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Gilabert A, Rieux A, Robert S, Vitalis R, Zapater M, Abadie C, Carlier J, Ravigné V. Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa. Ecol Evol 2023; 13:e10013. [PMID: 37091563 PMCID: PMC10116021 DOI: 10.1002/ece3.10013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step toward improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana Pseudocercospora fijiensis, by testing the historical hypothesis against other plausible hypotheses. We analyzed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.
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Affiliation(s)
- A. Gilabert
- Université de la Réunion, UMR PVBMTSaint‐PierreFrance
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
- Present address:
CIRAD, UMR AGAP InstitutMontpellierFrance
- Present address:
UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - A. Rieux
- CIRAD, UMR PVBMTSaint‐PierreFrance
| | - S. Robert
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - R. Vitalis
- CBGPUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - M.‐F. Zapater
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - C. Abadie
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - J. Carlier
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - V. Ravigné
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
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Gallet R, Di Mattia J, Ravel S, Zeddam JL, Vitalis R, Michalakis Y, Blanc S. Gene Copy Number Variations at the Within-Host Population Level Modulate Gene Expression in a Multipartite Virus. Virus Evol 2022; 8:veac058. [PMID: 35799884 PMCID: PMC9255600 DOI: 10.1093/ve/veac058] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/02/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022] Open
Abstract
Multipartite viruses have a segmented genome, with each segment encapsidated separately. In all multipartite virus species for which the question has been addressed, the distinct segments reproducibly accumulate at a specific and host-dependent relative frequency, defined as the ‘genome formula’. Here, we test the hypothesis that the multipartite genome organization facilitates the regulation of gene expression via changes of the genome formula and thus via gene copy number variations. In a first experiment, the faba bean necrotic stunt virus (FBNSV), whose genome is composed of eight DNA segments each encoding a single gene, was inoculated into faba bean or alfalfa host plants, and the relative concentrations of the DNA segments and their corresponding messenger RNAs (mRNAs) were monitored. In each of the two host species, our analysis consistently showed that the genome formula variations modulate gene expression, the concentration of each genome segment linearly and positively correlating to that of its cognate mRNA but not of the others. In a second experiment, twenty parallel FBNSV lines were transferred from faba bean to alfalfa plants. Upon host switching, the transcription rate of some genome segments changes, but the genome formula is modified in a way that compensates for these changes and maintains a similar ratio between the various viral mRNAs. Interestingly, a deep-sequencing analysis of these twenty FBNSV lineages demonstrated that the host-related genome formula shift operates independently of DNA-segment sequence mutation. Together, our results indicate that nanoviruses are plastic genetic systems, able to transiently adjust gene expression at the population level in changing environments, by modulating the copy number but not the sequence of each of their genes.
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Affiliation(s)
- Romain Gallet
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
- CBGP, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Jérémy Di Mattia
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Sébastien Ravel
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Jean-Louis Zeddam
- PHIM, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
| | - Renaud Vitalis
- CBGP, Univ Montpellier, INRAE, CIRAD, IRD, Institut Agro, Montpellier, France
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Gay L, Dhinaut J, Jullien M, Vitalis R, Navascués M, Ranwez V, Ronfort J. Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift. Ecol Evol 2022; 12:e8555. [PMID: 35127051 PMCID: PMC8794724 DOI: 10.1002/ece3.8555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/10/2022] Open
Abstract
Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced.
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Affiliation(s)
- Laurène Gay
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Julien Dhinaut
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
Evolutionary Biology and Ecology of AlgaeUPMCUniversity of Paris VI, UC, UACH, UMI 3614CNRSSorbonne UniversitésRoscoffFrance
| | - Margaux Jullien
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
INRAUniv. Paris‐SudCNRSAgroParisTechGQE – Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Renaud Vitalis
- CIRADINRAEInstitut AgroIRDCBGPUniv MontpellierMontpellierFrance
| | | | - Vincent Ranwez
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Joëlle Ronfort
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
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Gautier M, Vitalis R, Flori L, Estoup A. ƒ-statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat. Mol Ecol Resour 2021; 22:1394-1416. [PMID: 34837462 DOI: 10.1111/1755-0998.13557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/16/2021] [Accepted: 11/08/2021] [Indexed: 11/27/2022]
Abstract
By capturing various patterns of the structuring of genetic variation across populations, f -statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariance of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly relevant for the analysis of pooled sequencing (Pool-Seq) data. We here propose a reinterpretation of the F (and D) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool-Seq data and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three-population test of admixture; (ii) four-population test of treeness; (iii) F4-ratio estimation of admixture rates; and (iv) fitting, visualization and (semi-automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool-Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost-effective Pool-Seq design involving relatively low sequencing coverages. We further analyzed a real Pool-Seq data made of 14 populations of the invasive species Drosophila suzukii which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user-friendly and efficient all-in-one tool to unravel complex population genetic histories from large-size Pool-Seq or allele count SNP data.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Renaud Vitalis
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Laurence Flori
- SelMet, INRAE, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Arnaud Estoup
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Collin FD, Durif G, Raynal L, Lombaert E, Gautier M, Vitalis R, Marin JM, Estoup A. Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest. Mol Ecol Resour 2021; 21:2598-2613. [PMID: 33950563 PMCID: PMC8596733 DOI: 10.1111/1755-0998.13413] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 03/29/2021] [Accepted: 04/28/2021] [Indexed: 01/07/2023]
Abstract
Simulation-based methods such as approximate Bayesian computation (ABC) are well-adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. Random Forest allows conducting inferences at a low computational cost, without preliminary selection of the relevant components of the ABC summary statistics, and bypassing the derivation of ABC tolerance levels. We have implemented a set of RF algorithms to process inferences using simulated data sets generated from an extended version of the population genetic simulator implemented in DIYABC v2.1.0. The resulting computer package, named DIYABC Random Forest v1.0, integrates two functionalities into a user-friendly interface: the simulation under custom evolutionary scenarios of different types of molecular data (microsatellites, DNA sequences or SNPs) and RF treatments including statistical tools to evaluate the power and accuracy of inferences. We illustrate the functionalities of DIYABC Random Forest v1.0 for both scenario choice and parameter estimation through the analysis of pseudo-observed and real data sets corresponding to pool-sequencing and individual-sequencing SNP data sets. Because of the properties inherent to the implemented RF methods and the large feature vector (including various summary statistics and their linear combinations) available for SNP data, DIYABC Random Forest v1.0 can efficiently contribute to the analysis of large SNP data sets to make inferences about complex population genetic histories.
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Affiliation(s)
| | - Ghislain Durif
- IMAG, Univ Montpellier, CNRS, UMR 5149, Montpellier, France
| | - Louis Raynal
- IMAG, Univ Montpellier, CNRS, UMR 5149, Montpellier, France
| | - Eric Lombaert
- ISA, INRAE, CNRS, Univ Côte d'Azur, Sophia Antipolis, France
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Arnaud Estoup
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Rohfritsch A, Galan M, Gautier M, Gharbi K, Olsson G, Gschloessl B, Zeimes C, VanWambeke S, Vitalis R, Charbonnel N. Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden. Ecol Evol 2018; 8:11273-11292. [PMID: 30519443 PMCID: PMC6262921 DOI: 10.1002/ece3.4603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Natural reservoirs of zoonotic pathogens generally seem to be capable of tolerating infections. Tolerance and its underlying mechanisms remain difficult to assess using experiments or wildlife surveys. High-throughput sequencing technologies give the opportunity to investigate the genetic bases of tolerance, and the variability of its mechanisms in natural populations. In particular, population genomics may provide preliminary insights into the genes shaping tolerance and potentially influencing epidemiological dynamics. Here, we addressed these questions in the bank vole Myodes glareolus, the specific asymptomatic reservoir host of Puumala hantavirus (PUUV), which causes nephropathia epidemica (NE) in humans. Despite the continuous spatial distribution of M. glareolus in Sweden, NE is endemic to the northern part of the country. Northern bank vole populations in Sweden might exhibit tolerance strategies as a result of coadaptation with PUUV. This may favor the circulation and maintenance of PUUV and lead to high spatial risk of NE in northern Sweden. We performed a genome-scan study to detect signatures of selection potentially correlated with spatial variations in tolerance to PUUV. We analyzed six bank vole populations from Sweden, sampled from northern NE-endemic to southern NE-free areas. We combined candidate gene analyses (Tlr4, Tlr7, and Mx2 genes) and high-throughput sequencing of restriction site-associated DNA (RAD) markers. Outlier loci showed high levels of genetic differentiation and significant associations with environmental data including variations in the regional number of NE human cases. Among the 108 outliers that matched to mouse protein-coding genes, 14 corresponded to immune-related genes. The main biological pathways found to be significantly enriched corresponded to immune processes and responses to hantavirus, including the regulation of cytokine productions, TLR cascades, and IL-7, VEGF, and JAK-STAT signaling. In the future, genome-scan replicates and functional experimentations should enable to assess the role of these biological pathways in M. glareolus tolerance to PUUV.
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Affiliation(s)
- Audrey Rohfritsch
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Karim Gharbi
- Norwich Research ParkEarlham InstituteNorwich, NorfolkUK
| | - Gert Olsson
- Department of Wildlife, Fish, and Environmental StudiesSLUUmeåSweden
| | - Bernhard Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Caroline Zeimes
- Georges Lemaître Centre for Earth and Climate Research, Earth and Life InstituteUniversité Catholique de Louvain (UCL)Louvain‐la‐NeuveBelgium
| | - Sophie VanWambeke
- Georges Lemaître Centre for Earth and Climate Research, Earth and Life InstituteUniversité Catholique de Louvain (UCL)Louvain‐la‐NeuveBelgium
| | - Renaud Vitalis
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
| | - Nathalie Charbonnel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
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Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
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Frachon L, Libourel C, Villoutreix R, Carrère S, Glorieux C, Huard-Chauveau C, Navascués M, Gay L, Vitalis R, Baron E, Amsellem L, Bouchez O, Vidal M, Le Corre V, Roby D, Bergelson J, Roux F. Author Correction: Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nat Ecol Evol 2018; 2:194. [DOI: 10.1038/s41559-017-0405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Leblois R, Gautier M, Rohfritsch A, Foucaud J, Burban C, Galan M, Loiseau A, Sauné L, Branco M, Gharbi K, Vitalis R, Kerdelhué C. Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa. Mol Ecol 2017; 27:264-278. [DOI: 10.1111/mec.14411] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 01/01/2023]
Affiliation(s)
- R. Leblois
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
- Institut de Biologie Computationnelle (IBC); Université de Montpellier; Montpellier France
| | - M. Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
- Institut de Biologie Computationnelle (IBC); Université de Montpellier; Montpellier France
| | - A. Rohfritsch
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - J. Foucaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - C. Burban
- INRA, UMR1202 BIOGECO (INRA - Université de Bordeaux); Cestas Cedex France
| | - M. Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - A. Loiseau
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - L. Sauné
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
| | - M. Branco
- Centro de Estudos Florestais (CEF); Instituto Superior de Agronomia (ISA); University of Lisbon; Lisbon Portugal
| | - K. Gharbi
- Edinburgh Genomics; School of Biological Sciences; University of Edinburgh; Edinburgh UK
| | - R. Vitalis
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
- Institut de Biologie Computationnelle (IBC); Université de Montpellier; Montpellier France
| | - C. Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier; Montferrier sur Lez Cedex France
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10
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Frachon L, Libourel C, Villoutreix R, Carrère S, Glorieux C, Huard-Chauveau C, Navascués M, Gay L, Vitalis R, Baron E, Amsellem L, Bouchez O, Vidal M, Le Corre V, Roby D, Bergelson J, Roux F. Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nat Ecol Evol 2017. [PMID: 29185515 DOI: 10.1038/s41559-017-0297-91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Rapid phenotypic evolution of quantitative traits can occur within years, but its underlying genetic architecture remains uncharacterized. Here we test the theoretical prediction that genes with intermediate pleiotropy drive adaptive evolution in nature. Through a resurrection experiment, we grew Arabidopsis thaliana accessions collected across an 8-year period in six micro-habitats representative of that local population. We then used genome-wide association mapping to identify the single-nucleotide polymorphisms (SNPs) associated with evolved and unevolved traits in each micro-habitat. Finally, we performed a selection scan by testing for temporal differentiation in these SNPs. Phenotypic evolution was consistent across micro-habitats, but its associated genetic bases were largely distinct. Adaptive evolutionary change was most strongly driven by a small number of quantitative trait loci (QTLs) with intermediate degrees of pleiotropy; this pleiotropy was synergistic with the per-trait effect size of the SNPs, increasing with the degree of pleiotropy. In addition, weak selection was detected for frequent micro-habitat-specific QTLs that shape single traits. In this population, A. thaliana probably responded to local warming and increased competition, in part mediated by central regulators of flowering time. This genetic architecture, which includes both synergistic pleiotropic QTLs and distinct QTLs within particular micro-habitats, enables rapid phenotypic evolution while still maintaining genetic variation in wild populations.
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Affiliation(s)
- Léa Frachon
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France
| | - Cyril Libourel
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France
| | - Romain Villoutreix
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, 59655, Villeneuve d'Ascq Cedex, France
| | - Sébastien Carrère
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France
| | - Cédric Glorieux
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, 59655, Villeneuve d'Ascq Cedex, France
| | | | - Miguel Navascués
- INRA, UMR CBGP, 34988, Montferrier-sur-Lez, France
- Institut de Biologie Computationnelle, Montpellier, 34095, France
| | | | - Renaud Vitalis
- INRA, UMR CBGP, 34988, Montferrier-sur-Lez, France
- Institut de Biologie Computationnelle, Montpellier, 34095, France
| | - Etienne Baron
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, 59655, Villeneuve d'Ascq Cedex, France
| | - Laurent Amsellem
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, 59655, Villeneuve d'Ascq Cedex, France
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 31326, Castanet-Tolosan, France
| | - Marie Vidal
- INRA, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France
- INRA, UAR1209, 31326, Castanet-Tolosan, France
| | | | - Dominique Roby
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France.
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, 59655, Villeneuve d'Ascq Cedex, France.
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11
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Dubois A, Galan M, Cosson JF, Gauffre B, Henttonen H, Niemimaa J, Razzauti M, Voutilainen L, Vitalis R, Guivier E, Charbonnel N. Microevolution of bank voles (Myodes glareolus) at neutral and immune-related genes during multiannual dynamic cycles: Consequences for Puumala hantavirus epidemiology. Infect Genet Evol 2016; 49:318-329. [PMID: 27956196 DOI: 10.1016/j.meegid.2016.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 01/02/2023]
Abstract
Understanding how host dynamics, including variations of population size and dispersal, may affect the epidemiology of infectious diseases through ecological and evolutionary processes is an active research area. Here we focus on a bank vole (Myodes glareolus) metapopulation surveyed in Finland between 2005 and 2009. Bank vole is the reservoir of Puumala hantavirus (PUUV), the agent of nephropathia epidemica (NE, a mild form of hemorrhagic fever with renal symptom) in humans. M. glareolus populations experience multiannual density fluctuations that may influence the level of genetic diversity maintained in bank voles, PUUV prevalence and NE occurrence. We examine bank vole metapopulation genetics at presumably neutral markers and immune-related genes involved in susceptibility to PUUV (Tnf-promoter, Tlr4, Tlr7 and Mx2 gene) to investigate the links between population dynamics, microevolutionary processes and PUUV epidemiology. We show that genetic drift slightly and transiently affects neutral and adaptive genetic variability within the metapopulation. Gene flow seems to counterbalance its effects during the multiannual density fluctuations. The low abundance phase may therefore be too short to impact genetic variation in the host, and consequently viral genetic diversity. Environmental heterogeneity does not seem to affect vole gene flow, which might explain the absence of spatial structure previously detected in PUUV in this area. Besides, our results suggest the role of vole dispersal on PUUV circulation through sex-specific and density-dependent movements. We find little evidence of selection acting on immune-related genes within this metapopulation. Footprint of positive selection is detected at Tlr-4 gene in 2008 only. We observe marginally significant associations between Mx2 genotype and PUUV genogroups. These results show that neutral processes seem to be the main factors affecting the evolution of these immune-related genes at a contemporary scale, although the relative effects of neutral and adaptive forces could vary temporally with density fluctuations. Immune related gene polymorphism may in turn partly influence PUUV epidemiology in this metapopulation.
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Affiliation(s)
- Adelaïde Dubois
- INRA, UMR CBGP, F-34988 Montferrier-sur-Lez, France; Anses, Unité de Virologie, 31 avenue Tony Garnier, 69364 Lyon, France.
| | - Maxime Galan
- INRA, UMR CBGP, F-34988 Montferrier-sur-Lez, France
| | - Jean-François Cosson
- INRA, UMR CBGP, F-34988 Montferrier-sur-Lez, France; INRA-ANSES-ENVA, UMR 0956 BIPAR, Maisons-Alfort, France
| | | | | | - Jukka Niemimaa
- Natural Resources Institute Finland, FI-013012 Vantaa, Finland
| | | | - Liina Voutilainen
- Natural Resources Institute Finland, FI-013012 Vantaa, Finland; Department of Virology, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Emmanuel Guivier
- Biogeosciences, CNRS UMR 6282, Université de Bourgogne, Franche-Comté, 21000, Dijon, France
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Gautier M, Klassmann A, Vitalis R. rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Mol Ecol Resour 2016; 17:78-90. [PMID: 27863062 DOI: 10.1111/1755-0998.12634] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/29/2016] [Accepted: 10/31/2016] [Indexed: 01/01/2023]
Abstract
Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g. EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. The rehh package for r was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance was not sufficient to cope with the growing size of available data sets. Here, we propose a major upgrade of the rehh package, which includes an improved processing of the input files, a faster algorithm to enumerate haplotypes, as well as multithreading. As illustrated with the analysis of large human haplotype data sets, these improvements decrease the computation time by more than one order of magnitude. This new version of rehh will thus allow performing iHS-, Rsb- or XP-EHH-based scans on large data sets. The package rehh 2.0 is available from the CRAN repository (http://cran.r-project.org/web/packages/rehh/index.html) together with help files and a detailed manual.
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Affiliation(s)
- Mathieu Gautier
- INRA, UMR CBGP, Montferrier-sur-Lez, F-34988, France.,Institut de Biologie Computationnelle, Montpellier, F-34095, France
| | | | - Renaud Vitalis
- INRA, UMR CBGP, Montferrier-sur-Lez, F-34988, France.,Institut de Biologie Computationnelle, Montpellier, F-34095, France
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13
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Affiliation(s)
- Arnaud Estoup
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Virginie Ravigné
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
| | - Ruth Hufbauer
- Department of Bioagricultural Science and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Renaud Vitalis
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Mathieu Gautier
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Benoit Facon
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
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14
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Popkin M, Piffaretti J, Clamens AL, Qiao GX, Chen J, Vitalis R, Vanlerberghe-Masutti F, Gupta RK, Lamaari M, Langella O, Coeur d'acier A, Jousselin E. Large-scale phylogeographic study of the cosmopolitan aphid pestBrachycaudus helichrysireveals host plant associated lineages that evolved in allopatry. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Megan Popkin
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
| | - Josephine Piffaretti
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
| | - Anne-Laure Clamens
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; No. 1 Beichen West Road Chaoyang District Beijing 100101 China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; No. 1 Beichen West Road Chaoyang District Beijing 100101 China
| | - Renaud Vitalis
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
| | - Flavie Vanlerberghe-Masutti
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
| | - Rakesh K. Gupta
- Division of Entomology; Faculty of Agriculture; Sher-e-Kashmir University Agricultural & Technology of Jammu; Chatha Jammu 180009 India
| | - Malik Lamaari
- Laboratory of LATPPAM; Department of Agronomy; Institute of Veterinary and Agronomic Sciences; University of Batna; Batna Algeria
| | - Olivier Langella
- CNRS, UMR 0320/UMR 8120 Génétique Végétale; F-91190 Gif-sur-Yvette France
| | - Armelle Coeur d'acier
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
| | - Emmanuelle Jousselin
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro); 755 avenue du Campus Agropolis CS 30016 F-34 988 Montferrier-sur-Lez France
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Leblois R, Pudlo P, Néron J, Bertaux F, Reddy Beeravolu C, Vitalis R, Rousset F. Maximum-likelihood inference of population size contractions from microsatellite data. Mol Biol Evol 2014; 31:2805-23. [PMID: 25016583 DOI: 10.1093/molbev/msu212] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MSVAR) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared with alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that the violations of a single step mutation assumption induce very high bias toward false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the MIGRAINE software package.
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Affiliation(s)
- Raphaël Leblois
- INRA, UMR 1062 CBGP (INRA-IRD-CIRAD-Montpellier Supagro), Montpellier, France Muséum National d'Histoire Naturelle, CNRS, UMR OSEB, Paris, France Institut de Biologie Computationnelle, Montpellier, France
| | - Pierre Pudlo
- INRA, UMR 1062 CBGP (INRA-IRD-CIRAD-Montpellier Supagro), Montpellier, France Institut de Biologie Computationnelle, Montpellier, France Université Montpellier 2, CNRS, UMR I3M, Montpellier, France
| | - Joseph Néron
- Muséum National d'Histoire Naturelle, CNRS, UMR OSEB, Paris, France
| | - François Bertaux
- Muséum National d'Histoire Naturelle, CNRS, UMR OSEB, Paris, France INRIA Paris-Rocquencourt, BANG Team, Le Chesnay, France
| | | | - Renaud Vitalis
- INRA, UMR 1062 CBGP (INRA-IRD-CIRAD-Montpellier Supagro), Montpellier, France Institut de Biologie Computationnelle, Montpellier, France
| | - François Rousset
- Institut de Biologie Computationnelle, Montpellier, France Université Montpellier 2, CNRS, UMR ISEM, Montpellier, France
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Alexandre H, Ponsard S, Bourguet D, Vitalis R, Audiot P, Cros-Arteil S, Streiff R. When history repeats itself: exploring the genetic architecture of host-plant adaptation in two closely related lepidopteran species. PLoS One 2013; 8:e69211. [PMID: 23874914 PMCID: PMC3709918 DOI: 10.1371/journal.pone.0069211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 06/11/2013] [Indexed: 11/18/2022] Open
Abstract
The genus Ostrinia includes two allopatric maize pests across Eurasia, namely the European corn borer (ECB, O. nubilalis) and the Asian corn borer (ACB, O. furnacalis). A third species, the Adzuki bean borer (ABB, O. scapulalis), occurs in sympatry with both the ECB and the ACB. The ABB mostly feeds on native dicots, which probably correspond to the ancestral host plant type for the genus Ostrinia. This situation offers the opportunity to characterize the two presumably independent adaptations or preadaptations to maize that occurred in the ECB and ACB. In the present study, we aimed at deciphering the genetic architecture of these two adaptations to maize, a monocot host plant recently introduced into Eurasia. To this end, we performed a genome scan analysis based on 684 AFLP markers in 12 populations of ECB, ACB and ABB. We detected 2 outlier AFLP loci when comparing French populations of the ECB and ABB, and 9 outliers when comparing Chinese populations of the ACB and ABB. These outliers were different in both countries, and we found no evidence of linkage disequilibrium between any two of them. These results suggest that adaptation or preadaptation to maize relies on a different genetic architecture in the ECB and ACB. However, this conclusion must be considered in light of the constraints inherent to genome scan approaches and of the intricate evolution of adaptation and reproductive isolation in the Ostrinia spp. complex.
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Affiliation(s)
- Hermine Alexandre
- INRA, UMR CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
- Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
- CNRS, Université Paul Sabatier, UMR5174 EDB, Toulouse, France
| | - Sergine Ponsard
- Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
- CNRS, Université Paul Sabatier, UMR5174 EDB, Toulouse, France
| | - Denis Bourguet
- INRA, UMR CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Renaud Vitalis
- INRA, UMR CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Philippe Audiot
- INRA, UMR CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Sandrine Cros-Arteil
- INRA, UMR CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Réjane Streiff
- INRA, UMR CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
- * E-mail:
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17
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Vitalis R, Rousset F, Kobayashi Y, Olivieri I, Gandon S. The joint evolution of dispersal and dormancy in a metapopulation with local extinctions and kin competition. Evolution 2013; 67:1676-91. [PMID: 23730761 DOI: 10.1111/evo.12069] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/17/2013] [Indexed: 12/11/2022]
Abstract
Dispersal and dormancy are two strategies that allow recolonization of empty patches and escape from kin competition. Because they presumably respond to similar evolutionary forces, it is tempting to consider that these strategies may substitute for each other. Yet in order to predict the outcome of the evolution of dispersal and dormancy, and to characterize the emerging covariation between both traits, it is necessary to consider models where dispersal and dormancy evolve jointly. Here, we analyze the evolution of dispersal and dormancy as a function of direct fitness costs, environmental variation, and competition among relatives. We consider two scenarios depending on whether the rates of dormancy for philopatric and dispersed individuals are constrained to be the same (unconditional dormancy) or allowed to be different (conditional dormancy). We show that only philopatric individuals should enter dormancy, at a rate increasing with increasing rates of local extinction and decreasing population sizes. When dormancy and dispersal evolve jointly, we observe a wide range of evolutionary outcomes. In particular, we find that the pattern of covariation between the evolutionarily stable rates of dispersal and dormancy is molded by the rate of extinction and the local population size.
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Affiliation(s)
- Renaud Vitalis
- Institut des Sciences de l'Évolution, UMR 5554, CNRS, Université Montpellier 2, Montpellier cedex 5, Place Eugène Bataillon, France.
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18
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Ségurel L, Austerlitz F, Toupance B, Gautier M, Kelley JL, Pasquet P, Lonjou C, Georges M, Voisin S, Cruaud C, Couloux A, Hegay T, Aldashev A, Vitalis R, Heyer E. Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia. Eur J Hum Genet 2013; 21:1146-51. [PMID: 23340510 DOI: 10.1038/ejhg.2012.295] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 10/30/2012] [Accepted: 12/11/2012] [Indexed: 11/09/2022] Open
Abstract
The high prevalence of type 2 diabetes and its uneven distribution among human populations is both a major public health concern and a puzzle in evolutionary biology. Why is this deleterious disease so common, while the associated genetic variants should be removed by natural selection? The 'thrifty genotype' hypothesis proposed that the causal genetic variants were advantageous and selected for during the majority of human evolution. It remains, however, unclear whether genetic data support this scenario. In this study, we characterized patterns of selection at 10 variants associated with type 2 diabetes, contrasting one herder and one farmer population from Central Asia. We aimed at identifying which alleles (risk or protective) are under selection, dating the timing of selective events, and investigating the effect of lifestyle on selective patterns. We did not find any evidence of selection on risk variants, as predicted by the thrifty genotype hypothesis. Instead, we identified clear signatures of selection on protective variants, in both populations, dating from the beginning of the Neolithic, which suggests that this major transition was accompanied by a selective advantage for non-thrifty variants. Combining our results with worldwide data further suggests that East Asia was particularly prone to such recent selection of protective haplotypes. As much effort has been devoted so far to searching for thrifty variants, we argue that more attention should be paid to the evolution of non-thrifty variants.
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Affiliation(s)
- Laure Ségurel
- 1] Eco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle - Centre National de la Recherche Scientifique - Université Paris 7 Diderot, Paris, France [2] Department of Human Genetics, University of Chicago, Chicago, IL, USA
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Jaquiéry J, Stoeckel S, Nouhaud P, Mieuzet L, Mahéo F, Legeai F, Bernard N, Bonvoisin A, Vitalis R, Simon JC. Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex. Mol Ecol 2012; 21:5251-64. [PMID: 23017212 DOI: 10.1111/mec.12048] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/06/2012] [Indexed: 11/26/2022]
Abstract
A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome-wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of divergent host races, to explore the organization of the genomic divergence associated with host plant adaptation and ecological speciation. We analysed 390 microsatellite markers located at variable distances from predicted genes in replicate samples of sympatric populations of the pea aphid collected on alfalfa, red clover and pea, which correspond to three common host-adapted races reported in this species complex. Using a method that accounts for the hierarchical structure of our data set, we found a set of 11 outlier loci that show higher genetic differentiation between host races than expected under the null hypothesis of neutral evolution. Two of the outliers are close to olfactory receptor genes and three other nearby genes encoding salivary proteins. The remaining outliers are located in regions with genes of unknown functions, or which functions are unlikely to be involved in interactions with the host plant. This study reveals genetic signatures of divergent selection across the genome and provides an inventory of candidate genes responsible for plant specialization in the pea aphid, thereby setting the stage for future functional studies.
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Affiliation(s)
- J Jaquiéry
- INRA, UMR 1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, BP 35327, 35653, Le Rheu Cedex, France
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Smadja CM, Canbäck B, Vitalis R, Gautier M, Ferrari J, Zhou JJ, Butlin RK. Large-scale candidate gene scan reveals the role of chemoreceptor genes in host plant specialization and speciation in the pea aphid. Evolution 2012; 66:2723-38. [PMID: 22946799 DOI: 10.1111/j.1558-5646.2012.01612.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the drivers of speciation is critical to interpreting patterns of biodiversity. The identification of the genetic changes underlying adaptation and reproductive isolation is necessary to link barriers to gene flow to the causal origins of divergence. Here, we present a novel approach to the genetics of speciation, which should complement the commonly used approaches of quantitative trait locus mapping and genome-wide scans for selection. We present a large-scale candidate gene approach by means of sequence capture, applied to identifying the genetic changes underlying reproductive isolation in the pea aphid, a model system for the study of ecological speciation. Targeted resequencing enabled us to scale up the candidate gene approach, specifically testing for the role of chemosensory gene families in host plant specialization. Screening for the signature of divergence under selection at 172 candidate and noncandidate loci, we revealed a handful of loci that show high levels of differentiation among host races, which almost all correspond to odorant and gustatory receptor genes. This study offers the first indication that some chemoreceptor genes, often tightly linked together in the genome, could play a key role in local adaptation and reproductive isolation in the pea aphid and potentially other phytophagous insects. Our approach opens a new route toward the functional genomics of ecological speciation.
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Affiliation(s)
- Carole M Smadja
- Centre National de la Recherche Scientifique CNRS-Institut des Sciences de l'Evolution UMR 5554, cc065 Université Montpellier 2, 34095 Montpellier, France.
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Abstract
UNLABELLED With the development of next-generation sequencing and genotyping approaches, large single nucleotide polymorphism haplotype datasets are becoming available in a growing number of both model and non-model species. Identifying genomic regions with unexpectedly high local haplotype homozygosity relatively to neutral expectation represents a powerful strategy to ascertain candidate genes responding to natural or artificial selection. To facilitate genome-wide scans of selection based on the analysis of long-range haplotypes, we developed the R package rehh. It provides a versatile tool to detect the footprints of recent or ongoing selection with several graphical functions that help visual interpretation of the results. AVAILABILITY AND IMPLEMENTATION Stable version is available from CRAN: http://cran.r-project.org/. Development version is available from the R-forge repository: http://r-forge.r-project.org/projects/rehh. Both versions can be installed directly from R. Function documentation and example data files are provided within the package and a tutorial is available as Supplementary Material. rehh is distributed under the GNU General Public Licence (GPL ≥ 2).
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Abstract
In the new era of population genomics, surveys of genetic polymorphism ("genome scans") offer the opportunity to distinguish locus-specific from genome-wide effects at many loci. Identifying presumably neutral regions of the genome that are assumed to be influenced by genome-wide effects only, and excluding presumably selected regions, is therefore critical to infer population demography and phylogenetic history reliably. Conversely, detecting locus-specific effects may help identify those genes that have been, or still are, targeted by natural selection. The software package DETSEL has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations. Recently, two major improvements have been made: the analysis of dominant markers is now supported, and the estimation of empirical P-values has been implemented. These features, which are described below, have been incorporated into an R package, which replaces the stand-alone DETSEL software package.
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Affiliation(s)
- Renaud Vitalis
- CNRS, INRA, UMR CBGP (INRA-IRD-CIRAD-Montpellier SupAgro), Montferrier-sur-Lez Cedex, France.
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Midamegbe A, Vitalis R, Malausa T, Delava E, Cros-Arteil S, Streiff R. Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species. Mol Ecol 2011; 20:1414-30. [PMID: 21375617 DOI: 10.1111/j.1365-294x.2011.05035.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It has recently been shown that the European corn borer, a major pest of maize crops, is actually composed of two genetically differentiated and reproductively isolated taxa, which are found in sympatry over a wide geographical range in Eurasia. Each taxon is adapted to specific host plants: Ostrinia nubilalis feeds mainly on maize, while O. scapulalis feeds mainly on hop or mugwort. Here, we present a genome scan approach as a first step towards an integrated molecular analysis of the adaptive genomic divergence between O. nubilalis and O. scapulalis. We analysed 609 AFLP marker loci in replicate samples of sympatric populations of Ostrinia spp. collected on maize, hop and mugwort, in France. Using two genome scan methods based on the analysis of population differentiation, we found a set of 28 outlier loci that departed from the neutral expectation in one or the other method (of which a subset of 14 loci were common to both methods), which showed a significantly increased differentiation between O. nubilalis and O. scapulalis, when compared to the rest of the genome. A subset of 12 outlier loci were sequenced, of which 7 were successfully re-amplified as target candidate loci. Three of these showed homology with annotated lepidopteran sequences from public nucleotide databases.
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Affiliation(s)
- Afiwa Midamegbe
- Institut National de la Recherche Agronomique, UMR CBGP (INRA-IRD-CIRAD-Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier sur Lez Cedex, France
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26
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Facon B, Hufbauer R, Tayeh A, Loiseau A, Lombaert E, Vitalis R, Guillemaud T, Lundgren J, Estoup A. Inbreeding Depression Is Purged in the Invasive Insect Harmonia axyridis. Curr Biol 2011; 21:424-7. [DOI: 10.1016/j.cub.2011.01.068] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 11/24/2022]
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27
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Ayala D, Fontaine MC, Cohuet A, Fontenille D, Vitalis R, Simard F. Chromosomal inversions, natural selection and adaptation in the malaria vector Anopheles funestus. Mol Biol Evol 2011; 28:745-58. [PMID: 20837604 PMCID: PMC3002248 DOI: 10.1093/molbev/msq248] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Chromosomal polymorphisms, such as inversions, are presumably involved in the rapid adaptation of populations to local environmental conditions. Reduced recombination between alternative arrangements in heterozygotes may protect sets of locally adapted genes, promoting ecological divergence and potentially leading to reproductive isolation and speciation. Through a comparative analysis of chromosomal inversions and microsatellite marker polymorphisms, we hereby present biological evidence that strengthens this view in the mosquito Anopheles funestus s.s, one of the most important and widespread malaria vectors in Africa. Specimens were collected across a wide range of geographical, ecological, and climatic conditions in Cameroon. We observed a sharp contrast between population structure measured at neutral microsatellite markers and at chromosomal inversions. Microsatellite data detected only a weak signal for population structuring among geographical zones (F(ST) < 0.013, P < 0.01). By contrast, strong differentiation among ecological zones was revealed by chromosomal inversions (F(ST) > 0.190, P < 0.01). Using standardized estimates of F(ST), we show that inversions behave at odds with neutral expectations strongly suggesting a role of environmental selection in shaping their distribution. We further demonstrate through canonical correspondence analysis that heterogeneity in eco-geographical variables measured at specimen sampling sites explained 89% of chromosomal variance in A. funestus. These results are in agreement with a role of chromosomal inversions in ecotypic adaptation in this species. We argue that this widespread mosquito represents an interesting model system for the study of chromosomal speciation mechanisms and should provide ample opportunity for comparative studies on the evolution of reproductive isolation and speciation in major human malaria vectors.
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Affiliation(s)
- Diego Ayala
- Institut de Recherche pour le Développement, UR016 CCPV, Montpellier, France.
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28
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Martínez-Cruz B, Vitalis R, Ségurel L, Austerlitz F, Georges M, Théry S, Quintana-Murci L, Hegay T, Aldashev A, Nasyrova F, Heyer E. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. Eur J Hum Genet 2010; 19:216-23. [PMID: 20823912 DOI: 10.1038/ejhg.2010.153] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Located in the Eurasian heartland, Central Asia has played a major role in both the early spread of modern humans out of Africa and the more recent settlements of differentiated populations across Eurasia. A detailed knowledge of the peopling in this vast region would therefore greatly improve our understanding of range expansions, colonizations and recurrent migrations, including the impact of the historical expansion of eastern nomadic groups that occurred in Central Asia. However, despite its presumable importance, little is known about the level and the distribution of genetic variation in this region. We genotyped 26 Indo-Iranian- and Turkic-speaking populations, belonging to six different ethnic groups, at 27 autosomal microsatellite loci. The analysis of genetic variation reveals that Central Asian diversity is mainly shaped by linguistic affiliation, with Turkic-speaking populations forming a cluster more closely related to East-Asian populations and Indo-Iranian speakers forming a cluster closer to Western Eurasians. The scattered position of Uzbeks across Turkic- and Indo-Iranian-speaking populations may reflect their origins from the union of different tribes. We propose that the complex genetic landscape of Central Asian populations results from the movements of eastern, Turkic-speaking groups during historical times, into a long-lasting group of settled populations, which may be represented nowadays by Tajiks and Turkmen. Contrary to what is generally thought, our results suggest that the recurrent expansions of eastern nomadic groups did not result in the complete replacement of local populations, but rather into partial admixture.
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Affiliation(s)
- Begoña Martínez-Cruz
- Muséum National d'Histoire Naturelle - Centre National de la Recherche Scientifique-Université Paris 7, UMR 7206, Éco-Anthropologie et Ethnobiologie, Paris, France
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Alberto F, Niort J, Derory J, Lepais O, Vitalis R, Galop D, Kremer A. Population differentiation of sessile oak at the altitudinal front of migration in the French Pyrenees. Mol Ecol 2010; 19:2626-39. [PMID: 20561196 DOI: 10.1111/j.1365-294x.2010.04631.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- F Alberto
- INRA, UMR 1202 Biodiversité Gènes et Communautés, Cestas, F-33610, France
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Verdu P, Leblois R, Froment A, Théry S, Bahuchet S, Rousset F, Heyer E, Vitalis R. Limited dispersal in mobile hunter-gatherer Baka Pygmies. Biol Lett 2010; 6:858-61. [PMID: 20427330 DOI: 10.1098/rsbl.2010.0192] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hunter-gatherer Pygmies from Central Africa are described as being extremely mobile. Using neutral genetic markers and population genetics theory, we explored the dispersal behaviour of the Baka Pygmies from Cameroon, one of the largest Pygmy populations in Central Africa. We found a strong correlation between genetic and geographical distances: a pattern of isolation by distance arising from limited parent-offspring dispersal. Our study suggests that mobile hunter-gatherers do not necessarily disperse over wide geographical areas.
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Affiliation(s)
- Paul Verdu
- Department of Human Genetics, University of Michigan, Ann Arbor, USA.
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Rhoné B, Vitalis R, Goldringer I, Bonnin I. Evolution of flowering time in experimental wheat populations: a comprehensive approach to detect genetic signatures of natural selection. Evolution 2010; 64:2110-25. [PMID: 20148950 DOI: 10.1111/j.1558-5646.2010.00970.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In annual plant species, flowering time is a major adaptive trait that synchronizes the initiation of reproduction with favorable environmental conditions. Here, we aimed at studying the evolution of flowering time in three experimental populations of bread wheat, grown in contrasting environments (Northern to Southern France) for 12 generations. By comparing the distribution of phenotypic and presumably neutral variation, we first showed that flowering time responded to selection during the 12 generations of the experiment. To get insight into the genetic architecture of that trait, we then tested whether the distribution of genetic polymorphisms at six candidate genes, presumably involved in the trait expression, departed from neutral expectation. To that end, we focused on the temporal variation during the course of the experiment, and on the spatial differentiation at the end of the experiment, using previously published methods adapted to our experimental design. Only those genes that were strongly associated with flowering time variation were detected as responding to selection. For genes that had low-to-moderate phenotypic effects, or when there was interaction across different genes, we did not find evidence of selection using methods based on the distribution of temporal or spatial variation. In such cases, it might be more informative to consider multilocus and multiallelic combinations across genes, which could be the targets of selection.
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Affiliation(s)
- Bénédicte Rhoné
- AgroParisTech, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France.
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Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet JM, Huelsenbeck J, Foll M, Yang Z, Rousset F, Balding D, Excoffier L. In defence of model-based inference in phylogeography. Mol Ecol 2010; 19:436-446. [PMID: 29284924 DOI: 10.1111/j.1365-294x.2009.04515.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.
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Affiliation(s)
- Mark A Beaumont
- School of Animal and Microbial Sciences, University of Reading, Whiteknights, PO Box 228, Reading, RG6 6AJ, UK
| | - Rasmus Nielsen
- Integrative Biology, UC Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA
| | | | - Jody Hey
- Department of Genetics, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Oscar Gaggiotti
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, 38041 GRENOBLE, France
| | - Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Arnaud Estoup
- INRA UMR Centre de Biologie et de Gestion des Populations (INRA ⁄ IRD ⁄ Cirad ⁄ Montpellier SupAgro), Campus international de Baillarguet, Montferrier-sur-Lez, France
| | - Mahesh Panchal
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Jukka Corander
- Department of Mathematics and statistics, University of Helsinki, Finland
| | - Mike Hickerson
- Biology Department, Queens College, City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367-1597, USA
| | - Scott A Sisson
- School of Mathematics and Statistics, University of New South Wales, Sydney, Australia
| | - Nelson Fagundes
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lounès Chikhi
- Université Paul Sabatier-UMR EDB 5174 118, 31062 Toulouse Cedex 09, France
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Renaud Vitalis
- CNRS-INRA, CBGP, Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez, France
| | - Jean-Marie Cornuet
- INRA UMR Centre de Biologie et de Gestion des Populations (INRA ⁄ IRD ⁄ Cirad ⁄ Montpellier SupAgro), Campus international de Baillarguet, Montferrier-sur-Lez, France
| | - John Huelsenbeck
- Integrative Biology, UC Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA
| | - Matthieu Foll
- CMPG, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ziheng Yang
- Department of Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Francois Rousset
- Institut des Sciences de l'Évolution, Universté Montpellier 2, CNRS, Place Eugène Bataillon, CC065, Montpellier, Cedex 5, France
| | - David Balding
- Institute of Genetics, University College London, 2nd Floor, Kathleen Lonsdale Building, 5 Gower Place, London WC1E 6BT, UK
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Cooper JD, Vitalis R, Waser PM, Gopurenko D, Hellgren EC, Gabor TM, DeWoody JA. Quantifying male-biased dispersal among social groups in the collared peccary (Pecari tajacu) using analyses based on mtDNA variation. Heredity (Edinb) 2009; 104:79-87. [DOI: 10.1038/hdy.2009.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Meyer CL, Vitalis R, Saumitou-Laprade P, Castric V. Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal. Mol Ecol 2009; 18:2050-62. [PMID: 19434814 DOI: 10.1111/j.1365-294x.2009.04159.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pollution by heavy metals is one of the strongest environmental constraints in human-altered environments that only a handful of species can cope with. Identifying the genes conferring to those species the ability to grow in polluted areas is a first step towards a global understanding of the evolutionary processes involved and will eventually improve phytoremediation practices. We used a genome-scan approach to detect loci under divergent selection among four populations of Arabidopsis halleri growing on either polluted or nonpolluted habitats. Based on a high density of amplified fragment length polymorphism (AFLP) markers (820 AFLP markers, i.e. approximately 1 marker per 0.3Mb), evidence for selection was found for some markers in every sampled population. Four loci departed from neutrality in both metallicolous populations and thus constitute high-quality candidates for general adaptation to pollution. Interestingly, some candidates differed between the two metallicolous populations, suggesting the possibility that different loci may be involved in adaptation in the different metallicolous populations.
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Affiliation(s)
- Claire-Lise Meyer
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille, Bâtiment SN2, Villeneuve d'Ascq, France
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36
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Ségurel L, Martínez-Cruz B, Quintana-Murci L, Balaresque P, Georges M, Hegay T, Aldashev A, Nasyrova F, Jobling MA, Heyer E, Vitalis R. Sex-specific genetic structure and social organization in Central Asia: insights from a multi-locus study. PLoS Genet 2008; 4:e1000200. [PMID: 18818760 PMCID: PMC2535577 DOI: 10.1371/journal.pgen.1000200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 08/18/2008] [Indexed: 12/01/2022] Open
Abstract
In the last two decades, mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome (NRY) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations, and to infer sex-specific demography and history. Most studies converge towards the notion that among populations, women are genetically less structured than men. This has been mainly explained by a higher migration rate of women, due to patrilocality, a tendency for men to stay in their birthplace while women move to their husband's house. Yet, since population differentiation depends upon the product of the effective number of individuals within each deme and the migration rate among demes, differences in male and female effective numbers and sex-biased dispersal have confounding effects on the comparison of genetic structure as measured by uniparentally inherited markers. In this study, we develop a new multi-locus approach to analyze jointly autosomal and X-linked markers in order to aid the understanding of sex-specific contributions to population differentiation. We show that in patrilineal herder groups of Central Asia, in contrast to bilineal agriculturalists, the effective number of women is higher than that of men. We interpret this result, which could not be obtained by the analysis of mtDNA and NRY alone, as the consequence of the social organization of patrilineal populations, in which genetically related men (but not women) tend to cluster together. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter. Human evolutionary history has been investigated mainly through the prism of genetic variation of the Y chromosome and mitochondrial DNA. These two uniparentally inherited markers reflect the demographic history of males and females, respectively. Their contrasting patterns of genetic differentiation reveal that women are more mobile than men among populations, which might be due to specific marriage rules. However, these two markers provide only a limited understanding of the underlying demographic processes. To obtain an independent picture of sex-specific demography, we developed a new multi-locus approach based on the analysis of markers from the autosomal and X-chromosomal compartments. We applied our method to 21 human populations sampled in Central Asia, with contrasting social organizations and lifestyles. We found that, in patrilineal populations, not only the migration rate but also the number of reproductive individuals is likely to be higher for women. This result does not hold for bilineal populations, for which both the migration rate and the number of reproductive individuals can be equal for both sexes. The social organization of patrilineal populations is the likely cause of this pattern. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter.
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Affiliation(s)
- Laure Ségurel
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique UMR 5145, Université Paris 7, Eco-Anthropologie et Ethnobiologie, Musée de l'Homme, Paris, France.
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Abstract
We study the evolution of the dispersal rate in a metapopulation model with extinction and colonization dynamics, akin to the model as originally described by Levins. To do so we extend the metapopulation model with a description of the within patch dynamics. By means of a separation of time scales we analytically derive a fitness expression from first principles for this model. The fitness function can be written as an inclusive fitness equation (Hamilton's rule). By recasting this equation in a form that emphasizes the effects of competition we show the effect of the local competition and the local population size on the evolution of dispersal. We find that the evolution of dispersal cannot be easily interpreted in terms of avoidance of kin competition, but rather that increased dispersal reduces the competitive ability. Our model also yields a testable prediction in term of relatedness and life-history parameters.
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Affiliation(s)
- Vincent A A Jansen
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK.
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Vitalis R, Couvet D. estim1.0: a computer program to infer population parameters from one- and two-locus gene identity probabilities. ACTA ACUST UNITED AC 2005. [DOI: 10.1046/j.1471-8278.2001.00086.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vitalis R, Dubois MP, Olivieri I. Characterization of microsatellite loci in the endangered species of fern Marsilea strigosa
Willd. (Marsileaceae, Pteridophyta). ACTA ACUST UNITED AC 2005. [DOI: 10.1046/j.1471-8278.2001.00026.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vitalis R, Glémin S, Olivieri I. When Genes Go to Sleep: The Population Genetic Consequences of Seed Dormancy and Monocarpic Perenniality. Am Nat 2004; 163:295-311. [PMID: 14970929 DOI: 10.1086/381041] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2003] [Accepted: 08/20/2003] [Indexed: 11/03/2022]
Abstract
In many annual plant populations, seeds may be dormant for several seasons before they germinate. Here, we investigate the consequences of both conditional (dispersed seeds cannot enter a dormant stage) and unconditional seed dormancy on the amount and the distribution of neutral genetic diversity within and among populations. We present joint demographic and population genetics models for single and subdivided populations and derive the effective size and population differentiation at both local and metapopulation scales. We suggest that a Wahlund effect is unlikely to result from age structure alone. Furthermore, the differentiation among populations is decreased by the presence of seed banks. We also extend these models to describe monocarpic (semelparous) perennial life cycle, where the nonreproductive stages are vegetative rosettes instead of dormant seeds. The main difference between the models relies in the way the density-dependent regulation is acting. The effective size of monocarpic perennial species may be less than the census number of individuals, and among-population differentiation is always larger than in annual species. We discuss our results in the light of recent population genetics surveys of annual plants with seed banks.
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Affiliation(s)
- Renaud Vitalis
- Laboratoire Genetique et Environnement, C C 065, Institut des Sciences de l'Evolution de Montpellier, Universite Montpellier II, 34095 Montpellier Cedex 05, France.
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41
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Abstract
Estimating population parameters from polymorphism frequency data requires neutral genetic markers. Any departure from neutrality may invalidate the inferences drawn from such analyses. We recently discussed the possibility of identifying markers that show deviation from neutral expectations in pairwise comparisons of diverging populations. We are now releasing a user-friendly software package that implements all the necessary steps to identify the signature of selection among molecular markers in a set of polymorphism data. This software can be downloaded free of charge at http://www.univ-montp2.fr/~genetix/detsel/detsel.html.
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Affiliation(s)
- R Vitalis
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.
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Vitalis R, Riba M, Colas B, Grillas P, Olivieri I. Multilocus genetic structure at contrasted spatial scales of the endangered water fern Marsilea strigosa Willd. (Marsileaceae, Pteridophyta). Am J Bot 2002; 89:1142-1155. [PMID: 21665714 DOI: 10.3732/ajb.89.7.1142] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Marsilea strigosa (Marsileaceae, Pterydophyta) is a rare water fern found in the Mediterranean basin, in temporary flooded habitats only. We analyzed the level and the distribution of genetic variation at seven microsatellite loci, both at the Mediterranean scale and at a narrower scale within a highly fragmented French metapopulation. Genetic diversity among individuals within each pond suggests that M. strigosa reproduces predominantly through selfing. The very high population differentiation at the Mediterranean scale indicates that gene flow (if any) is highly restricted. Similar differentiation is also found at the scale of a single metapopulation. The distribution of multilocus genotypes suggests that the genetic variation in this species is maintained mainly through the interplay of mutation and low recombination.
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Affiliation(s)
- Renaud Vitalis
- Laboratoire Génétique et Environnement, C.C. 065, ISEM (UMR 5554), Université Montpellier II, 34095 Montpellier Cedex 05, France
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Abstract
I derive the equilibrium values of sex-specific FST parameters, in an island model for a dioecious species with sex-biased dispersal and binomial distribution of family size before dispersal (as assumed in a Wright-Fisher population). I show that FST may take different values among males and among females whenever dispersal is a trait conditioned on gender. This has not always been recognized, because some models assumed that genes are sampled before dispersal. In particular, the ratios of sex-specific FST parameters evaluated after dispersal over FST evaluated before dispersal are simple functions of sex-specific dispersal rates. Therefore, a simple moment-based estimator of sex-specific dispersal rate is proposed. This method is based on the comparison of FST estimated before and after dispersal and assumes equilibrium between migration and drift. I evaluate this method through stochastic simulations for a range of sex-specific dispersal rates and sampling effort (sample size, number of loci scored).
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Affiliation(s)
- Renaud Vitalis
- Laboratoire Génétique et Environnement, C.C. 065, Institut des Sciences de l'Evolution de Montpellier (UMR 5554), Université Montpellier II, F-34095 Montpellier Cedex 05, France. vitalis@isem,univ-montp2.fr
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44
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Abstract
Population structure and history have similar effects on the genetic diversity at all neutral loci. However, some marker loci may also have been strongly influenced by natural selection. Selection shapes genetic diversity in a locus-specific manner. If we could identify those loci that have responded to selection during the divergence of populations, then we may obtain better estimates of the parameters of population history by excluding these loci. Previous attempts were made to identify outlier loci from the distribution of sample statistics under neutral models of population structure and history. Unfortunately these methods depend on assumptions about population structure and history that usually cannot be verified. In this article, we define new population-specific parameters of population divergence and construct sample statistics that are estimators of these parameters. We then use the joint distribution of these estimators to identify outlier loci that may be subject to selection. We found that outlier loci are easier to recognize when this joint distribution is conditioned on the total number of allelic states represented in the pooled sample at each locus. This is so because the conditional distribution is less sensitive to the values of nuisance parameters.
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Affiliation(s)
- R Vitalis
- Laboratoire Génome, Populations et Interactions, Université Montpellier II, 34095 Montpellier Cedex 05, France.
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45
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Abstract
Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the 'within-subpopulation identity disequilibrium' as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.
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Affiliation(s)
- R Vitalis
- Laboratoire de Génétique et Environnement, C.C. 065, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier II Place Eugène Bataillon, 34095 Montpellier, France.
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46
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Abstract
Standard methods for inferring demographic parameters from genetic data are based mainly on one-locus theory. However, the association of genes at different loci (e.g., two-locus identity disequilibrium) may also contain some information about demographic parameters of populations. In this article, we define one- and two-locus parameters of population structure as functions of one- and two-locus probabilities for the identity in state of genes. Since these parameters are known functions of demographic parameters in an infinite island model, we develop moment-based estimators of effective population size and immigration rate from one- and two-locus parameters. We evaluate this method through simulation. Although variance and bias may be quite large, increasing the number of loci on which the estimates are derived improves the method. We simulate an infinite allele model and a K allele model of mutation. Bias and variance are smaller with increasing numbers of alleles per locus. This is, to our knowledge, the first attempt of a joint estimation of local effective population size and immigration rate.
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Affiliation(s)
- R Vitalis
- Laboratoire Génétique et Environnement, C.C. 065, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.
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47
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Fréville H, Imbert E, Justy F, Vitalis R, Olivieri I. Isolation and characterization of microsatellites in the endemic species Centaurea corymbosa Pourret (Asteraceae) and other related species. Mol Ecol 2000; 9:1671-2. [PMID: 11050567 DOI: 10.1046/j.1365-294x.2000.01045-7.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- H Fréville
- Université Montpellier 2, ISEM, CC065, F-34095 Montpellier cedex 05, France.
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48
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Godelle B, Austerlitz F, Brachet S, Colas B, Cuguen J, Gandon S, Gouyon PH, Lefranc M, Olivieri I, Reboud X, Vitalis R. Système génétique, polymorphisme neutre et sélectionné: implications en biologie de la conservation. Genet Sel Evol 1998. [DOI: 10.1186/1297-9686-30-s1-s15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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49
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Vitalis R, Colas B, Riba Rovira M, Olivieri I. Marsilea strigosa Willd. : statut génétique et démographique d’une espèce menacée. ACTA ACUST UNITED AC 1998. [DOI: 10.3406/ecmed.1998.1858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Capy P, Vitalis R, Langin T, Higuet D, Bazin C. Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor? J Mol Evol 1996; 42:359-68. [PMID: 8661997 DOI: 10.1007/bf02337546] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The integrase domain of RNA-mediated elements (class I) and the transposase domain of DNA-mediated transposable elements (class II) were compared. A number of elements contain the DDE signature, which plays an important role in their integration. The possible relationships between mariner-Tc1 and IS elements, retrotransposons, and retroviruses were analyzed from an alignment of this region. The mariner-Tc1 superfamily, and LTR retrotransposons and retroviruses were found to be monophyletic groups. However, the IS elements of bacteria were found in several groups. These results were used to propose an evolutionary history that suggests a common ancestor for some integrases and transposases.
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Affiliation(s)
- P Capy
- Laboratoire Populations, Génétique et Evolution, CNRS, 91198 Gif/Yvette Cedex, France
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