CHV1 is a biocontrol agent for the chestnut blight fungus (Cryphonectria parasitica), which co-invaded Europe alongside the fungus. We characterized the mutational and haplotypic intra-host virus diversity of thirty-eight natural CHV1 infections spread across four locations in Croatia and Switzerland. Intra-host CHV1 diversity values were shaped by purifying selection and accumulation of mutations over time as well as epistatic interactions within the host genome at defense loci. Geographical landscape features impacted CHV1 inter-host relationships through restricting dispersal and causing founder effects. Interestingly, a small number of intra-host viral haplotypes showed high sequence similarity across large geographical distances unlikely to be linked by dispersal.
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Affiliation(s)
- Deborah M Leigh
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Karla Peranić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Simone Prospero
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Carolina Cornejo
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | | | | | - Lucija Nuskern
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Daniel Rigling
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Marin Ježić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
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Zuykova EI, Bochkarev NA, Kotov AA. Specific and Genetic Structure of the Daphnia longispina s. l. Complex (Cladocera, Daphniidae) in Water Bodies of Southern Siberia. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021070323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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5
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Martin GK, Beisner BE, Chain FJJ, Cristescu ME, Del Giorgio PA, Derry AM. Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation. Ecology 2020; 102:e03224. [PMID: 33067865 DOI: 10.1002/ecy.3224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/22/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022]
Abstract
Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales.
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Affiliation(s)
- Gillian K Martin
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Beatrix E Beisner
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Frédéric J J Chain
- Department of Biological Science, University of Massachusetts Lowell, Massachusetts, 01854, USA
| | - Melania E Cristescu
- Department of Biology, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), McGill University, Québec, H3A 1B1, Canada
| | - Paul A Del Giorgio
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
| | - Alison M Derry
- Department of Biological Sciences, Groupe de Recherche Interuniversitaire en Limnologie (GRIL), University of Québec at Montreal, Québec, H2X 3Y7, Canada
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6
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Millette KL, Gonzalez A, Cristescu ME. Breaking ecological barriers: Anthropogenic disturbance leads to habitat transitions, hybridization, and high genetic diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140046. [PMID: 32563876 DOI: 10.1016/j.scitotenv.2020.140046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Genetic diversity is expected to erode in disturbed habitats through strong selection, local extinctions, and recolonization associated with genetic bottlenecks and restricted gene flow. Despite this general prediction and over three decades of population genetics studies, our understanding of the long-term effect of environmental disturbance on local and regional genetic diversity remains limited. We conducted a population genetic survey of the microcrustacean Daphnia across a landscape subject to anthropogenic stressors from a century of industrial mining. At the local scale we found moderate genetic diversity (i.e., low clonal diversity), characteristic of habitat-specific selective sweeps and local extinctions, but high diversity and strong genetic structure at the regional scale despite the shared watershed of many lakes and exceptional dispersal ability of daphniids. Many habitats experienced changes in species assemblages, with the obligate asexual Daphnia pulex lineages-known only to inhabit ponds-dominating disrupted urban lakes. This habitat transition (pond to lake) was likely facilitated by the disruption of ecological barriers maintaining the genomic separation of these young species. Thus, disrupted habitats can exhibit complex and unexpected genetic patterns of local extinctions and recolonizations, followed by habitat transitions, hybridization and potential speciation events that are difficult to predict and should not be underestimated.
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Affiliation(s)
- Katie L Millette
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada; Quebec Centre for Biodiversity Science, Canada.
| | - Andrew Gonzalez
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada; Quebec Centre for Biodiversity Science, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada; Quebec Centre for Biodiversity Science, Canada
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7
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Lucati F, Poignet M, Miró A, Trochet A, Aubret F, Barthe L, Bertrand R, Buchaca T, Calvez O, Caner J, Darnet E, Denoël M, Guillaume O, Le Chevalier H, Martínez-Silvestre A, Mossoll-Torres M, O'Brien D, Osorio V, Pottier G, Richard M, Sabás I, Souchet J, Tomàs J, Ventura M. Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees. Mol Ecol 2020; 29:2904-2921. [PMID: 32563209 DOI: 10.1111/mec.15521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 12/31/2022]
Abstract
Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.
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Affiliation(s)
- Federica Lucati
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculty of Sciences, University of Lisbon, Lisbon, Portugal.,Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Manon Poignet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Alexandre Miró
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Audrey Trochet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France.,Société Herpétologique de France, Muséum National d'Histoire Naturelle, Paris, France
| | - Fabien Aubret
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Laurent Barthe
- Association Nature En Occitanie, Maison de l'Environnement de Midi-Pyrénées, Toulouse, France
| | - Romain Bertrand
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Teresa Buchaca
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Olivier Calvez
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Jenny Caner
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Elodie Darnet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liege, Liege, Belgium
| | - Olivier Guillaume
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Hugo Le Chevalier
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | | | | | | | - Víctor Osorio
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Gilles Pottier
- Association Nature En Occitanie, Maison de l'Environnement de Midi-Pyrénées, Toulouse, France
| | - Murielle Richard
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Ibor Sabás
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Jérémie Souchet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Jan Tomàs
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Marc Ventura
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
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8
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Rodríguez-Flores PC, Recuero E, Jiménez-Ruiz Y, García-París M. Limited long-distance dispersal success in a Western European fairy shrimp evidenced by nuclear and mitochondrial lineage structuring. Curr Zool 2020; 66:227-237. [PMID: 32440283 PMCID: PMC7234018 DOI: 10.1093/cz/zoz054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 11/12/2022] Open
Abstract
Anostraca are known by their ability for long-distance dispersal, but the existence in several species of deep, geographically structured mtDNA lineages suggests their populations are subjected to allopatric differentiation, isolation, and prevalence of local scale dispersion. Tanymastix stagnalis is one of the most widespread species of Anostraca and previous studies revealed an unclear geographical pattern of mtDNA genetic diversity. Here, we analyze populations from the Iberian and Italian Peninsulas, Central Europe, and Scandinavia, with the aim to characterize the patterns of genetic diversity in a spatio-temporal framework using mtDNA and nuclear markers to test gene flow among close populations. For these aims we built a time-calibrated phylogeny and carried out Bayesian phylogeographic analyses using a continuous diffusion model. Our results indicated that T. stagnalis presents a deeply structured genetic diversity, including 7 ancient lineages, some of them even predating the Pleistocene. The Iberian Peninsula harbors high diversity of lineages, with strong isolation and recent absence of gene flow between populations. Dispersal at local scale seems to be the prevailing dispersal mode of T. stagnalis, which exhibits a pattern of isolation-by-distance in the Iberian Peninsula. We remark the vulnerability of most of these lineages, given the limited known geographic distribution of some of them, and the high risk of losing important evolutionary potential for the species.
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Affiliation(s)
- Paula C Rodríguez-Flores
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid 28006, Spain
- Centre d’Estudis Avançats de Blanes (CEAB-CSIC), C. d’Accés Cala Sant Francesc 14, Blanes 17300, Spain
| | - Ernesto Recuero
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid 28006, Spain
| | - Yolanda Jiménez-Ruiz
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid 28006, Spain
| | - Mario García-París
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid 28006, Spain
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Ortiz‐Álvarez R, Cáliz J, Camarero L, Casamayor EO. Regional community assembly drivers and microbial environmental sources shaping bacterioplankton in an alpine lacustrine district (Pyrenees, Spain). Environ Microbiol 2019; 22:297-309. [DOI: 10.1111/1462-2920.14848] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Rüdiger Ortiz‐Álvarez
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Joan Cáliz
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Emilio O. Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
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10
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García-Roger EM, Lubzens E, Fontaneto D, Serra M. Facing Adversity: Dormant Embryos in Rotifers. THE BIOLOGICAL BULLETIN 2019; 237:119-144. [PMID: 31714860 DOI: 10.1086/705701] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An in-depth look at the basic aspects of dormancy in cyclic parthenogenetic organisms is now possible thanks to research efforts conducted over the past two decades with rotifer dormant embryos. In this review, we assemble and compose the current knowledge on four central themes: (1) distribution of dormancy in animals, with an overview on the phylogenetic distribution of embryo dormancy in metazoans, and (2) physiological and cellular processes involved in dormancy, with a strong emphasis on the dormant embryos of cyclically parthenogenetic monogonont rotifers; and discussions of (3) the selective pressures and (4) the evolutionary and population implications of dormancy in these animals. Dormancy in metazoans is a widespread phenomenon with taxon-specific features, and rotifers are among the animals in which dormancy is an intrinsic feature of their life cycle. Our review shows that embryo dormancy in rotifers shares common functional pathways with other taxa at the molecular and cellular level, despite the independent evolution of dormancy across phyla. These pathways include the arrest of similar metabolic routes and the usage of common metabolites for the stabilization of cellular structures and to confer stress resistance. We conclude that specific features of recurrent harsh environmental conditions are a powerful selective pressure for the fine-tuning of dormancy patterns in rotifers. We hypothesize that similar mechanisms at the organism level will lead to similar adaptive consequences at the population level across taxa, among which the formation of egg banks, the coexistence of species, and the possibility of differentiation among populations and local adaptation stand out. Our review shows how studies of rotifers have contributed to improved knowledge of all of these aspects.
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Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia. PLoS One 2019; 14:e0221527. [PMID: 31479467 PMCID: PMC6719860 DOI: 10.1371/journal.pone.0221527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 02/01/2023] Open
Abstract
The biological significance of regional cladoceran morphotypes in the montane regions of the central Palearctic remains poorly understood. In the Holarctic Daphnia longispina complex (Cladocera: Daphniidae), several variants, lineages and species have been proposed as endemic for Southern Siberia. Daphnia turbinata Sars, for example, named after its unusual head shape, is known only from Southern Siberia. Here we sequence DNA of Daphnia from three mitochondrial genes (12S rRNA, 16S rRNA, and NADH dehydrogenase subunit 2, ND2) from 57 localities in Russia and Mongolia (the majority being from Southern Siberia) and place them in evolutionary context with existing data. Our aim was to examine regional endemism of the Daphnia longispina complex in Southern Siberian; to improve the phylogenetic understanding with improved taxonomic and regional sampling, and to better understand the influence of Pleistocene glaciation on the biogeography of these lineages. At least three lineages showed genetic evidence for endemism in Southern Siberia. There was strong support for D. turbinata as a sister lineage to to D. longispina/D. dentifera. Another endemic, Siberian D. cf. longispina, is a sister group to the longispina group in general. Within D. longispina s. str. there was an endemic Siberian clade with a western range boundary near the Yenisei River Basin. Gene flow estimates among populations (based on FST values) were very low for clades of D. longispina on a regional (the original 12S dataset), and on a pan-Eurasian (the extended 12S dataset) scale. Negative values of Fu’s FS and Tajima’s D tests prevailed for the species examined with significant values found for two D. longispina clades, D. dentifera, D. galeata and D. cristata. Our results support the notion that Southern Siberia is an important biogeographic region for cladocerans as it contained unexpected diversity of endemics (such as D. turbinata, D. cf. longispina and lineages of D. umbra and D. longsipina s.str.) and from being the geographic meeting place of expanding postglacial lineages from eastern and western refugia.
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13
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Zuykova EI. Identification and Phylogeny of Cryptic Species of the Daphnia Longispina Complex (Anomopoda, Daphniidae) Using ITS2 Secondary Structure. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541905017x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Hessen DO, Jensen TC, Walseng B. Zooplankton Diversity and Dispersal by Birds; Insights From Different Geographical Scales. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Vávra J, Fiala I, Krylová P, Petrusek A, Hyliš M. Establishment of a new microsporidian genus and species, Pseudoberwaldia daphniae (Microsporidia, Opisthosporidia), a common parasite of the Daphnia longispina complex in Europe. J Invertebr Pathol 2019; 162:43-54. [DOI: 10.1016/j.jip.2019.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 01/10/2023]
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16
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Ravindran SP, Herrmann M, Cordellier M. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. Ecol Evol 2019; 9:2487-2504. [PMID: 30891195 PMCID: PMC6405927 DOI: 10.1002/ece3.4894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.
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Affiliation(s)
| | - Maike Herrmann
- Department of Veterinary MedicinePaul‐Ehrlich‐InstitutLangenGermany
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17
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Zuykova EI, Simonov EP, Bochkarev NA, Abramov SA, Sheveleva NG, Kotov AA. Contrasting phylogeographic patterns and demographic history in closely related species of Daphnia longispina group (Crustacea: Cladocera) with focus on North-Eastern Eurasia. PLoS One 2018; 13:e0207347. [PMID: 30427905 PMCID: PMC6235318 DOI: 10.1371/journal.pone.0207347] [Citation(s) in RCA: 12] [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: 06/23/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Species with large geographic distributions present a challenge for phylogeographic studies due to the logistic difficulties of obtaining adequate samples. Daphnia O.F. Müller (Anomopoda: Daphniidae) is a model genus for evolutionary biology and ecology, but many regions such as the remote areas of Siberia, remain poorly studied. Here we examined genetic polymorphism in the ribosomal 12S and the protein-coding ND2 mitochondrial genes of three closely related taxa of the Daphnia (Daphnia) longispina complex, namely D. galeata Sars, D. longispina O.F. Müller and D. dentifera Forbes. We estimated the phylogenetic relationships among these taxa based on a concatenated alignment of these two genes. Using sequences from the present study and those available in GenBank, we investigated the geographic distributions of the mitochondrial haplotypes of these species and proposed an evolutionary scenario for each taxon. Network structures, haplotype distribution patterns, and FST values indicated significant differences in the evolutionary history of the examined species. Our analysis of D. galeata populations confirmed its recent and fast expansion, without a previous phase of a strong population disconnection. In contrast, the high haplotype diversity in D. dentifera and D. longispina could be explained by the survival of different phylogroups in several glacial refugia located in different geographic regions. For all studied species, maximum haplotype diversity was recorded in the remote regions of Siberia-lakes of the Yenisei River and Transbaikalia. Our study is an important step in our understanding of the evolutionary history of the Daphnia longispina group and provides further evidence of the biogeographic significance of Siberia for freshwater taxa.
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Affiliation(s)
- Elena I. Zuykova
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniy P. Simonov
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nickolai A. Bochkarev
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey A. Abramov
- Laboratory for Ecology of Vertebrate Communities, Institute of Systematics and Ecology of Animals of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia G. Sheveleva
- Laboratory of Biology of Aquatic Invertebrates, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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18
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Yin M, Wang X, Ma X, Gießler S, Petrusek A, Griebel J, Hu W, Wolinska J. Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres. BMC Evol Biol 2018; 18:130. [PMID: 30176793 PMCID: PMC6122193 DOI: 10.1186/s12862-018-1256-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 08/27/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci. RESULTS Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe. CONCLUSIONS Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.
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Affiliation(s)
- Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China.
| | - Xiaoyu Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Sabine Gießler
- Department Biologie II, Aquatic Evolutionary Ecology, Ludwig-Maximilians-Universität, Großhaderner Str. 2, 82152 Planegg-, Martinsried, Germany
| | - Adam Petrusek
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, 12844, Prague, Czechia
| | - Johanna Griebel
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mueggelseedamm 301, 12587, Berlin, Germany
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road, Shanghai, 2005, China
| | - Justyna Wolinska
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mueggelseedamm 301, 12587, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str. 1-3, 14195, Berlin, Germany
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19
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Zuykova EI, Simonov EP, Bochkarev NA, Taylor DJ, Kotov AA. Resolution of the Daphnia umbra problem (Crustacea: Cladocera) using an integrated taxonomic approach. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Elena I Zuykova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniy P Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Siberian Federal University, Svobodny pr., Krasnoyarsk, Russia
| | - Nikolay A Bochkarev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution, Leninsky Prospect, Moscow, Russia
- Kazan Federal University, Kazan, Russia
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20
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Xu L, Lin Q, Xu S, Gu Y, Hou J, Liu Y, Dumont HJ, Han B. Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy. Ecol Evol 2018; 8:5069-5078. [PMID: 29876082 PMCID: PMC5980554 DOI: 10.1002/ece3.4071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 02/04/2023] Open
Abstract
Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4-year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.
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Affiliation(s)
- Lei Xu
- South China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Institute of HydrobiologyJinan UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Fishery Ecology and EnvironmentGuangzhouChina
- Key Laboratory of South China Sea Fishery ResourcesDevelopment and UtilizationMinistry of AgricultureGuangzhouChina
| | - Qiuqi Lin
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Shaolin Xu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Yangliang Gu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Juzhi Hou
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | - Yongqin Liu
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | | | - Bo‐Ping Han
- Institute of HydrobiologyJinan UniversityGuangzhouChina
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21
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Tethyan changes shaped aquatic diversification. Biol Rev Camb Philos Soc 2017; 93:874-896. [DOI: 10.1111/brv.12376] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 01/19/2023]
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22
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Tokishita SI, Shibuya H, Kobayashi T, Sakamoto M, Ha JY, Yokobori SI, Yamagata H, Hanazato T. Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): Comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan. Gene 2017; 611:38-46. [PMID: 28219780 DOI: 10.1016/j.gene.2017.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/20/2017] [Accepted: 02/13/2017] [Indexed: 02/02/2023]
Abstract
To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions. Several non-synonymous substitutions were found in ATPase8 and ATPase6 even in the comparison that no synonymous substitution was found. Comparison of the total number of nt variations among the mt DNAs suggested the phylogenetic relationship ((((Shirakaba/Suwa, Kizaki), Kasumigaura), Biwa), D. pulex). Maximum-likelihood analysis using the total nt sequences of mt protein-coding genes confirmed this relationship with bootstrap values higher than 98%. All the mtDNAs of the analyzed Japanese D. galeata clones contained a control region of essentially the same structure that is distinct from those of the previously reported European Daphnia species of the D. longispina complex. The two control regions of different structures spread among mtDNAs of the Japanese and European Daphnia species, respectively, probably after the divergence of the Japanese D. galeata under different selection pressures associated with their habitats.
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Affiliation(s)
- Shin-Ichi Tokishita
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Hiroyuki Shibuya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Taku Kobayashi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Masaki Sakamoto
- Department of Environmental Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Jin-Yong Ha
- Department of Environmental Sciences, Faculty of Science, Shinshu University, Matsumoto Asahi 3-1-1, Nagano 390-8621, Japan
| | - Shin-Ichi Yokobori
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hideo Yamagata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Takayuki Hanazato
- Suwa Hydrobiological Station, Shinshu University, 5-2-4 Kogandori, Suwa, Nagano 392-0027, Japan
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Muñoz J, Chaturvedi A, De Meester L, Weider LJ. Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS). Sci Rep 2016; 6:28569. [PMID: 27346179 PMCID: PMC4921830 DOI: 10.1038/srep28569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/01/2016] [Indexed: 12/01/2022] Open
Abstract
The keystone aquatic herbivore Daphnia has been studied for more than 150 years in the context of evolution, ecology and ecotoxicology. Although it is rapidly becoming an emergent model for environmental and population genomics, there have been limited genome-wide level studies in natural populations. We report a unique resource of novel Single Nucleotide Polymorphic (SNP) markers for Daphnia pulicaria using the reduction in genomic complexity with the restriction enzymes approach, genotyping-by-sequencing. Using the genome of D. pulex as a reference, SNPs were scored for 53 clones from five natural populations that varied in lake trophic status. Our analyses resulted in 32,313 highly confident and bi-allelic SNP markers. 1,364 outlier SNPs were mapped on the annotated D. pulex genome, which identified 2,335 genes, including 565 within functional genes. Out of 885 EuKaryotic Orthologous Groups that we found from outlier SNPs, 294 were involved in three metabolic and four regulatory pathways. Bayesian-clustering analyses showed two distinct population clusters representing the possible combined effects of geography and lake trophic status. Our results provide an invaluable tool for future population genomics surveys in Daphnia targeting informative regions related to physiological processes that can be linked to the ecology of this emerging eco-responsive taxon.
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Affiliation(s)
- Joaquín Muñoz
- Doñana Biological Station (CSIC), Isla de La Cartuja, Av. Américo Vespucio S/N, 41092-Seville, Spain.,Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Anurag Chaturvedi
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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24
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Haileselasie TH, Mergeay J, Weider LJ, Jeppesen E, De Meester L. Colonization history and clonal richness of asexual Daphnia in periglacial habitats of contrasting age in West Greenland. J Anim Ecol 2016; 85:1108-17. [PMID: 27279332 DOI: 10.1111/1365-2656.12513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/25/2016] [Indexed: 12/01/2022]
Abstract
Due to climate change, Arctic ice sheets are retreating. This leads to the formation of numerous new periglacial ponds and lakes, which are being colonized by planktonic organisms such as the water flea Daphnia. This system provides unique opportunities to test genotype colonization dynamics and the genetic assemblage of populations. Here, we studied clonal richness of the Daphnia pulex species complex in novel periglacial habitats created by glacial retreat in the Jakobshavn Isbrae area of western Greenland. Along a 10 km transect, we surveyed 73 periglacial habitats out of which 61 were colonized by Daphnia pulex. Hence, for our analysis, we used 21 ponds and 40 lakes in two clusters of habitats differing in age (estimated <50 years vs. >150 years). We tested the expectation that genetic diversity would be low in recently formed (i.e. young), small habitats, but would increase with increasing age and size. We identified a total of 42 genetically distinct clones belonging to two obligately asexual species of the D. pulex species complex: D. middendorffiana and the much more abundant D. pulicaria. While regional clonal richness was high, most clones were rare: 16 clones were restricted to a single habitat and the five most widespread clones accounted for 68% of all individuals sampled. On average, 3·2 clones (range: 1-12) coexisted in a given pond or lake. There was no relationship between clonal richness and habitat size when we controlled for habitat age. Whereas clonal richness was statistically higher in the cluster of older habitats when compared with the cluster of younger ponds and lakes, most young habitats were colonized by multiple genotypes. Our data suggest that newly formed (periglacial) ponds and lakes are colonized within decades by multiple genotypes via multiple colonization events, even in the smallest of our study systems (4 m(2) ).
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Affiliation(s)
| | - Joachim Mergeay
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium.,Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, OK, 73071, USA
| | - Erik Jeppesen
- Department of Bioscience and Arctic Research Centre, Aarhus University, Silkeborg, Denmark.,Sino-Danish Centre for Education and Research (SDC), UCAS, Beijing, China
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
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25
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Dibble CJ, Rudolf VHW. Intraspecific trait variation and colonization sequence alter community assembly and disease epidemics. OIKOS 2016. [DOI: 10.1111/oik.02373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Volker H. W. Rudolf
- Dept of Ecology and Evolutionary Biology; Rice Univ.; MS 170 Houston TX 77005 USA
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26
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Sassenhagen I, Sefbom J, Säll T, Godhe A, Rengefors K. Freshwater protists do not go with the flow: population structure in
G
onyostomum semen
independent of connectivity among lakes. Environ Microbiol 2015; 17:5063-72. [DOI: 10.1111/1462-2920.12987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 01/08/2023]
Affiliation(s)
| | - Josefin Sefbom
- Department of Marine Sciences University of Gothenburg Box 461 Gothenburg 40530 Sweden
| | - Torbjörn Säll
- Evolutionary Genetics Lund University Sölvegatan 35 Lund 22362 Sweden
| | - Anna Godhe
- Department of Marine Sciences University of Gothenburg Box 461 Gothenburg 40530 Sweden
| | - Karin Rengefors
- Aquatic Ecology Lund University Sölvegatan 37 22362 Lund Sweden
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27
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Yin M, Li H, McManus DP, Blair D, Su J, Yang Z, Xu B, Feng Z, Hu W. Geographical genetic structure of Schistosoma japonicum revealed by analysis of mitochondrial DNA and microsatellite markers. Parasit Vectors 2015; 8:150. [PMID: 25881113 PMCID: PMC4372230 DOI: 10.1186/s13071-015-0757-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/20/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Schistosoma japonicum is a significant public health risk in parts of China and elsewhere in Southeast Asia. To gain an insight into the epidemiology of schistosomiasis japonica, a detailed investigation of S. japonicum genetic population structure is needed. METHODS Using three mitochondrial DNA fragments and ten microsatellite loci, we investigated the genetic diversity within and structure among twelve populations of S. japonicum sampled on a geographical scale covering most major endemic areas. RESULTS Schistosoma japonicum lineages from Indonesia, the Philippines and Chinese Taiwan were clearly distinct from each other and from those in mainland China. Within mainland China, there was some evidence for genetic divergence between populations from the mountain and lake regions. However, the analysis inferred no clear sub-population structure in the lake region of mainland China. High genetic diversity was found among S. japonicum populations of mainland China and this was significantly higher than those from island regions. CONCLUSIONS High genetic diversity within and substantial differentiation among populations were demonstrated in S. japonicum.
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Affiliation(s)
- Mingbo Yin
- School of Life Science, Fudan University, Handan Road 220, Shanghai, 200433, China.
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025, China.
| | - Hongyan Li
- School of Life Science, Fudan University, Handan Road 220, Shanghai, 200433, China.
| | - Donald P McManus
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Qld 4029, Australia.
| | - David Blair
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld 4811, Australia.
| | - Jing Su
- School of Life Science, Fudan University, Handan Road 220, Shanghai, 200433, China.
| | - Zhong Yang
- School of Life Science, Fudan University, Handan Road 220, Shanghai, 200433, China.
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025, China.
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025, China.
| | - Wei Hu
- School of Life Science, Fudan University, Handan Road 220, Shanghai, 200433, China.
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025, China.
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28
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Affiliation(s)
- David Johnson
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
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29
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Population structure of a microparasite infecting Daphnia: spatio-temporal dynamics. BMC Evol Biol 2014; 14:247. [PMID: 25471262 PMCID: PMC4265321 DOI: 10.1186/s12862-014-0247-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/18/2014] [Indexed: 11/21/2022] Open
Abstract
Background Detailed knowledge of spatial and temporal variation in the genetic population structure of hosts and parasites is required for understanding of host − parasite coevolution. As hot-spots of contemporary coevolution in natural systems are difficult to detect and long-term studies are restricted to few systems, additional population genetic data from various host − parasite systems may provide important insights into the topic. This is particularly true for parasites, as these players have been under-investigated so far due to the lower availability of suitable molecular markers. Here, we traced genetic variation (based on sequence variants in the internal transcribed spacer region, ITS) among seven geographically isolated populations of the ichthyosporean Caullerya mesnili, a common microparasite of the cladoceran Daphnia (here, the D. longispina hybrid complex). At three sites, we also studied parasite genetic variation over time (three to four sampling points) and tested for associations between parasite genotypes and host species. Results Parasite (and host) populations were significantly structured across space, indicating limited dispersal. Moreover, the frequency of parasite genotypes varied significantly over time, suggesting rapid evolutionary change in Caullerya. However, the distribution of parasite genotypes was similar across different host species, which might in turn have important consequences for parasite epidemiology. Conclusions The approach proposed here can be applied to track spatial and temporal changes in the population structure of other microparasite species for which sequence variation in the ITS or other highly variable genome regions has been documented but other types of polymorphic markers are lacking. Screening of parasite sequence variants allows for reliable detection of cross-species infections and, using advanced sequencing techniques in the near future, for detailed studies of parasite evolution in natural host − parasite systems. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0247-3) contains supplementary material, which is available to authorized users.
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30
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Thielsch A, Glass N, Streit B, Meester LD, Ortells R, Schwenk K. Fitness differences and persistent founder effects determine the clonal composition during population build-up inDaphnia. OIKOS 2014. [DOI: 10.1111/oik.01575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anne Thielsch
- Inst. for Environmental Science, Molecular Ecology, Univ. of Koblenz-Landau; Fortstraße 7 DE-76829 Landau Germany
| | - Nicole Glass
- Dept of Ecology and Evolution; Goethe-Univ. - Biologicum; Max-von-Laue-Straße 13 DE-60438 Frankfurt am Main Germany
| | - Bruno Streit
- Dept of Ecology and Evolution; Goethe-Univ. - Biologicum; Max-von-Laue-Straße 13 DE-60438 Frankfurt am Main Germany
| | - Luc De Meester
- Laboratory Aquatic Ecology, Evolution and Conservation, KU Leuven - Univ. of Leuven; Charles Deberiotstraat 32 BE-3000 Leuven Belgium
| | - Raquel Ortells
- Inst. Cavanilles de Biodiversitat i Biologia Evolutiva, Univ. of Valencia; C/Catedrático José Beltrán, 2 ES-46980 Paterna Spain
| | - Klaus Schwenk
- Inst. for Environmental Science, Molecular Ecology, Univ. of Koblenz-Landau; Fortstraße 7 DE-76829 Landau Germany
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Bellati A, Tiberti R, Cocca W, Galimberti A, Casiraghi M, Bogliani G, Galeotti P. A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanicDaphniapopulations in the Alps. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Adriana Bellati
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Rocco Tiberti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
- Alpine Wildlife Research Centre; Gran Paradiso National Park; Degioz 11 11010 Valsavarenche Aosta Italy
| | - Walter Cocca
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Galimberti
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Maurizio Casiraghi
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Giuseppe Bogliani
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Paolo Galeotti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
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