1
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Venta PJ, Nguyen AK, Senut MC, Poulos WG, Prukudom S, Cibelli JB. A 13-plex of tetra- and penta-STRs to identify zebrafish. Sci Rep 2020; 10:3851. [PMID: 32123258 PMCID: PMC7052278 DOI: 10.1038/s41598-020-60842-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/09/2020] [Indexed: 11/09/2022] Open
Abstract
The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage ("stutter") that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10-5 and the PI for siblings (PIsib) was 6.4 × 10-3, as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model.
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Affiliation(s)
- Patrick J Venta
- Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA. .,Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA.
| | - Anthony K Nguyen
- Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA
| | - Marie-Claude Senut
- Biomilab LLC, Lansing, MI, 48910, USA.,Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA
| | - William G Poulos
- Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA
| | - Sukumal Prukudom
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University (CASAF, NRU-KU), Bangkok, 10900, Thailand
| | - Jose B Cibelli
- Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA. .,Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA.
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2
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Gonzalez EG, Cunha C, Ghanavi HR, Oliva-Paterna FJ, Torralva M, Doadrio I. Phylogeography and Population Genetic Analyses in the Iberian Toothcarp (Aphanius iberus Valenciennes, 1846) at Different Time Scales. J Hered 2018; 109:253-263. [PMID: 29036328 DOI: 10.1093/jhered/esx076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Secondary freshwater fish species inhabiting fluctuating and extreme environments are susceptible to changes in dispersion, effective population size, and genetic structure. The Iberian toothcarp Aphanius iberus is an endemic cyprinodontid of the Iberian Peninsula restricted to brackish water of salt marshes and coastal lagoons on the eastern Spanish Mediterranean coast. In this study, we analyzed mitochondrial cytochrome b (cyt b) DNA and microsatellite variation to evaluate ways in which the processes of extinction, dispersal, and colonization of A. iberus across its geographic distribution have affected its population genetic structure over time and space. The A. iberus network reconstruction indicated subtle levels of phylogeographic structuring. This, combined with substantial mitochondrial DNA (mtDNA) genetic diversity, suggests that Pleistocene glaciations had a lesser effect on the demographic structure of its populations than was the case for Iberian freshwater species with a similar distribution. Haplotype network, hierarchical analysis of molecular variance, and pairwise ΦST comparisons involving some Levantine samples showed a relatively high degree of mtDNA differentiation, which could be explained by historical isolation of the Villena Lagoon population. Conversely, significant genetic differentiation that follows an isolation-by-distance pattern, and a reduction in Ne though time was detected with microsatellites, suggesting extensive habitat fragmentation on the Mediterranean coast of the Iberian Peninsula over the past hundreds of years. At a smaller geographical scale (Mar Menor Lagoon), habitat fragmentation, probably due to human activity, appears to have resulted in substantially reduced migration and increased genetic drift, as shown by expanded genetic differentiation of populations.
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Affiliation(s)
- Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutiérrez Abascal, Madrid, Spain
| | - Carina Cunha
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutiérrez Abascal, Madrid, Spain
| | - Hamid R Ghanavi
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutiérrez Abascal, Madrid, Spain.,Biology Department, Lund, Sweden
| | | | - Mar Torralva
- Departamento de Zoología y Antropología Física, Universidad de Murcia, Murcia, Spain
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutiérrez Abascal, Madrid, Spain
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3
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Panagiotopoulou H, Austin JD, Zalewska K, Gonciarz M, Czarnogórska K, Gawor J, Weglenski P, Popovic D. Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus). J Hered 2017; 108:686-692. [PMID: 28821182 DOI: 10.1093/jhered/esx057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/02/2017] [Indexed: 11/14/2022] Open
Abstract
Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10-4 per locus per generation (95% confidence interval: 1.48 × 10-3, 4.15 × 10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.
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Affiliation(s)
- Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - James D Austin
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Katarzyna Zalewska
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Magdalena Gonciarz
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Kinga Czarnogórska
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Jan Gawor
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Piotr Weglenski
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Danijela Popovic
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
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4
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Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0867-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Rougemont Q, Roux C, Neuenschwander S, Goudet J, Launey S, Evanno G. Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations. PeerJ 2016; 4:e1910. [PMID: 27077007 PMCID: PMC4830234 DOI: 10.7717/peerj.1910] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/17/2016] [Indexed: 12/19/2022] Open
Abstract
Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.
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Affiliation(s)
- Quentin Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Camille Roux
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Sophie Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Guillaume Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
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6
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Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C. Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations. Mol Ecol 2015; 24:6107-19. [PMID: 26562076 DOI: 10.1111/mec.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023]
Abstract
Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e(-4) per generation per untranscribed dinucleotide locus. This is close to vertebrate estimates and one order of magnitude higher than estimates from species of other arthropod orders, such as Drosophila melanogaster and Daphnia pulex. We also found evidence of a directional bias towards expansions even for long alleles and exceptionally large ranges of allele sizes. Finally, at transcribed microsatellites, the mean rate of mutation was half the rate found at untranscribed loci and the mutational model deviated from that usually considered, with most mutations involving multistep changes that avoid disrupting the reading frame. Our direct estimates of mutation rate were discussed in the light of peculiar biological and genomic features of S. gregaria, including specificities in mismatch repair and the dependence of its activity to allele length. Shedding new light on the mutational dynamics of grasshopper microsatellites is of critical importance for a number of research fields. As an illustration, we showed how our findings improve microsatellite application in population genetics, by obtaining a more precise estimation of S. gregaria effective population size from a published data set based on the same microsatellites.
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Affiliation(s)
- M-P Chapuis
- CIRAD, UMR CBGP, Montpellier, F-34398, France
| | - C Plantamp
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Villeurbanne, 69622, France
| | - R Streiff
- INRA, UMR CBGP, Montpellier, F-34398, France.,INRA, UMR DGIMI, Montpellier, F-34000, France
| | - L Blondin
- CIRAD, UPR B-AMR, Montpellier, F-34398, France
| | - C Piou
- CIRAD, UMR CBGP, Montpellier, F-34398, France
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7
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Araki H, Berejikian BA, Ford MJ, Blouin MS. Fitness of hatchery-reared salmonids in the wild. Evol Appl 2015; 1:342-55. [PMID: 25567636 PMCID: PMC3352433 DOI: 10.1111/j.1752-4571.2008.00026.x] [Citation(s) in RCA: 430] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 02/02/2008] [Indexed: 11/28/2022] Open
Abstract
Accumulating data indicate that hatchery fish have lower fitness in natural environments than wild fish. This fitness decline can occur very quickly, sometimes following only one or two generations of captive rearing. In this review, we summarize existing data on the fitness of hatchery fish in the wild, and we investigate the conditions under which rapid fitness declines can occur. The summary of studies to date suggests: nonlocal hatchery stocks consistently reproduce very poorly in the wild; hatchery stocks that use wild, local fish for captive propagation generally perform better than nonlocal stocks, but often worse than wild fish. However, the data above are from a limited number of studies and species, and more studies are needed before one can generalize further. We used a simple quantitative genetic model to evaluate whether domestication selection is a sufficient explanation for some observed rapid fitness declines. We show that if selection acts on a single trait, such rapid effects can be explained only when selection is very strong, both in captivity and in the wild, and when the heritability of the trait under selection is high. If selection acts on multiple traits throughout the life cycle, rapid fitness declines are plausible.
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Affiliation(s)
- Hitoshi Araki
- Department of Zoology, Oregon State University Corvallis, OR, USA ; Eawag, The Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum, Switzerland
| | | | - Michael J Ford
- NOAA, Northwest Fisheries Science Center Seattle, WA, USA
| | - Michael S Blouin
- Department of Zoology, Oregon State University Corvallis, OR, USA
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8
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Plough LV, Moran A, Marko P. Density drives polyandry and relatedness influences paternal success in the Pacific gooseneck barnacle, Pollicipes elegans. BMC Evol Biol 2014; 14:81. [PMID: 24739102 PMCID: PMC4021092 DOI: 10.1186/1471-2148-14-81] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 03/31/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyandry is a common mating strategy in animals, increasing female fitness through direct (material) and indirect (genetic) benefits. Most theories about the benefits of polyandry come from studies of terrestrial animals, which have relatively complex mating systems and behaviors; less is known about the potential benefits of polyandry in sessile marine animals, for which potential mates may be scarce and females have less control over pre-copulatory mate choice. Here, we used microsatellite markers to examine multiple paternity in natural aggregations of the Pacific gooseneck barnacle Pollicipes elegans, testing the effect of density on paternity and mate relatedness on male reproductive success. RESULTS We found that multiple paternity was very common (79% of broods), with up to five fathers contributing to a brood, though power was relatively low to detect more than four fathers. Density had a significant and positive linear effect on the number of fathers siring a brood, though this relationship leveled off at high numbers of fathers, which may reflect a lack of power and/or an upper limit to polyandry in this species. Significant skew in male reproductive contribution in multiply-sired broods was observed and we found a positive and significant relationship between the proportion of offspring sired and the genetic similarity between mates, suggesting that genetic compatibility may influence reproductive success in this species. CONCLUSIONS To our knowledge, this is the first study to show high levels of multiple paternity in a barnacle, and overall, patterns of paternity in P. elegans appear to be driven primarily by mate availability. Evidence of paternity bias for males with higher relatedness suggests some form of post-copulatory sexual selection is taking place, but more work is needed to determine whether it operates during or post-fertilization. Overall, our results suggest that while polyandry in P. elegans is driven by mate availability, it may also provide a mechanism for females to ensure fertilization by compatible gametes and increase reproductive success in this sessile species.
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Affiliation(s)
- Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, P,O, Box 775, Cambridge, MD 21601, USA.
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9
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Lotterhos KE, Dick SJ, Haggarty DR. Evaluation of rockfish conservation area networks in the United States and Canada relative to the dispersal distance for black rockfish (Sebastes melanops). Evol Appl 2013; 7:238-59. [PMID: 24567745 PMCID: PMC3927886 DOI: 10.1111/eva.12115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022] Open
Abstract
Marine reserves networks are implemented as a way to mitigate the impact of fishing on marine ecosystems. Theory suggests that a reserve network will function synergistically when connected by dispersal, but the scale of dispersal is often unknown. On the Pacific coast of the United States and Canada, both countries have recently implemented a number of rockfish conservation areas (RCAs) to protect exploited rockfish species, but no study has evaluated the connectivity within networks in each country or between the two countries. We used isolation-by-distance theory to estimate the scale of dispersal from microsatellite data in the black rockfish, Sebastes melanops, and compared this estimate with the distance between RCAs that would protect this species. Within each country, we found that the distance between RCAs was generally within the confidence intervals of mean dispersal per generation. The distance between these two RCA networks, however, was greater than the average dispersal per generation. The data were also consistent with a genetic break between southern Oregon and central Oregon. We discuss whether additional nearshore RCAs in southern Oregon and Washington would help promote connectivity between RCA's for shallow-water rockfishes.
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Affiliation(s)
- Katie E Lotterhos
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
| | - Stefan J Dick
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
| | - Dana R Haggarty
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
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10
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Lapinski AG, Solovenchuk LL, Gorbachev VV. Informativity of some of the molecular markers most frequently used in population genetics of salmonids. BIOL BULL+ 2013. [DOI: 10.1134/s1062359013050087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Beal MA, Glenn TC, Lance SL, Somers CM. Characterization of unstable microsatellites in mice: no evidence for germline mutation induction following gamma-radiation exposure. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:599-607. [PMID: 22930577 DOI: 10.1002/em.21726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/19/2012] [Indexed: 06/01/2023]
Abstract
Large tandem repeat DNA loci such as expanded simple tandem repeats and minisatellites are efficient markers for detecting germline mutations; however, mutation detection using these loci can be imprecise and difficult to standardize across labs. Short-tandem repeats, such as microsatellites, offer more precise and high-throughput mutation detection, but germline mutation induction at these loci has not yet been studied in model organisms such as mice. In this study, we used microsatellite enrichment and large-scale DNA sequencing of several closely related inbred mouse lines to identify a panel of 19 polymorphic microsatellites with potentially high spontaneous mutation frequencies. We used this panel and four additional loci from other sources to quantify spontaneous mutation frequency in pedigrees of outbred Swiss-Webster mice. In addition, we also examined mutation induction in families in which sires were treated with acute doses of either 0.5 Gy or 1.0 Gy gamma-irradiation to spermatogonial stem cells. Per locus mutation frequencies ranged from 0 to 5.03 × 10(-3). Considering only the 11 loci with mutations, the mutation frequencies were: control 2.78 × 10(-3), 0.5 Gy 4.09 × 10(-3), and 1.0 Gy 1.82 × 10(-3). There were no statistically significant changes in mutation frequencies among treatment groups. Our study provides the first direct quantification of microsatellite mutation frequency in the mouse germline, but shows no evidence for mutation induction at pre-meiotic male germ cells following acute gamma-irradiation. Further work using the panel is needed to examine mutation induction at different doses of radiation, exposure durations, and stages during spermatogenesis.
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Affiliation(s)
- Marc A Beal
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada S4S 0A2
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12
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Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-Bëer E, Robinson S, Vásquez-Carrillo C, Pauli JN, Palsbøll PJ. Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 2012; 21:3403-18. [PMID: 22646281 DOI: 10.1111/j.1365-294x.2012.05635.x] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.
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Affiliation(s)
- M Zachariah Peery
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA.
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13
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Fitzpatrick JM, Carlon DB, Lippe C, Robertson DR. The West Pacific diversity hotspot as a source or sink for new species? Population genetic insights from the Indo-Pacific parrotfish Scarus rubroviolaceus. Mol Ecol 2010; 20:219-34. [PMID: 21143329 DOI: 10.1111/j.1365-294x.2010.04942.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We used a population genetic approach to quantify major population subdivisions and patterns of migration within a broadly distributed Indo-Pacific parrotfish. We genotyped 15 microsatellite loci in Scarus rubroviolaceus collected from 20 localities between Africa and the Americas. A STRUCTURE model indicates the presence of four major populations: Eastern Pacific, Hawaii, Central-West Pacific and a less well-differentiated Indian Ocean. We used the isolation and migration model to estimate splitting times, population sizes and migration patterns between sister population pairs. To eliminate loci under selection, we used BayeScan to select loci for three isolation and migration models: Eastern Pacific and Central-West Pacific, Hawaii and the Central-West Pacific, and Indian Ocean and the Central-West Pacific. To test the assumption of a stepwise mutation model (SMM), we used likelihood to test the SMM against a two-phase model that allowed mutational complexity. A posteriori, minor departures from SMM were estimated to affect ≤2% of the alleles in the data. The data were informative about the contemporary and ancestral population sizes, migration rates and the splitting time in the eastern Pacific/Central-West Pacific comparison. The model revealed a splitting time ∼17,000 BP, a larger contemporary N(e) in the Central-West Pacific than in the eastern Pacific and a strong bias of east to west migration. These characteristics support the Center of Accumulation model of peripatric diversification in low-diversity peripheral sites and perhaps migration from those sites to the western Pacific diversity hotspot.
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Affiliation(s)
- J M Fitzpatrick
- Department of Zoology, University of Hawaii, Honolulu, HI 96822, USA
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14
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Genetic variation and effective population size in isolated populations of coastal cutthroat trout. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0083-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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16
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Hemmer-Hansen J, Nielsen EE, Grønkjaer P, Loeschcke V. Evolutionary mechanisms shaping the genetic population structure of marine fishes; lessons from the European flounder (Platichthys flesusL.). Mol Ecol 2007; 16:3104-18. [PMID: 17651190 DOI: 10.1111/j.1365-294x.2007.03367.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A number of evolutionary mechanisms have been suggested for generating low but significant genetic structuring among marine fish populations. We used nine microsatellite loci and recently developed methods in landscape genetics and coalescence-based estimation of historical gene flow and effective population sizes to assess temporal and spatial dynamics of the population structure in European flounder (Platichthys flesus L.). We collected 1062 flounders from 13 localities in the northeast Atlantic and Baltic Seas and found temporally stable and highly significant genetic differentiation among samples covering a large part of the species' range (global F(ST) = 0.024, P < 0.0001). In addition to historical processes, a number of contemporary acting evolutionary mechanisms were associated with genetic structuring. Physical forces, such as oceanographic and bathymetric barriers, were most likely related with the extreme isolation of the island population at the Faroe Islands. A sharp genetic break was associated with a change in life history from pelagic to benthic spawners in the Baltic Sea. Partial Mantel tests showed that geographical distance per se was not related with genetic structuring among Atlantic and western Baltic Sea samples. Alternative factors, such as dispersal potential and/or environmental gradients, could be important for generating genetic divergence in this region. The results show that the magnitude and scale of structuring generated by a specific mechanism depend critically on its interplay with other evolutionary mechanisms, highlighting the importance of investigating species with wide geographical and ecological distributions to increase our understanding of evolution in the marine environment.
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Affiliation(s)
- Jakob Hemmer-Hansen
- Department of Genetics and Ecology, University of Aarhus, Building 1540, Ny Munkegade, 8000 Aarhus C, Denmark.
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Yue GH, David L, Orban L. Mutation rate and pattern of microsatellites in common carp (Cyprinus carpio L.). Genetica 2006; 129:329-31. [PMID: 16897452 DOI: 10.1007/s10709-006-0003-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 03/13/2006] [Indexed: 11/26/2022]
Abstract
Microsatellites are popular molecular markers in genetic and evolutionary studies. Their mutational dynamics have been extensively studied in humans and fruit flies, but few data were available in fish. By genotyping 55 individuals of a F1 pedigree, we investigated the mutation rates and patterns of 49 microsatellites in one of the most important fresh water fish species, the common carp (Cyprinus carpio L.). The overall mutation rate of the 49 loci was 5.56 x 10(-4)/locus/generation (95% confidence interval 1.52 x 10(-4) and 1.63 x 10(-3)). The change of allele size was between +2 to -5 repeat units, assuming that the mutation allele arose from the parental allele most similar in size to the mutant.
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Affiliation(s)
- G H Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.
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18
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Woodruff RC, Thomson JN. The Fundamental Theorem of Neutral Evolution: Rates of Substitution and Mutation Should Factor in Premeiotic Clusters. Genetica 2005; 125:333-9. [PMID: 16247704 DOI: 10.1007/s10709-005-4982-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Accepted: 04/01/2005] [Indexed: 01/27/2023]
Abstract
Mutations do not always arise as single events. Many new mutations actually occur in the cell lineage before germ cell formation or meiosis and are therefore replicated pre-meiotically. The increased likelihood of substitutions caused by these clusters of new mutant alleles can change the fundamental theorem of neutral evolution.
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Affiliation(s)
- R C Woodruff
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
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Hartig JS, Kool ET. Efficient isothermal expansion of human telomeric and minisatellite repeats by Thermococcus litoralis DNA polymerase. Nucleic Acids Res 2005; 33:4922-7. [PMID: 16284196 PMCID: PMC1199558 DOI: 10.1093/nar/gki803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Repeating DNA sequences, such as telomeres, centromeres, and micro- and mini-satellites, comprise 50% of the genome and play important roles in regulatory and pathogenic mechanisms. In order to study structures and functions of such repeating sequences, it is important to have simple and efficient methods for making them in vitro. Here, we describe the efficient and convenient expansion of repetitive telomeric and minisatellite DNA sequences starting from small synthetic templates to final product lengths of several hundreds to thousands of nucleotides by the thermostable DNA polymerase from Thermococcus litoralis (Vent DNA polymerase). This enzyme was so far unknown to catalyze repeat expansion. Either single-stranded or double-stranded DNAs could be produced, depending on nucleotides present. Compared to earlier results obtained with other enzymes, the expansion reaction is highly efficient both in its yield and product length, and proceeds without thermal cycling. Moreover, the products are characterized by a narrow length distribution.
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Affiliation(s)
| | - Eric T. Kool
- To whom correspondence should be addressed. Tel: +1 650 724 4741; Fax: +1 650 725 0259;
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Gow JL, Noble LR, Rollinson D, Jones CS. A high incidence of clustered microsatellite mutations revealed by parent-offspring analysis in the African freshwater snail, Bulinus forskalii (Gastropoda, Pulmonata). Genetica 2005; 124:77-83. [PMID: 16011005 DOI: 10.1007/s10709-005-0204-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Genotyping of 11 microsatellites in 432 offspring from 28 families of the hermaphroditic, freshwater snail Bulinusforskalii detected 10 de novo mutant alleles. This gave an estimated mutation rate of 1.1 x 10(-3) per locus per gamete per generation. There was a trend towards repeat length expansion and, unlike most studies, multi-step mutations predominated, suggesting that the microsatellite mutation process does not conform to a strict stepwise mutation model. Interestingly, the ten mutant alleles appear to have arisen from only six independent germline mutation events within the microsatellite array, with seven of them residing in three mutational clusters. Our results extend observations of clustered microsatellite mutations to another taxonomic group and type of mating system, self-fertile gastropods, and provide compelling evidence of premeiotic germline mutations, a phenomenon that could greatly impact upon our understanding of mutation dynamics but which has received little attention.
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Affiliation(s)
- Jennifer L Gow
- Department of Zoology, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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Adams RI, Brown KM, Hamilton MB. The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis). Mol Ecol 2004; 13:2579-88. [PMID: 15315672 DOI: 10.1111/j.1365-294x.2004.02256.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microsatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical tree Corythophora alta and 11 loci in the anadromous fish Morone saxatilis by sequencing 14-23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy for M. saxatilis loci. Seven C. alta loci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy in C. alta generally produced little or no change in single-locus estimates of RST, except for two loci in which some additional differentiation among populations was revealed. Twelve-locus estimates of RST (including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% for C. alta and M. saxatilis, respectively. Simulations showed that the increase in RST produced by homoplasy correction was only slightly larger than variation in RST estimates expected to be caused by methodological errors.
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Affiliation(s)
- Rachel I Adams
- Georgetown University, Department of Biology, Reiss Sciences Building 406, 37th and O Streets NW, Washington, DC 20057-1229 USA
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Lian C, Oishi R, Miyashita N, Hogetsu T. High somatic instability of a microsatellite locus in a clonal tree, Robinia pseudoacacia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:836-841. [PMID: 14625672 DOI: 10.1007/s00122-003-1500-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Accepted: 10/09/2003] [Indexed: 05/24/2023]
Abstract
Robinia pseudoacacia L. is a clonal tree species. To investigate a mutation within eight microsatellite loci of R. pseudoacacia, we analyzed DNA samples obtained from different leaf samples within each ramet, leaves from ramets within the genet, and seeds. Of the eight loci, locus Rops15 (AG motif) displayed hypermutability. The mutation rates of Rops15 within each ramet, among ramets within the genet, and offspring were 6.27% (ranging from 0 to 31.1%), 6.11% (from 0 to 25.0%) and 3.78% (from 0 to 10.9%), respectively. The mutation rate increased with allele size (13-71 repeat units). The mutation patterns observed in Rops15 were distinctive in two ways. First, there was a significant bias toward additions over deletions, and both addition and deletion of single repeats were dominant at alleles with lengths less than 232 bp (63 repeats). Second, for the longest allele of 248 bp (71 repeats), the number of losses was higher than the number of gains. These observations suggest that the mutation patterns of microsatellites in R. pseudoacacia may follow a generalized stepwise mutation model, and that the tendency of long alleles to mutate to shorter lengths acts to prevent infinite growth. Finally, the observation of somatic hypermutability at locus Rops15 highlights the need for caution when using highly polymorphic microsatellites for population genetic structure and paternity analysis in tree species.
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Affiliation(s)
- Chunlan Lian
- Asian Natural Environmental Science Center, The University of Tokyo, Midori-cho 1-1-8, Nishitokyo-shi, 188-0002, Tokyo, Japan.
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Crane PA, Lewis CJ, Kretschmer EJ, Miller SJ, Spearman WJ, DeCicco AL, Lisac MJ, Wenburg JK. Characterization and inheritance of seven microsatellite loci from Dolly Varden, Salvelinus malma, and cross-species amplification in Arctic char, S. alpinus. CONSERV GENET 2004. [DOI: 10.1007/s10592-004-1853-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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