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Molinier C, Lenormand T, Haag CR. No recombination suppression in asexually produced males of Daphnia pulex. Evolution 2023; 77:1987-1999. [PMID: 37345677 DOI: 10.1093/evolut/qpad114] [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: 12/09/2021] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Obligate parthenogenesis (OP) is often thought to evolve by disruption of reductional meiosis and suppression of crossover recombination. In the crustacean Daphnia pulex, OP lineages, which have evolved from cyclical parthenogenetic (CP) ancestors, occasionally produce males that are capable of reductional meiosis. Here, by constructing high-density linkage maps, we find that these males show only slightly and nonsignificantly reduced recombination rates compared to CP males and females. Both meiosis disruption and recombination suppression are therefore sex-limited (or partly so), which speaks against the evolution of OP by disruption of a gene that is essential for meiosis or recombination in both sexes. The findings may be explained by female-limited action of genes that suppress recombination, but previously identified candidate genes are known to be expressed in both sexes. Alternatively, and equally consistent with the data, OP might have evolved through a reuse of the parthenogenesis pathways already present in CP and through their extension to all events of oogenesis. The causal mutations for the CP to OP transition may therefore include mutations in genes involved in oogenesis regulation and may not necessarily be restricted to genes of the "meiosis toolkit." More generally, our study emphasizes that there are many ways to achieve asexuality, and elucidating the possible mechanisms is key to ultimately identify the genes and traits involved.
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Affiliation(s)
- Cécile Molinier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tuebingen, Germany
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2
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Multiple Recent Colonizations of the Australian Region by the Chydorus sphaericus Group (Crustacea: Cladocera). WATER 2022. [DOI: 10.3390/w14040594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biotic introductions are an ongoing disruption for many ecosystems. For passively dispersed freshwater zooplankton, transcontinental introductions have been common but are poorly studied in the southern hemisphere. Here we assess the hypothesis of recent introduction for populations of the Chydorus sphaericus group (Crustacea: Cladocera) in Australia. We analyzed 254 sequences (63 original sequences) from the cytochrome oxidase I region of mitochondrial DNA of Chydorus sp., which included global representation. Three Australian populations were connected with separate clades in the northern hemisphere, suggesting multiple colonization events for Australia. The timescale of the divergences was consistent with recent (Quaternary) dispersal. As Australian populations are exposed to migrating birds from the northern hemisphere, both avian and anthropogenic sources are candidates for dispersal vectors. We concluded that recent cross-hemisphere dispersal in the Chydorus sphaericus group is more common than previously believed.
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3
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Garibian PG, Karabanov DP, Neretina AN, Taylor DJ, Kotov AA. Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 2021; 9:e11310. [PMID: 33981506 PMCID: PMC8074845 DOI: 10.7717/peerj.11310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
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Affiliation(s)
- Petr G. Garibian
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I.D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Anna N. Neretina
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, New York, United States
| | - 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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4
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Chin TA, Cristescu ME. Speciation in Daphnia. Mol Ecol 2021; 30:1398-1418. [PMID: 33522056 DOI: 10.1111/mec.15824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022]
Abstract
The microcrustacean Daphnia is arguably one of the most studied zooplankton species, having a well understood ecology, life history, and a relatively well studied evolutionary history. Despite this wealth of knowledge, species boundaries within closely related species in this genus often remain elusive and the major evolutionary forces driving the diversity of daphniids remain controversial. This genus contains more than 80 species with multiple cryptic species complexes, with many closely related species able to hybridize. Here, we review speciation research in Daphnia within the framework of current speciation theory. We evaluate the role of geography, ecology, and biology in restricting gene flow and promoting diversification. Of the 253 speciation studies on Daphnia, the majority of studies examine geographic barriers (55%). While evidence shows that geographic barriers play a role in species divergence, ecological barriers are also probably prominent in Daphnia speciation. We assess the contribution of ecological and nonecological reproductive isolating barriers between closely related species of Daphnia and found that none of the reproductive isolating barriers are restricting gene flow completely. Research on reproductive isolating barriers has disproportionally focused on two species complexes, the Daphnia pulex and Daphnia longispina species complexes. Finally, we identify areas of research that remain relatively unexplored and discuss future research directions that build our understanding of speciation in daphniids.
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Affiliation(s)
- Tiffany A Chin
- Department of Biology, McGill University, Montreal, QC, Canada
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5
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Lohr JN, Haag CR. Parasite-driven replacement of a sexual by a closely related asexual taxon in nature. Ecology 2020; 101:e03105. [PMID: 32452541 DOI: 10.1002/ecy.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/22/2020] [Accepted: 04/15/2020] [Indexed: 11/09/2022]
Abstract
Asexual species are thought to suffer more from coevolving parasites than related sexuals. Yet a variety of studies do not find the patterns predicted by theory. Here, to shine light on this conundrum, we investigate one such case of an asexual advantage in the presence of parasites. We follow the frequency dynamics of sexual and asexual Daphnia pulex in a natural pond that was initially dominated by sexuals. Coinciding with an epidemic of a microsporidian parasite infecting both sexuals and asexuals, the pond was rapidly taken over by the initially rare asexuals. With experiments comparing multiple sexual and asexual clones from across the local metapopulation, we confirm that asexuals are less susceptible and also suffer less from the parasite once infected. These results are consistent with the parasite-driven, ecological replacement of dominant sexuals by closely related, but more resistant asexuals, ultimately leading to the extinction of the formerly superior sexual competitor. Our study is one of the clearest examples from nature, backed up by experimental verification, showing a parasite-mediated reversal of competition dynamics. The experiments show that, across the metapopulation, asexuals have an advantage in the presence of parasites. In this metapopulation, asexuals are relatively rare, likely due to their recent invasion. While we cannot rule out other reasons for the observed patterns, the results are consistent with a temporary parasite-mediated advantage of asexuals due to the fact that they are rare, which is an underappreciated aspect of the Red Queen Hypothesis.
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Affiliation(s)
- Jennifer N Lohr
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Tvärminne Zoological Station, J.A. Palménin tie 260, 10900, Hanko, Finland.,Department of Genetics, Evolution and Environment, University College London, Institute of Healthy Ageing, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Christoph R Haag
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Tvärminne Zoological Station, J.A. Palménin tie 260, 10900, Hanko, Finland.,CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919, route de Mende, 34293, Montpellier Cedex 5, France
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6
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Fernández CE, Campero M, Bianco G, Ekvall MT, Rejas D, Uvo CB, Hansson L. Local adaptation to
UV
radiation in zooplankton: a behavioral and physiological approach. Ecosphere 2020. [DOI: 10.1002/ecs2.3081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Carla E. Fernández
- Unidad de Limnología y Recursos Acuáticos Universidad Mayor de San Simón Calle Sucre s/n frente al Parque La Torre Cochabamba Bolivia
- Division of Water Resources Engineering Lund University V‐building, 3rd Floor John Ericssons väg 1 SE‐223 63 Lund Sweden
| | - Melina Campero
- Unidad de Limnología y Recursos Acuáticos Universidad Mayor de San Simón Calle Sucre s/n frente al Parque La Torre Cochabamba Bolivia
| | - Giuseppe Bianco
- Department of Biology/Aquatic Ecology Lund University Sölvegatan 37223 62 Lund Sweden
| | - Mikael T. Ekvall
- Department of Biology/Aquatic Ecology Lund University Sölvegatan 37223 62 Lund Sweden
| | - Danny Rejas
- Unidad de Limnología y Recursos Acuáticos Universidad Mayor de San Simón Calle Sucre s/n frente al Parque La Torre Cochabamba Bolivia
| | - Cintia B. Uvo
- Division of Water Resources Engineering Lund University V‐building, 3rd Floor John Ericssons väg 1 SE‐223 63 Lund Sweden
| | - Lars‐Anders Hansson
- Department of Biology/Aquatic Ecology Lund University Sölvegatan 37223 62 Lund Sweden
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7
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Lopes JML, de Carvalho HH, Zorzatto C, Azevedo ALS, Machado MA, Salimena FRG, Grazul RM, Gitzendanner MA, Soltis DE, Soltis PS, Viccini LF. Genetic relationships and polyploid origins in the Lippia alba complex. AMERICAN JOURNAL OF BOTANY 2020; 107:466-476. [PMID: 32115694 DOI: 10.1002/ajb2.1443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Plant genomes vary in size and complexity due in part to polyploidization. Latitudinal analyses of polyploidy are biased toward floras of temperate regions, with much less research done in the tropics. Lippia alba has been described as a tropical polyploid complex with diploid, triploid, tetraploid, and hexaploid accessions. However, no data regarding relationships among the ploidal levels and their origins have been reported. Our goals are to clarify the relationships among accessions of Lippia alba and the origins of each ploidal level. METHODS We investigated 98 samples representing all five geographical regions of Brazil and all ploidal levels using microsatellite (SSR) allelic variation and DNA sequences of ITS and trnL-F. Nine morphological structures were analyzed from 33 herbarium samples, and the chemical compounds of 78 accessions were analyzed by GC-MS. RESULTS Genetic distance analysis, the alignment block pattern, as well as RAxML and Bayesian trees showed that accessions grouped by ploidal level. The triploids form a well-defined group that originated from a single group of diploids. The tetraploids and hexaploid grouped together in SSR and trnL-F analyses. The recovered groups agree with chemical data and morphology. CONCLUSIONS The accessions grouped by ploidal level. Only one origin of triploids from a single group of diploids was observed. The tetraploid origin is uncertain; however, it appears to have contributed to the origin of the hexaploid. This framework reveals linkages among the ploidal levels, providing new insights into the evolution of a polyploid complex of tropical plants.
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Affiliation(s)
- Juliana M L Lopes
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - Cristiane Zorzatto
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
| | | | | | | | - Richard M Grazul
- Department of Chemistry, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
| | | | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Lyderson F Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
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8
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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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9
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Ma X, Petrusek A, Wolinska J, Hu W, Yin M. Lineage diversity and reproductive modes of the Daphnia pulex group in Chinese lakes and reservoirs. Mol Phylogenet Evol 2019; 130:424-433. [DOI: 10.1016/j.ympev.2018.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/24/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022]
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10
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Brans KI, Jansen M, Vanoverbeke J, Tüzün N, Stoks R, De Meester L. The heat is on: Genetic adaptation to urbanization mediated by thermal tolerance and body size. GLOBAL CHANGE BIOLOGY 2017; 23:5218-5227. [PMID: 28614592 DOI: 10.1111/gcb.13784] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
Worldwide, urbanization leads to tremendous anthropogenic environmental alterations, causing strong selection pressures on populations of animals and plants. Although a key feature of urban areas is their higher temperature ("urban heat islands"), adaptive thermal evolution in organisms inhabiting urban areas has rarely been studied. We tested for evolution of a higher heat tolerance (CTMAX ) in urban populations of the water flea Daphnia magna, a keystone grazer in freshwater ecosystems, by carrying out a common garden experiment at two temperatures (20°C and 24°C) with genotypes of 13 natural populations ordered along a well-defined urbanization gradient. We also assessed body size and haemoglobin concentration to identify underlying physiological drivers of responses in CTMAX . We found a higher CTMAX in animals isolated from urban compared to rural habitats and in animals reared at higher temperatures. We also observed substantial genetic variation in thermal tolerance within populations. Overall, smaller animals were more heat tolerant. While urban animals mature at smaller size, the effect of urbanization on thermal tolerance is only in part caused by reductions in body size. Although urban Daphnia contained higher concentrations of haemoglobin, this did not contribute to their higher CTMAX . Our results provide evidence of adaptive thermal evolution to urbanization in the water flea Daphnia. In addition, our results show both evolutionary potential and adaptive plasticity in rural as well as urban Daphnia populations, facilitating responses to warming. Given the important ecological role of Daphnia in ponds and lakes, these adaptive responses likely impact food web dynamics, top-down control of algae, water quality, and the socio-economic value of urban ponds.
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Affiliation(s)
- Kristien I Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Mieke Jansen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Joost Vanoverbeke
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
- Research Institute for Nature and Forest (INBO), Brussel, Belgium
| | - Nedim Tüzün
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Robby Stoks
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
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11
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Kake-Guena S, Touisse K, Warren B, Scott K, Dufresne F, Blier P, Lemieux H. Temperature-related differences in mitochondrial function among clones of the cladoceran Daphnia pulex. J Therm Biol 2017; 69:23-31. [DOI: 10.1016/j.jtherbio.2017.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/10/2017] [Accepted: 05/20/2017] [Indexed: 10/19/2022]
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12
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Haileselasie TH, Mergeay J, Weider LJ, Sommaruga R, Davidson TA, Meerhoff M, Arndt H, Jürgens K, Jeppesen E, De Meester L. Environment not dispersal limitation drives clonal composition of Arctic Daphnia in a recently deglaciated area. Mol Ecol 2016; 25:5830-5842. [PMID: 27662259 DOI: 10.1111/mec.13843] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/24/2016] [Accepted: 09/02/2016] [Indexed: 12/11/2022]
Abstract
One of the most prominent manifestations of the ongoing climate warming is the retreat of glaciers and ice sheets around the world. Retreating glaciers result in the formation of new ponds and lakes, which are available for colonization. The gradual appearance of these new habitat patches allows us to determine to what extent the composition of asexual Daphnia (water flea) populations is affected by environmental drivers vs. dispersal limitation. Here, we used a landscape genetics approach to assess the processes structuring the clonal composition of species in the D. pulex species complex that have colonized periglacial habitats created by ice-sheet retreat in western Greenland. We analysed 61 populations from a young (<50 years) and an old cluster (>150 years) of lakes and ponds. We identified 42 asexual clones that varied widely in spatial distribution. Beta-diversity was higher among older than among younger systems. Lineage sorting by the environment explained 14% of the variation in clonal composition whereas the pure effect of geographical distance was very small and statistically insignificant (Radj2 = 0.010, P = 0.085). Dispersal limitation did not seem important, even among young habitat patches. The observation of several tens of clones colonizing the area combined with environmentally driven clonal composition of populations illustrates that population assembly of asexual species in the Arctic is structured by environmental gradients reflecting differences in the ecology of clones.
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Affiliation(s)
- Tsegazeabe H Haileselasie
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B-3000, Leuven, Belgium.,Department of Biology, College of Natural and Computational Sciences (CNCS), Mekelle University, P.O.Box: 231, Mekelle, Ethiopia
| | - Joachim Mergeay
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B-3000, Leuven, Belgium.,Research Institute for Nature and Forest, Gaverstraat 4, Geraardsbergen, 9500, Belgium
| | - Lawrence J Weider
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, 73071, USA
| | - Ruben Sommaruga
- Lake and Glacier Research Group, Institute of Ecology, University of Innsbruck, Technikerstr. 25, Innsbruck, Austria
| | - Thomas A Davidson
- Department of Bioscience, Arctic Research Centre, Aarhus University, Vejlsøvej 25, Silkeborg, 8600, Denmark
| | - Mariana Meerhoff
- Department of Bioscience, Arctic Research Centre, Aarhus University, Vejlsøvej 25, Silkeborg, 8600, Denmark.,Department of Ecology and Environmental Management, CURE-Faculty of Sciences, University of the Republic (Uruguay), Maldonado, 20000, Uruguay
| | - Hartmut Arndt
- Cologne Biocenter, Institute for Zoology, General Ecology, University of Cologne, Zülpicher Str. 47b, D-50674, Köln, Germany
| | - Klaus Jürgens
- Biological Oceanography Department, Leibniz Institute for Baltic Sea Research, Seestrasse 15, D-18119, Rostock, Germany
| | - Erik Jeppesen
- Department of Bioscience, Arctic Research Centre, Aarhus University, Vejlsøvej 25, Silkeborg, 8600, Denmark.,Sino-Danish Centre for Education and Research (SDC), University of Chinese Academy of Sciences, 3 Zhongguancun South 1st Alley, Haidian District, 100190, Beijing, China
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B-3000, Leuven, Belgium
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13
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Quenta E, Molina-Rodriguez J, Gonzales K, Rebaudo F, Casas J, Jacobsen D, Dangles O. Direct and indirect effects of glaciers on aquatic biodiversity in high Andean peatlands. GLOBAL CHANGE BIOLOGY 2016; 22:3196-3205. [PMID: 27058991 DOI: 10.1111/gcb.13310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 03/11/2016] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
The rapid melting of glacier cover is one of the most obvious impacts of climate change on alpine ecosystems and biodiversity. Our understanding of the impact of a decrease in glacier runoff on aquatic biodiversity is currently based on the 'glacier-heterogeneity-diversity' paradigm, according to which there is high α-diversity at intermediate levels of glacial influence due to the high degree of environmental heterogeneity caused by glacier water. This α-diversity pattern generates high levels of between-site aquatic community variation (high β diversity) and increases regional diversity (γ-diversity). There is a rich conceptual background in favor of this paradigm, but empirical data supporting it are scarce. We investigated this paradigm by analyzing the different diversity patterns (α, β and γ-diversity) of four aquatic groups (zooplankton, macroinvertebrates, algae and macrophytes) living in high-elevation peatlands (>4500 m above sea level). We sampled 200 pools from 20 peatlands along a glacier gradient in the Cordillera Real of Bolivia. We performed structural equation modeling (SEM) to analyze the potential mechanisms underlying the observed diversity patterns. Intermediate levels of glacial influence (15-20% cover) resulted in high heterogeneity, but α-diversity responded to glacial influence only for the zooplankton group (Cladocera). Our SEM analysis did not identify environmental heterogeneity as a significant variable explaining the relationship between glacier and α-diversity. Peatland area had a strong positive effect on heterogeneity and diversity. β-diversity was significantly associated with glacier gradient, and 12.9% of the total regional diversity (γ-diversity) was restricted to peatlands with a high degree of glacial influence. These species might be lost in a context of glacial retreat. These findings provide new insight into the potential effects of glacial retreat on the aquatic environment and biodiversity in the peatlands of the tropical Andes.
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Affiliation(s)
- Estefania Quenta
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), Université François-Rabelais, Tours, Tours, 37200, France
- Institut de Recherche pour le Développement (IRD), UMR EGCE-UnivParisSud-CNRS-IRD-ParisSaclay, Gif-sur Yvette, 91198, France
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor San Andrés, calle 27 Cota Cota, La Paz, Bolivia
| | - Jorge Molina-Rodriguez
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor San Andrés, calle 27 Cota Cota, La Paz, Bolivia
| | - Karina Gonzales
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor San Andrés, calle 27 Cota Cota, La Paz, Bolivia
| | - François Rebaudo
- Institut de Recherche pour le Développement (IRD), UMR EGCE-UnivParisSud-CNRS-IRD-ParisSaclay, Gif-sur Yvette, 91198, France
- Centro de Análisis Espacial, Instituto de Ecología, Universidad Mayor San Andrés, calle 27 Cota Cota, La Paz, Bolivia
| | - Jérôme Casas
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), Université François-Rabelais, Tours, Tours, 37200, France
| | - Dean Jacobsen
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, 2100, Copenhagen, Denmark
- Escuela de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, 12 de Octubre, 1076 y Roca, Quito, Ecuador
| | - Olivier Dangles
- Institut de Recherche pour le Développement (IRD), UMR EGCE-UnivParisSud-CNRS-IRD-ParisSaclay, Gif-sur Yvette, 91198, France
- Escuela de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, 12 de Octubre, 1076 y Roca, Quito, Ecuador
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Bekker EI, Karabanov DP, Galimov YR, Kotov AA. DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera). PLoS One 2016; 11:e0161737. [PMID: 27556403 PMCID: PMC4996527 DOI: 10.1371/journal.pone.0161737] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/10/2016] [Indexed: 11/19/2022] Open
Abstract
Species of the genus Moina Baird (Cladocera: Moinidae) often dominate freshwater crustacean communities in temporary water bodies. Several species of Moina are used as food for fish larvae in aquaculture, as bioindicators in toxicological studies, and as common subjects for physiological studies. The aim of this paper is to estimate biodiversity of Moina in northern Eurasia using the standard DNA barcoding approach based on the cytochrome c oxidase subunit I (COI) gene. We analysed 160 newly obtained and 157 existing COI sequences, and found evidence for 21 phylogroups of Moina, some of which were detected here for the first time. Our study confirmed the opinion that the actual species diversity of cladocerans is several times higher than is presently accepted. Our results also indicated that Moina has the second richest species diversity among the cladoceran genera (with only Daphnia O. F. Mueller having a greater diversity of species). Our study strongly supports division of Moina into two faunistic groups: European-Western Siberian and Eastern Siberian-Far Eastern, with a transitional zone at the Yenisey River basin (Eastern Siberia). Here, we refrain from taxonomic descriptions of new species, as this requires a thorough morphological and taxonomic study for each putative taxon.
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Affiliation(s)
- Eugeniya I. Bekker
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
- Laboratory of Fish Ecology, I. D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Yan R. Galimov
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
- Laboratory of Experimental Embryology, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, 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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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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Wang W, Zhang K, Deng D, Zhang YN, Peng S, Xu X. Genetic Diversity of Daphnia pulex in the Middle and Lower Reaches of the Yangtze River. PLoS One 2016; 11:e0152436. [PMID: 27015539 PMCID: PMC4807850 DOI: 10.1371/journal.pone.0152436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/14/2016] [Indexed: 11/29/2022] Open
Abstract
Increased human activities and environmental changes may lead to genetic diversity variations of Cladocerans in water. Daphnia pulex are distributed throughout the world and often regarded as a model organism. The 16S rDNA, cytochrome c oxidase subunit I (COI), and 18S genes were used as molecular marks. The genetic diversity and phylogeny of D. pulex obtained from 10 water bodies in the middle and lower reaches of the Yangtze River were studied. For 16S rDNA, COI gene, and 18S gene, the A+T content (65.4%, 58.4%, and 54.6%) was significantly higher than the G+C content (34.6%, 41.6% and 45.4%). This result was consistent with higher A and T contents among invertebrates. Based on the genetic distances of 16S rDNA and COI genes, the genetic differences of D. pulex from 10 water bodies located in the middle and lower reaches of the Yangtze River in China was minimal (0%-0.8% for 16S rDNA and 0%-1.5% for COI gene). However, D. pulex evolved into two branches in the phylogenetic trees, which coincided with its geographical distribution. Compared with D. pulex from other countries, the average genetic distance of D. pulex obtained from 10 water bodies in the middle and lower reaches of the Yangtze River reached 9.1%-10.5%, thereby indicating that D. pulex may have evolved into different subspecies.
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Affiliation(s)
- Wenping Wang
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Kun Zhang
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Daogui Deng
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Ya-Nan Zhang
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Shuixiu Peng
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
| | - Xiaoxue Xu
- School of Life Science, Huaibei Normal University, Anhui Key Laboratory of Resource and Plant Biology, Huaibei, 235000, China
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17
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Özdemir E, Altındağ A, Kandemir İ. Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:424-433. [PMID: 27159716 DOI: 10.3109/19401736.2015.1136303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.
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Affiliation(s)
- Ebru Özdemir
- a Department of Molecular Biology and Genetics, Faculty of Science and Letters , University of Kafkas , Kars , Turkey.,b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
| | - Ahmet Altındağ
- b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
| | - İrfan Kandemir
- b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
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18
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Alfsnes K, Hobæk A, Weider LJ, Hessen DO. Birds, nutrients, and climate change: mtDNA haplotype diversity of Arctic Daphnia on Svalbard revisited. Polar Biol 2016. [DOI: 10.1007/s00300-015-1868-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Kake-Guena SA, Touisse K, Vergilino R, Dufresne F, Blier PU, Lemieux H. Assessment of mitochondrial functions inDaphnia pulexclones using high-resolution respirometry. ACTA ACUST UNITED AC 2015; 323:292-300. [DOI: 10.1002/jez.1913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 12/25/2022]
Affiliation(s)
| | - Kamal Touisse
- Campus Saint-Jean; University of Alberta; Edmonton Alberta Canada
| | - Roland Vergilino
- Département de biologie; Laboratoire de Physiologie Animale Intégrative; Université du Québec à Rimouski; Rimouski Québec Canada
| | - France Dufresne
- Département de biologie; Laboratoire de Physiologie Animale Intégrative; Université du Québec à Rimouski; Rimouski Québec Canada
| | - Pierre U. Blier
- Département de biologie; Laboratoire de Physiologie Animale Intégrative; Université du Québec à Rimouski; Rimouski Québec Canada
| | - Hélène Lemieux
- Campus Saint-Jean; University of Alberta; Edmonton Alberta Canada
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20
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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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21
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Ventura M, Petrusek A, Miró A, Hamrová E, Buñay D, De Meester L, Mergeay J. Local and regional founder effects in lake zooplankton persist after thousands of years despite high dispersal potential. Mol Ecol 2014; 23:1014-27. [DOI: 10.1111/mec.12656] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/22/2013] [Accepted: 12/30/2013] [Indexed: 02/02/2023]
Affiliation(s)
- M. Ventura
- Center for Advanced Studies of Blanes; Spanish Research Council (CEAB-CSIC); Biodiversity and Biogeodynamics Group; Blanes 17300 Catalonia Girona Spain
- Institut de Recerca de l'Aigua; Universitat de Barcelona; Av. Diagonal 684 08034 Barcelona Catalonia Spain
| | - A. Petrusek
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-12844 Prague 2 Czech Republic
| | - A. Miró
- Center for Advanced Studies of Blanes; Spanish Research Council (CEAB-CSIC); Biodiversity and Biogeodynamics Group; Blanes 17300 Catalonia Girona Spain
| | - E. Hamrová
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-12844 Prague 2 Czech Republic
| | - D. Buñay
- Center for Advanced Studies of Blanes; Spanish Research Council (CEAB-CSIC); Biodiversity and Biogeodynamics Group; Blanes 17300 Catalonia Girona Spain
| | - L. De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven; University of Leuven; Deberiotstraat 32 B-3000 Leuven Belgium
| | - J. Mergeay
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven; University of Leuven; Deberiotstraat 32 B-3000 Leuven Belgium
- Research Institute for Nature and Forest; Gaverstraat 4 B-9500 Geraardsbergen Belgium
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22
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Marková S, Dufresne F, Manca M, Kotlík P. Mitochondrial capture misleads about ecological speciation in the Daphnia pulex complex. PLoS One 2013; 8:e69497. [PMID: 23869244 PMCID: PMC3711805 DOI: 10.1371/journal.pone.0069497] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/11/2013] [Indexed: 11/18/2022] Open
Abstract
The North American ecological species Daphniapulicaria and Daphniapulex are thought to have diverged from a common ancestor by adaptation to sympatric but ecologically distinct lake and pond habitats respectively. Based on mtDNA relationships, European D. pulicaria is considered a different species only distantly related to its North American counterpart, but both species share a lactate dehydrogenase (Ldh) allele F supposedly involved in lake adaptation in North America, and the same allele is also carried by the related Holarctic Daphniatenebrosa. The correct inference of the species' ancestral relationships is therefore critical for understanding the origin of their adaptive divergence. Our species tree inferred from unlinked nuclear loci for D. pulicaria and D. pulex resolved the European and North American D. pulicaria as sister clades, and we argue that the discordant mtDNA gene tree is best explained by capture of D. pulex mtDNA by D. pulicaria in North America. The Ldh gene tree shows that F-class alleles in D. pulicaria and D. tenebrosa are due to common descent (as opposed to introgression), with D. tenebrosa alleles paraphyletic with respect to D. pulicaria alleles. That D. tenebrosa still segregates the ancestral and derived amino acids at the two sites distinguishing the pond and lake alleles suggests that D. pulicaria inherited the derived states from the D. tenebrosa ancestry. Our results suggest that some adaptations restricting the gene flow between D. pulicaria and D. pulex might have evolved in response to selection in ancestral environments rather than in the species' current sympatric habitats. The Arctic (D. tenebrosa) populations are likely to provide important clues about these issues.
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Affiliation(s)
- Silvia Marková
- Institute of Animal Physiology and Genetics, Laboratory of Molecular Ecology, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
| | - France Dufresne
- Département de Biologie, Centre d’Études Nordiques, Université du Québec à Rimouski, Québec, Canada
| | - Marina Manca
- CNR Istituto per lo Studio degli Ecosistemi, Verbania, Italy
| | - Petr Kotlík
- Institute of Animal Physiology and Genetics, Laboratory of Molecular Ecology, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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23
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Arkhipova IR, Rodriguez F. Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids. Cytogenet Genome Res 2013; 140:295-311. [PMID: 23899811 DOI: 10.1159/000352069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.
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Affiliation(s)
- I R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA. iarkhipova @ mbl.edu
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24
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HAMROVÁ EVA, KRAJICEK MARTIN, KARANOVIC TOMISLAV, ČERNÝ MARTIN, PETRUSEK ADAM. Congruent patterns of lineage diversity in two species complexes of planktonic crustaceans,Daphnia longispina(Cladocera) andEucyclops serrulatus(Copepoda), in East European mountain lakes. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00864.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Crease TJ, Omilian AR, Costanzo KS, Taylor DJ. Transcontinental phylogeography of the Daphnia pulex species complex. PLoS One 2012; 7:e46620. [PMID: 23056371 PMCID: PMC3463573 DOI: 10.1371/journal.pone.0046620] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022] Open
Abstract
Daphnia pulex is quickly becoming an attractive model species in the field of ecological genomics due to the recent release of its complete genome sequence, a wide variety of new genomic resources, and a rich history of ecological data. Sequences of the mitochondrial NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit 1 genes were used to assess the global phylogeography of this species, and to further elucidate its phylogenetic relationship to other members of the Daphnia pulex species complex. Using both newly acquired and previously published data, we analyzed 398 individuals from collections spanning five continents. Eleven strongly supported lineages were found within the D. pulex complex, and one lineage in particular, panarctic D. pulex, has very little phylogeographical structure and a near worldwide distribution. Mismatch distribution, haplotype network, and population genetic analyses are compatible with a North American origin for this lineage and subsequent spatial expansion in the Late Pleistocene. In addition, our analyses suggest that dispersal between North and South America of this and other species in the D. pulex complex has occurred multiple times, and is predominantly from north to south. Our results provide additional support for the evolutionary relationships of the eleven main mitochondrial lineages of the D. pulex complex. We found that the well-studied panarctic D. pulex is present on every continent except Australia and Antarctica. Despite being geographically very widespread, there is a lack of strong regionalism in the mitochondrial genomes of panarctic D. pulex--a pattern that differs from that of most studied cladocerans. Moreover, our analyses suggest recent expansion of the panarctic D. pulex lineage, with some continents sharing haplotypes. The hypothesis that hybrid asexuality has contributed to the recent and unusual geographic success of the panarctic D. pulex lineage warrants further study.
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Affiliation(s)
- Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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26
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Mergeay J, De Meester L, Eggermont H, Verschuren D. Priority effects and species sorting in a long paleoecological record of repeated community assembly through time. Ecology 2012; 92:2267-75. [PMID: 22352166 DOI: 10.1890/10-1645.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We studied the relative roles of environmental species sorting and priority effects in the assembly of ecological communities on long time scales, by analyzing community turnover of water fleas (Daphnia) in response to strong and recurrent environmental change in a fluctuating tropical lake. During the past 1800 years, Lake Naivasha (Kenya) repeatedly fluctuated between a small saline pond habitat during lowstands and a large freshwater lake habitat during highstands. Starting from a paleoecological reconstruction, we estimated the role of priority effects in Daphnia community assembly across 16 of these habitat turnovers and compared this with the response of the community to reconstructed changes in three environmental variables important for species sorting. Our results indicate that the best predictor of Daphnia community composition during highstands was the community composition just prior to the transition from lowstands to highstands. This reflects a long-lasting priority effect of late lowstand communities on highstand communities, arising when remnant lowstand populations fill newly available ecological space in the rapidly expanding lake habitat. Species sorting and priority effects had a comparable but relatively small influence on community composition during the lowstands. Moreover, these priority effects decayed rapidly with time as Daphnia communities responded to environmental change, in contrast with the highstand communities where priority effects lasted for several decades.
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Affiliation(s)
- Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500 Geraardsbergen, Belgium.
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28
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Vanschoenwinkel B, Mergeay J, Pinceel T, Waterkeyn A, Vandewaerde H, Seaman M, Brendonck L. Long distance dispersal of zooplankton endemic to isolated mountaintops--an example of an ecological process operating on an evolutionary time scale. PLoS One 2011; 6:e26730. [PMID: 22102865 PMCID: PMC3213101 DOI: 10.1371/journal.pone.0026730] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/03/2011] [Indexed: 11/18/2022] Open
Abstract
Recent findings suggest a convergence of time scales between ecological and evolutionary processes which is usually explained in terms of rapid micro evolution resulting in evolution on ecological time scales. A similar convergence, however, can also emerge when slow ecological processes take place on evolutionary time scales. A good example of such a slow ecological process is the colonization of remote aquatic habitats by passively dispersed zooplankton. Using variation at the protein coding mitochondrial COI gene, we investigated the balance between mutation and migration as drivers of genetic diversity in two Branchipodopsis fairy shrimp species (Crustacea, Anostraca) endemic to remote temporary rock pool clusters at the summit of isolated mountaintops in central South Africa. We showed that both species colonized the region almost simultaneously c. 0.8 My ago, but exhibit contrasting patterns of regional genetic diversity and demographic history. The haplotype network of the common B. cf. wolfi showed clear evidence of 11 long distance dispersal events (up to 140 km) with five haplotypes that are shared among distant inselbergs, as well as some more spatially isolated derivates. Similar patterns were not observed for B. drakensbergensis presumably since this rarer species experienced a genetic bottleneck. We conclude that the observed genetic patterns reflect rare historic colonization events rather than frequent ongoing gene flow. Moreover, the high regional haplotype diversity combined with a high degree of haplotype endemicity indicates that evolutionary- (mutation) and ecological (migration) processes in this system operate on similar time scales.
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Affiliation(s)
- Bram Vanschoenwinkel
- Laboratory of Aquatic Ecology and Evolutionary Biology, Katholieke Universiteit Leuven, Leuven, Belgium.
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29
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Crease TJ, Floyd R, Cristescu ME, Innes D. Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex. BMC Evol Biol 2011; 11:212. [PMID: 21767386 PMCID: PMC3231769 DOI: 10.1186/1471-2148-11-212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 07/18/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. RESULTS We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. CONCLUSIONS Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.
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Affiliation(s)
- Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robin Floyd
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- School of Clinical Sciences, Southmead Hospital, University of Bristol, Bristol BS105NB, UK
| | - Melania E Cristescu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - David Innes
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B 3X9, Canada
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Abstract
Understanding nucleotide variation in natural populations has been a subject of great interest for decades. However, many taxonomic groups, especially those with atypical life history attributes remain unstudied, and Drosophila is the only arthropod genus for which DNA polymorphism data are presently abundant. As a result of the recent release of the complete genome sequence and a wide variety of new genomic resources, the Daphnia system is quickly becoming a promising new avenue for expanding our knowledge of nucleotide variation in natural populations. Here, we examine nucleotide variation in six protein-coding loci for Daphnia pulex and its congeners with particular emphasis on D. pulicaria, the closest extant relative of D. pulex. Levels of synonymous intraspecific variation, pi(s), averaged 0.0136 for species in the Daphnia genus, and are slightly lower than most prior estimates in invertebrates. Tests of neutrality indicated that segregating variation conforms to neutral model expectations for the loci that we examined in most species, while K(a)/K(s) ratios revealed strong purifying selection. Using a full maximum-likelihood coalescent-based method, the ratio of the recombination rate to the mutation rate (c/u), averaged 0.5255 for species of the Daphnia genus. Lastly, a divergence population-genetics approach was used to investigate gene flow and divergence between D. pulex and D. pulicaria.
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Adamowicz SJ, Petrusek A, Colbourne JK, Hebert PD, Witt JD. The scale of divergence: A phylogenetic appraisal of intercontinental allopatric speciation in a passively dispersed freshwater zooplankton genus. Mol Phylogenet Evol 2009; 50:423-36. [DOI: 10.1016/j.ympev.2008.11.026] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 11/24/2008] [Accepted: 11/26/2008] [Indexed: 11/16/2022]
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Petrusek A, Hobaek A, Nilssen JP, Skage M, Černý M, Brede N, Schwenk K. A taxonomic reappraisal of the EuropeanDaphnia longispinacomplex (Crustacea, Cladocera, Anomopoda). ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00336.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Scientists in various subdisciplines of biology have long relied on model organisms to push the frontiers of knowledge forward as far as possible in their specific field. Today, interdisciplinary science requires model organisms that can push our understanding on multiple frontiers and help us formulate and address more complex questions. Members of the genus Daphnia represent just such an interdisciplinary model. Daphnia are aquatic microcrustaceans (also known as waterfleas) that have long been central to the study of ecology and toxicology and have recently been developed as a genomic model. A recent survey of both nuclear and mitochondrial markers in populations of the Daphnia pulex complex from high-altitude lakes in South America (Mergeay et al. 2008, this issue) provides an excellent example of how genetic data and ecological information can be used to push the boundaries of our understanding in molecular ecology. In this species complex, extensive hybridization has occurred resulting in polyploidization and, consequently, asexuality. Their data reveal high levels of genetic diversity, incongruence in phylogenetic signal among genomes (nuclear and mitochondrial), cryptic species in the complex, and a new model for the historical spread of the species throughout the Americas. Their data indicate that genome-level changes have occurred in this species which have profound consequences in an ecological context, the implications of which can be more fully appreciated because of our extensive knowledge of the ecology and natural history of the genus Daphnia.
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Affiliation(s)
- Sarah Schaack
- Department of Biology, Indiana University, Bloomington, IN 47401, USA.
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