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Murray CS, Karram M, Bass DJ, Doceti M, Becker D, Nunez JCB, Ratan A, Bergland AO. Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589693. [PMID: 38659826 PMCID: PMC11042267 DOI: 10.1101/2024.04.16.589693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in the Daphnia pulex species complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and European D. pulex and several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that while North American and European D. pulex diverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and European D. pulex cannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.
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Affiliation(s)
- Connor S. Murray
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Madison Karram
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - David J. Bass
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Madison Doceti
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | | | - Aakrosh Ratan
- Center of Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Alan O. Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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2
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Wersebe MJ, Sherman RE, Jeyasingh PD, Weider LJ. The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex. Mol Ecol 2023; 32:1478-1496. [PMID: 35119153 DOI: 10.1111/mec.16383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.
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Affiliation(s)
- Matthew J Wersebe
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Ryan E Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
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3
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Ramos-Rodríguez E, Pérez-Martínez C, Conde-Porcuna JM. A Non-Stressful Temperature Rise and Greater Food Availability Could Increase Tolerance to Calcium Limitation of Daphnia cf. pulex (Sensu Hebert, 1995) Populations in Cold Soft-Water Lakes. BIOLOGY 2022; 11:biology11101539. [PMID: 36290443 PMCID: PMC9598739 DOI: 10.3390/biology11101539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 11/05/2022]
Abstract
Calcium (Ca) is an important driver of community structure in freshwaters. We examined the combined effects of increased temperatures and variations in food quantity on the tolerance to low Ca of Daphnia pulex. The aim was to predict the impact of climate warming on this keystone zooplanktonic species in cold-climate lakes. We conducted a factorial life-history experiment in a clone of North American Daphnia cf. pulex to analyse the interaction effects of a temperature increase (17.5 °C−21 °C) within their physiological preferred range and expected by climate warming over the next few decades and a narrow Ca gradient (0.25−1.74 mg Ca L−1) under stressful vs. abundant food conditions. We found a striking positive synergistic effect of Ca and temperature on D. pulex reproduction at high food conditions. Although the increase in temperature to 21 °C greatly reduced survival, high energy allocation to reproduction at high food levels allowed the population to succeed in poor Ca (<0.25 mg Ca L−1). Results suggest that climate warming and higher food availability will make the populations of many cold and Ca-limited lakes more tolerant to low Ca levels with higher growth population rates, thereby altering zooplanktonic community structures and inducing potential cascading effects on the food web.
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Affiliation(s)
- Eloísa Ramos-Rodríguez
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
- Instituto del Agua, Universidad de Granada, 18003 Granada, Spain
- Correspondence: ; Tel.: +34-958-24-10-00 (ext. 20094)
| | - Carmen Pérez-Martínez
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
- Instituto del Agua, Universidad de Granada, 18003 Granada, Spain
| | - José María Conde-Porcuna
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
- Instituto del Agua, Universidad de Granada, 18003 Granada, Spain
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Tian X, Ohtsuki H, Urabe J. Competitive consequences determined by phenotypic but not genetic distance: A study with asexual water flea genotypes. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaofei Tian
- Fishery College Zhejiang Ocean University Zhoushan China
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Hajime Ohtsuki
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Jotaro Urabe
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Sendai Japan
- Institute of Freshwater Biology Nagano University Ueda Japan
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5
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Mitochondrial Lineage Diversity and Phylogeography of Daphnia (Daphnia) (Crustacea: Cladocera) in North-East Russia. WATER 2022. [DOI: 10.3390/w14121946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The variability of the 12S gene fragment of the mtDNA for taxa belonging to subgenus Daphnia (Daphnia) O.F. Müller, 1776 (Crustacea: Cladocera) in NE Russia is studied, and their phylogenetic analysis performed. We identified (based both on morphological and molecular data) nine species belonging to four species complexes, namely: (A) D. longispina s.l.: (1) D. longispina O.F. Müller, 1776; (2) D. dentifera Forbes, 1893; (3) D. galeata Sars, 1864; (4) D. umbra Taylor, Hebert et Colbourne, 1996; (B) D. cristata s.l.: (5) D. cristata Sars, 1862; (6) D. longiremis Sars, 1862; (C) D. curvirostris s.l.: (7) D. curvirostris Eylmann, 1887; (D) D. pulex s.l.: (8) D. pulex Leydig, 1860; (9) D. middendorffiana Fischer, 1851. Rare arcto-mountainous taxon D. umbra was found in the mountains of the Sakha (Yakutia) Republic for the first time. Species diversity in NE Asia is relatively low, and the most revealed taxa are trans-Beringian. We also performed a phylogeographic analysis of D. dentifera and D. pulex s.l., the two most common species in NE Russia. Our new data allow us to assume that the daphniids of NE Asia have undergone various evolutionary scenarios during the Pleistocene period: survival is within some local refugia, and re-colonization from these areas and from North America through the Beringian land bridge, etc. We agree with previous authors who revealed that the patterns in the studied species groups are relatively recent (of Late Pleistocene or even Holocene age), although the main phylogenetic daphniid lineages (mainly congruent with the biological species) are very old. Our results provide convincing evidence for the hypothesis that NE Russia is a very important source of modern haplotypic diversity for the cladocerans.
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Ohtsuki H, Norimatsu H, Makino T, Urabe J. Invasions of an obligate asexual daphnid species support the nearly neutral theory. Sci Rep 2022; 12:7305. [PMID: 35508526 PMCID: PMC9068809 DOI: 10.1038/s41598-022-11218-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.
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Affiliation(s)
- Hajime Ohtsuki
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hirotomo Norimatsu
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Jotaro Urabe
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
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7
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Ye Z, Zhao C, Raborn RT, Lin M, Wei W, Hao Y, Lynch M. Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Mol Biol Evol 2022; 39:msac059. [PMID: 35325186 PMCID: PMC9004417 DOI: 10.1093/molbev/msac059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chaoxian Zhao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - R. Taylor Raborn
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Man Lin
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wen Wei
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yue Hao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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8
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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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9
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Relationship between oxidative stress and lifespan in Daphnia pulex. Sci Rep 2022; 12:2354. [PMID: 35149730 PMCID: PMC8837783 DOI: 10.1038/s41598-022-06279-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Macromolecular damage leading to cell, tissue and ultimately organ dysfunction is a major contributor to aging. Intracellular reactive oxygen species (ROS) resulting from normal metabolism cause most damage to macromolecules and the mitochondria play a central role in this process as they are the principle source of ROS. The relationship between naturally occurring variations in the mitochondrial (MT) genomes leading to correspondingly less or more ROS and macromolecular damage that changes the rate of aging associated organismal decline remains relatively unexplored. MT complex I, a component of the electron transport chain (ETC), is a key source of ROS and the NADH dehydrogenase subunit 5 (ND5) is a highly conserved core protein of the subunits that constitute the backbone of complex I. Using Daphnia as a model organism, we explored if the naturally occurring sequence variations in ND5 correlate with a short or long lifespan. Our results indicate that the short-lived clones have ND5 variants that correlate with reduced complex I activity, increased oxidative damage, and heightened expression of ROS scavenger enzymes. Daphnia offers a unique opportunity to investigate the association between inherited variations in components of complex I and ROS generation which affects the rate of aging and lifespan.
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10
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Fedosov A, Achaz G, Gontchar A, Puillandre N. MOLD, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Mol Ecol Resour 2022; 22:2038-2053. [DOI: 10.1111/1755-0998.13590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Leninsky prospect 33 119071 Moscow Russia
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
- UMR7206 Eco‐Anthropologie Université de Paris‐CNRS‐MNHN Paris
- UMR7241 Centre Interdisciplinaire de Recherche en Biologie Collége de France‐CNRS‐INSERM Paris
| | - Andrey Gontchar
- Molecular Immunology Laboratory Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology Samory Mashela street 1 117997 Moscow Russia
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
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11
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Genitsaris S, Stefanidou N, Beeri-Shlevin Y, Viner-Mozzini Y, Moustaka-Gouni M, Ninio S, Sukenik A. Air-dispersed aquatic microorganisms show establishment and growth preferences in different freshwater colonisation habitats. FEMS Microbiol Ecol 2021; 97:6356561. [PMID: 34424315 DOI: 10.1093/femsec/fiab122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022] Open
Abstract
We attempted to mimic aeolian ecosystems to examine how filters posed by regional characteristics can influence the establishment and growth of airborne microcolonisers of a common air source. Using a natural single source of aerosols we applied a combined microscopy and high-throughput sequencing approach to examine the diversity, settling and growth potential of air-dispersed microbes in water containers representing newly formed aquatic colonisation habitats of different trophic states and salinity. Heterotrophic microeukaryotes were favoured as initial settlers when nutrients were low, while autotrophs rapidly proliferated in the high-nutrient containers, possibly due to favourable germinating conditions for their preferred mode of dispersal with resting spores. Following settling of colonisers, we investigated two contrasting hypotheses: if the different water colonisation habitats harboured the same microbial communities after establishment and growth periods, this would point towards a selection of best-fit cosmopolitan colonisers, regardless of habitat-specific characteristics. Alternatively, community dissimilarities after the growth period would suggest a selection of settlers due to bottom-up controls combined with priority effects. Both analyses suggested that the structure of the microbial communities in the different colonisation habitats were driven by nutrient content and salinity, showing clustering to similar bottom-up forces and dissimilarities in significantly different colonisation habitats.
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Affiliation(s)
- Savvas Genitsaris
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece.,Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yaron Beeri-Shlevin
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
| | - Yehudit Viner-Mozzini
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Shira Ninio
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
| | - Assaf Sukenik
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
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12
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Ye Z, Williams E, Zhao C, Burns CW, Lynch M. The rapid, mass invasion of New Zealand by North American Daphnia " pulex". LIMNOLOGY AND OCEANOGRAPHY 2021; 66:2672-2683. [PMID: 39175934 PMCID: PMC11340258 DOI: 10.1002/lno.11780] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/08/2021] [Indexed: 08/24/2024]
Abstract
Nonindigenous members of the Daphnia pulex complex have been found in many lakes in New Zealand (NZ) in the past 20 years, suggesting a recent invasion. However, very little is known about the precise phylogenetic origin of invasive Daphnia, whether each lake is invaded by a single clone or multiple clones, the lineage of the invasive clones, and whether they are obligately asexual clones. Furthermore, the source and time of arrival of the invasive genotype(s) are unclear. We address these questions by genomic sequencing of Daphnia populations from 13 lakes in the South Island and 1 lake in the North Island, NZ. All biallelic sites in these NZ populations have similar numbers of reads for the two parental alleles, suggesting each NZ population originates from a single asexual clone. Based on 25,643 monomorphic lineage-specific markers, the invasive Daphnia in the South Island were found to be Daphnia pulicaria Forbes, while those in the North Island are hybrids of D. pulicaria Forbes and D. cf. pulex sensu Hebert. Both the South and North Island Daphnia are phylogenetically clustered with North American Daphnia, thereby suggesting their North American origins. We found also that all South Island clones contain identical mitochondrial genomes, suggesting the origin and proliferation from a single founder clone, which we experimentally verified to be an obligate asexual. Estimates from molecular data imply a colonization time for the South Island clones of ~60 years ago, with a likely invasion route associated with the introduction of salmonids from North America.
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Affiliation(s)
- Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Emily Williams
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Chaoxian Zhao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Carolyn W. Burns
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
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Oliveira dos Anjos TB, Polazzo F, Arenas‐Sánchez A, Cherta L, Ascari R, Migliorati S, Vighi M, Rico A. Eutrophic status influences the impact of pesticide mixtures and predation on Daphnia pulex populations. Ecol Evol 2021; 11:4046-4057. [PMID: 33976793 PMCID: PMC8093730 DOI: 10.1002/ece3.7305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 11/11/2022] Open
Abstract
Pesticides, nutrients, and ecological stressors such as competition or predation co-occur in freshwater ecosystems impacted by agriculture. The extent to which combinations of these stressors affect aquatic populations and the role of nutrients availability in modulating these responses requires further understanding. In this study, we assessed how pesticides affecting different taxonomic groups and predation influence the response of Daphnia pulex populations under different trophic conditions. An outdoor experiment was designed following a factorial design, with the insecticide chlorpyrifos, the herbicide diuron, and the predation by Notonecta sp. individuals as key stressors. The single impact of each of these stressors, and their binary and tertiary combinations, was evaluated on D. pulex abundance and population structure under mesotrophic and eutrophic conditions for 21 days. Data were analyzed using generalized linear mixed models estimated by means of a novel Bayesian shrinkage technique. Our study shows a significant influence of each of the evaluated stressors on D. pulex abundance; however, the impacts of the herbicide and predation were lower under eutrophic conditions as compared to the mesotrophic ones. We found that binary stressor interactions were generally additive in the mesotrophic scenario, except for the herbicide-predation combination, which resulted in synergistic effects. The impacts of the binary stressor combinations in the eutrophic scenario were classified as antagonistic, except for the insecticide-herbicide combination, which was additive. The tertiary interaction resulted in significant effects on some sampling dates; however, these were rather antagonistic and resembled the most important binary stressor combination in each trophic scenario. Our study shows that the impact of pesticides on freshwater populations depends on the predation pressure, and demonstrates that the combined effect of pesticides and ecological stressors is influenced by the food availability and organism fitness related to the trophic status of freshwater ecosystems.
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Affiliation(s)
- Talles Bruno Oliveira dos Anjos
- IMDEA Water InstituteScience and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
- University of Koblenz‐LandauLandau in der PfalzGermany
| | - Francesco Polazzo
- IMDEA Water InstituteScience and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
| | - Alba Arenas‐Sánchez
- IMDEA Water InstituteScience and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
| | - Laura Cherta
- IMDEA Water InstituteScience and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
| | - Roberto Ascari
- Department of Economics, Management and StatisticsUniversity of Milano‐BicoccaMilanItaly
| | - Sonia Migliorati
- Department of Economics, Management and StatisticsUniversity of Milano‐BicoccaMilanItaly
| | - Marco Vighi
- IMDEA Water InstituteScience and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
| | - Andreu Rico
- IMDEA Water InstituteScience and Technology Campus of the University of AlcaláAlcalá de HenaresSpain
- Cavanilles Institute of Biodiversity and Evolutionary BiologyUniversity of ValenciaPaternaSpain
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14
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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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15
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Neretina AN, Karabanov DP, Sacherova V, Kotov AA. Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere. PeerJ 2021; 9:e10804. [PMID: 33585083 PMCID: PMC7860113 DOI: 10.7717/peerj.10804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 02/05/2023] Open
Abstract
Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.
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Affiliation(s)
- Anna N. Neretina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- I.D. Papanin Institute for Biology of Inland Waters, Borok, Yaroslavl State, Russia
| | | | - Alexey A. Kotov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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16
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Zhang X, Ohtsuki H, Makino W, Kato Y, Watanabe H, Urabe J. Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of
Daphnia
fed different algal diets. Ecol Res 2020. [DOI: 10.1111/1440-1703.12194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Xuan Zhang
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Aoba‐ku Sendai Japan
| | - Hajime Ohtsuki
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Aoba‐ku Sendai Japan
| | - Wataru Makino
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Aoba‐ku Sendai Japan
| | - Yasuhiko Kato
- Department of Biotechnology, Graduate School of Engineering Osaka University Suita Osaka Japan
| | - Hajime Watanabe
- Department of Biotechnology, Graduate School of Engineering Osaka University Suita Osaka Japan
| | - Jotaro Urabe
- Aquatic Ecology Lab, Graduate School of Life Sciences Tohoku University Aoba‐ku Sendai Japan
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17
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Pleistocene Branchiopods (Cladocera, Anostraca) from Transbaikalian Siberia Demonstrate Morphological and Ecological Stasis. WATER 2020. [DOI: 10.3390/w12113063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pleistocene water bodies have been studied using the paleolimnological approach, which traces environmental changes using particular subfossils as ecological proxies, rather than analysis of the paleocommunities themselves. Within a given taphocoenosis, the presence and quantity of animals are related to environmental conditions rather than to community types where relationships between taxa are stabilized during their long-term co-occurrence and are (at least partially) more important than the particular environmental conditions at the time of deposition, which may have experienced significant seasonal and inter-seasonal variations. Here, we analyze Branchiopoda (Crustacea) of two paleolocalities in the Transbaikalian Region of Russia: Urtuy (MIS3) and Nozhiy (older than 1.5 million years). Cladocerans Daphnia (Ctenodaphnia) magna, D. (C.) similis, D. (Daphnia) pulex, Ceriodaphnia pulchella-reticulata, C. laticaudata, Simocephalus sp., Moina cf. brachiata, M. macropopa clade, Chydorus cf. sphaericus, Capmtocercus sp. and anostracans Branchinecta cf. paludosa, and Streptocephalus (Streptocephalus) sp. are found in two localities. With the exception of the last taxon, which now occurs in the southern Holarctic, all other taxa inhabit the Transbaikalian Region. Within Eurasia, the steppe zone has the greatest diversity of large branchiopods and a high diversity of some cladocerans, such as subgenus Daphnia (Ctenodaphnia) and Moina sp. Here we demonstrated that the branchiopod community in shallow steppe water bodies has been unchanged since at least the Pleistocene, demonstrating long-term morphological and ecological stasis.
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18
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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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19
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Taylor DJ, Connelly SJ, Kotov AA. The Intercontinental phylogeography of neustonic daphniids. Sci Rep 2020; 10:1818. [PMID: 32020006 PMCID: PMC7000678 DOI: 10.1038/s41598-020-58743-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/07/2020] [Indexed: 11/30/2022] Open
Abstract
Organisms that live at the freshwater surface layer (the neuston) occupy a high energy habitat that is threatened by human activities. Daphniids of the genera Scapholeberis and Megafenestra are adapted to the neuston but are poorly studied for biogeography and diversity. Here we assess the global phylogeography of neustonic daphniids. We obtained 402 new multigene sequences from the 12S rRNA, 16S rRNA, and tRNA (val) regions of the mitochondrial genomes of daphniids from 186 global sites. We assessed the intercontinental origins and boundaries of mitochondrial lineages and the relative rates of evolution in neustonic and planktonic daphniids. We identified 17 divergent lineages in the neustonic daphniids that were associated with biogeographic regions. Six of these lineages had intercontinental ranges – four of these were Transberingian. Patagonian populations of Scapholeberis rammneri were monophyletic and nested within a closely related clade of western North American haplotypes, suggesting an introduction from the Western Nearctic to South America. The Eastern Palearctic was more diverse than other regions, containing eight of the major lineages detected in the Scapholeberinae. The Genus Scapholeberis had high levels of divergence compared to non-neustonic daphniids. Neustonic daphniids have more divergent biogeographic lineages than previously appreciated.
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Affiliation(s)
- Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, 14260, USA.
| | - Sandra J Connelly
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution, Leninsky Prospect 33, 119071, Moscow, Russia
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20
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Cornetti L, Fields PD, Van Damme K, Ebert D. A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Mol Phylogenet Evol 2019; 137:250-262. [DOI: 10.1016/j.ympev.2019.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
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21
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Abstract
Daphnia normally reproduce by cyclical parthenogenesis, with offspring sex being determined by environmental cues. However, some females have lost the ability to produce males. Our results demonstrate that this loss of male-producing ability is controlled by a dominant allele at a single locus. We identified the locus by comparing whole-genome sequences of 67 nonmale-producing (NMP) and 100 male-producing (MP) clones from 5 Daphnia pulex populations, revealing 132 NMP-linked SNPs and 59 NMP-linked indels within a single 1.1-Mb nonrecombining region on chromosome I. These markers include 7 nonsynonymous mutations, all of which are located within one unannotated protein-coding gene (gene 8960). Within this single gene, all of the marker-linked NMP haplotypes from different populations form a monophyletic clade, suggesting a single origin of the NMP phenotype, with the NMP haplotype originating by introgression from a sister species, Daphnia pulicaria Methyl farnesoate (MF) is the innate juvenile hormone in daphnids, which induces the production of males and whose inhibition results in female-only production. Gene 8960 is sensitive to treatment by MF in MP clones, but such responsiveness is greatly reduced in NMP clones. Thus, we hypothesize that gene 8960 is located downstream of the MF-signaling pathway in D. pulex, with the NMP phenotype being caused by expression change of gene 8960.
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22
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Kotov AA, Taylor DJ. Contrasting endemism in pond-dwelling cyclic parthenogens: the Daphnia curvirostris species group (Crustacea: Cladocera). Sci Rep 2019; 9:6812. [PMID: 31048750 PMCID: PMC6497905 DOI: 10.1038/s41598-019-43281-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/17/2019] [Indexed: 01/08/2023] Open
Abstract
Pond-dwelling cyclic parthenogens are often proposed to be highly vagile. However, the Holarctic biogeography of parthenogens has been hampered by very limited sampling in the eastern Palearctic. Here we examine the geographic boundaries, diversity, and connectivity across the Palearctic for the Daphnia curvirostris complex (Cladocera: Daphniidae). Nuclear (HSP90) and mitochondrial (ND2) sequence data supported the existence of five main clades (most of which corresponded to presumptive species) with one eastern Palearctic clade being novel to this study (the average mitochondrial genetic divergence from known species was 19.2%). D. curvirostris s.s. was geographically widespread in the Palearctic, with a population genetic signature consistent with postglacial expansion. The Eastern Palearctic had local nine endemic species and/or subclades (other Holarctic regions lacked more than one endemic subclade). Even though several endemic species appeared to have survived Pleistocene glaciation in the eastern Palearctic, much of the Palearctic has been recolonized by D. curvirostris s.str. from a Western Palearctic refugium. A disjunct population in Mexico also shared its haplotypes with D. curvirostris s.str., consistent with a recent introduction. The only apparently endemic North American lineage was detected in a thermally disturbed pond system in northwestern Alaska. Our results for pond-dwelling cyclic parthenogens further support the hypothesis that the Eastern Palearctic is a diversity hotspot for freshwater invertebrates.
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Affiliation(s)
- Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution, Leninsky Prospect 33, Moscow, 119071, Russia.
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, 14260, USA
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23
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Makino T, Kawata M. Invasive invertebrates associated with highly duplicated gene content. Mol Ecol 2019; 28:1652-1663. [PMID: 30811716 DOI: 10.1111/mec.15019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/15/2018] [Accepted: 12/27/2018] [Indexed: 01/14/2023]
Abstract
Invasion of alien species has led to serious problems, including the destruction of native ecosystems. In general, invasive species adapt to new environments rapidly, suggesting that they have high genetic diversity that can directly influence environmental adaptability. However, it is not known how genomic architecture causes genetic diversity that leads to invasiveness. Recent studies have showed that the proportion of duplicated genes (PD ) in whole animal genomes correlate with environmental variability within a habitat. Here, we show that PD and propagule size significantly explain the differences in species categories (invasive species, noninvasive species, and parasites). PD correlated negatively with the propagule size. The residual values of regression of PD on propagule size revealed that the invasive species had higher PD values and larger propagule size than those of the noninvasive species, whereas the parasites had lower PD values and smaller propagule size than those of others. There were no correlations between the invasive species and other genomic factors including the genome size, number of genes, and certain gene families. Our results suggest that the PD values of a genome might be a potential genomic source causing genetic variations for adaptation to diverse environments. The results also showed that the invasiveness status of a species would be predicted by the residual values of regression of PD on propagule size. Our innovative approach provides a measure to estimate the environmental adaptability of organisms based on genomic data.
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Affiliation(s)
- Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masakado Kawata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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24
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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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25
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Camp AA, Haeba MH, LeBlanc GA. Complementary roles of photoperiod and temperature in environmental sex determination in Daphnia spp. J Exp Biol 2019; 222:jeb.195289. [DOI: 10.1242/jeb.195289] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/07/2019] [Indexed: 11/20/2022]
Abstract
Daphnia spp, a keystone genus in freshwater lentic habitats, are subject to environmental sex determination wherein environmental conditions dictate offspring sex and whether they reproduce asexually or sexually. The introduction of males into a population denotes the first step in the switch from asexual parthenogenetic reproduction to sexual reproduction. We tested the hypothesis that photoperiod and temperature co-regulate male sex determination and that these environmental stimuli would activate elements of the male sex determination signaling cascade. Results revealed that photoperiod was a critical cue in creating permissive conditions for male production. Further, under photoperiod-induced permissive conditions, male sex determination was temperature dependent. The two daphnid species evaluated, Daphnia pulex and D. magna, exhibited different temperature dependencies. D. pulex produced fewer males with increasing temperatures between 16-22°C, and D. magna exhibited the opposite trend. We found consistent expression patterns of key genes along the male sex determining signaling pathway in D. pulex independent of environmental stimuli. mRNA levels for the enzyme responsible for synthesis of the male sex determining hormone, methyl farnesoate, were elevated early in the reproductive cycle, followed by increased mRNA levels of the methyl farnesoate receptor subunits, Met and SRC. Environmental conditions that stimulated male offspring production significantly increased Met mRNA levels. Results indicate that male sex determination in daphnids is under the permissive control of photoperiod and the regulatory control of temperature. Further, these environmental cues may stimulate male sex determination by increasing levels of the Met subunit of the methyl farnesoate receptor.
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Affiliation(s)
- Allison A. Camp
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695 USA
| | - Maher H. Haeba
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695 USA
| | - Gerald A. LeBlanc
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695 USA
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26
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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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27
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Miyakawa H, Sato T, Song Y, Tollefsen KE, Iguchi T. Ecdysteroid and juvenile hormone biosynthesis, receptors and their signaling in the freshwater microcrustacean Daphnia. J Steroid Biochem Mol Biol 2018; 184:62-68. [PMID: 29247785 DOI: 10.1016/j.jsbmb.2017.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
Abstract
The two essential insect hormones, ecdysteroids and juvenile hormones, are possessed not only by insects, but also widely by arthropods, and regulate various developmental and physiological processes. In contrast to the abundant information about molecular endocrine mechanisms in insects, the knowledge of non-insect arthropod endocrinology is still limited. In this review, we summarize recent reports about the molecular basis of these two major insect hormones in the freshwater microcrustacean Daphnia, a keystone taxon in limnetic ecology and a bioindicator in environmental studies. Comprehensive comparisons of endocrine signaling pathways between insects and daphnids may shed light on the regulatory mechanisms of various biological phenomena and, moreover, evolutionary processes of arthropod species.
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Affiliation(s)
- Hitoshi Miyakawa
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi 321-8505, Japan.
| | - Tomomi Sato
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - You Song
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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28
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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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29
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Bekker EI, Karabanov DP, Galimov YR, Haag CR, Neretina TV, Kotov AA. Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages. PLoS One 2018; 13:e0194045. [PMID: 29543844 PMCID: PMC5854346 DOI: 10.1371/journal.pone.0194045] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/25/2018] [Indexed: 11/30/2022] Open
Abstract
Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.
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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 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 Experimental Embryology, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Christoph R. Haag
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Tatiana V. Neretina
- N.A.Pertsov White Sea Biological Station, Biological Faculty, M.V. Lomonosov Moscow State University, 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
- Kazan Federal University, Kazan, Russia
- * E-mail:
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Kotov AA. Faunistic complexes of the Cladocera (Crustacea, Branchiopoda) of Eastern Siberia and the Far East of Russia. BIOL BULL+ 2017. [DOI: 10.1134/s1062359016090041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kotov AA, Karabanov DP, Bekker EI, Neretina TV, Taylor DJ. Phylogeography of the Chydorus sphaericus Group (Cladocera: Chydoridae) in the Northern Palearctic. PLoS One 2016; 11:e0168711. [PMID: 27992559 PMCID: PMC5167426 DOI: 10.1371/journal.pone.0168711] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/05/2016] [Indexed: 11/28/2022] Open
Abstract
The biodiversity and the biogeography are still poorly understood for freshwater invertebrates. The crustacean Chydorus sphaericus-brevilabris complex (Cladocera: Chydoridae) is composed of species that are important components of Holarctic freshwater food webs. Recent morphological and genetic study of the complex has indicated a substantial species diversity in the northern hemisphere. However, we know little of the geographic boundaries of these novel lineages. Moreover, a large section of the Palearctic remains unexamined at the genetic level. Here we attempt to address the biodiversity knowledge gap for the Chydorus sphaericus group in the central Palearctic and assess its diversity and biogeographic boundaries. We sequenced nuclear (ITS-2) and mitochondrial (COI) gene regions of Chydorus specimens across the Palearctic and compared them with already available Holarctic sequences. We detected six main clades in the C. sphaericus group in the Palearctic, of which two of the groups are novel. Three of the more divergent clades are geographically widespread. The central portion of Eurasia (the Yenisey River basin) appears to be a narrow zone of secondary contact for phylogroups that expanded from European and Beringian refugia. As such, the previously unsampled central Palearctic represents an important region for understanding the evolutionary consequences of Pleistocene climatic oscillations on the Chydorus sphaericus group.
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Affiliation(s)
- Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
- * E-mail:
| | - 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
| | - Eugeniya I. Bekker
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Neretina
- White Sea Biological Station, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Derek J. Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, United States of America
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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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Rakowski C, Cardinale BJ. Herbivores control effects of algal species richness on community biomass and stability in a laboratory microcosm experiment. OIKOS 2016. [DOI: 10.1111/oik.03105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chase Rakowski
- School of Natural Resources and Environment; Univ. of Michigan; 440 Church St Ann Arbor MI 48109 USA
| | - Bradley J. Cardinale
- School of Natural Resources and Environment; Univ. of Michigan; 440 Church St Ann Arbor MI 48109 USA
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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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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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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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Miyakawa H, Sugimoto N, Kohyama TI, Iguchi T, Miura T. Intra-specific variations in reaction norms of predator-induced polyphenism in the water flea Daphnia pulex. Ecol Res 2015. [DOI: 10.1007/s11284-015-1272-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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Jeong H, Kotov AA, Lee W. Checklist of the freshwater Cladocera (Crustacea: Branchiopoda) of South Korea. P BIOL SOC WASH 2014. [DOI: 10.2988/0006-324x-127.1.216] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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40
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Ballinger MJ, Bruenn JA, Kotov AA, Taylor DJ. Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses. Virology 2013; 446:276-82. [PMID: 24074591 DOI: 10.1016/j.virol.2013.07.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/21/2013] [Accepted: 07/23/2013] [Indexed: 11/29/2022]
Abstract
The ecological model, Daphnia pulex (Cladocera: Daphniidae), is broadly distributed in Holarctic freshwater habitats and has been the subject of multidisciplinary study for over half a century, but never has a natural RNA virus infection been reported in daphnids. Here we report on a group of paleoviruses related to RNA dependent RNA polymerase in the genome of D. pulex. Phylogenetic analysis suggests that these paleoviruses are derived from a viral lineage within the genus Phlebovirus. Comparison of the genomic sequences flanking individual paleoviruses reveal that some are orthologous viral insertions having been present in the common ancestor of the D. pulex species complex, which is millions of years old. Still, we detected some sites that have the signature of purifying selection. In contrast, other paleoviruses in this group seem to be unique to specific host lineages and even contain undisrupted open reading frames, suggesting either more recent acquisition, or selective maintenance.
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Affiliation(s)
- Matthew J Ballinger
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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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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