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Rouger B, Goldringer I, Barbillon P, Miramon A, Naino Jika AK, Thomas M. Sensitivity analysis of a crop metapopulation model. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2022.110174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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2
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Metakovsky E, Melnik V, Pascual L, Wrigley CW. Some intra-varietal non-uniformities in Triticum aestivum can be explained as repeated spontaneous mutations at the Gli loci. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Richard MMS, Gratias A, Alvarez Diaz JC, Thareau V, Pflieger S, Meziadi C, Blanchet S, Marande W, Bitocchi E, Papa R, Miklas PN, Geffroy V. A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungus Colletotrichum lindemuthianum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3569-3581. [PMID: 33693665 DOI: 10.1093/jxb/erab082] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/05/2021] [Indexed: 05/27/2023]
Abstract
Identifying the molecular basis of resistance to pathogens is critical to promote a chemical-free cropping system. In plants, nucleotide-binding leucine-rich repeat constitute the largest family of disease resistance (R) genes, but this resistance can be rapidly overcome by the pathogen, prompting research into alternative sources of resistance. Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the most important diseases of common bean. This study aimed to identify the molecular basis of Co-x, an anthracnose R gene conferring total resistance to the extremely virulent C. lindemuthianum strain 100. To that end, we sequenced the Co-x 58 kb target region in the resistant JaloEEP558 (Co-x) common bean and identified KTR2/3, an additional gene encoding a truncated and chimeric CRINKLY4 kinase, located within a CRINKLY4 kinase cluster. The presence of KTR2/3 is strictly correlated with resistance to strain 100 in a diversity panel of common beans. Furthermore, KTR2/3 expression is up-regulated 24 hours post-inoculation and its transient expression in a susceptible genotype increases resistance to strain 100. Our results provide evidence that Co-x encodes a truncated and chimeric CRINKLY4 kinase probably resulting from an unequal recombination event that occurred recently in the Andean domesticated gene pool. This atypical R gene may act as a decoy involved in indirect recognition of a fungal effector.
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Affiliation(s)
- Manon M S Richard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Juan C Alvarez Diaz
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Chouaib Meziadi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Sophie Blanchet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Phillip N Miklas
- USDA ARS, Grain Legume Genet & Physiol Res Unit, Prosser, WA, USA
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
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Metakovsky E, Melnik V, Pascual L, Wrigley CW. Over 40% of 450 registered wheat cultivars (Triticum aestivum) worldwide are composed of multiple biotypes. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.103088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Nowicki M, Houston LC, Boggess SL, Aiello AS, Payá‐Milans M, Staton ME, Hayashida M, Yamanaka M, Eda S, Trigiano RN. Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites. Ecol Evol 2020; 10:8299-8312. [PMID: 32788980 PMCID: PMC7417245 DOI: 10.1002/ece3.6537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023] Open
Abstract
Cornus kousa (Asian dogwood), an East Asia native tree, is the most economically important species of the dogwood genus, owing to its desirable horticultural traits and ability to hybridize with North America-native dogwoods. To assess the species genetic diversity and to better inform the ongoing and future breeding efforts, we assembled an herbarium and arboretum collection of 131 noncultivated C. kousa specimens. Genotyping and capillary electrophoresis analyses of our C. kousa collection with the newly developed genic and published nuclear genomic microsatellites permitted assessment of genetic diversity and evolutionary history of the species. Regardless of the microsatellite type used, the study yielded generally similar insights into the C. kousa diversity with subtle differences deriving from and underlining the marker used. The accrued evidence pointed to the species distinct genetic pools related to the plant country of origin. This can be helpful in the development of the commercial cultivars for this important ornamental crop with increased pyramided utility traits. Analyses of the C. kousa evolutionary history using the accrued genotyping datasets pointed to an unsampled ancestor population, possibly now extinct, as per the phylogeography of the region. To our knowledge, there are few studies utilizing the same gDNA collection to compare performance of genomic and genic microsatellites. This is the first detailed report on C. kousa species diversity and evolutionary history inference.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | - Logan C. Houston
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | - Sarah L. Boggess
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | | | - Miriam Payá‐Milans
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
- Present address:
Centro de Biotecnología y Genómica de PlantasUPM‐INIAMadridSpain
| | - Margaret E. Staton
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | | | - Masahiro Yamanaka
- Department of Pharmaceytical SciencesInternational University of Health and WelfareOhtawaraJapan
| | - Shigetoshi Eda
- Department of Forestry, Wildlife and FisheriesCenter for Wildlife Health ORUKnoxvilleTNUSA
- Department of MicrobiologyCenter for Wildlife Health ORUKnoxvilleTNUSA
| | - Robert N. Trigiano
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
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Metakovsky E, Melnik V, Pascual L, Wrigley C. Gliadin genotypes worldwide for spring wheats (Triticum aestivum L.) 2. Strong differentiation of polymorphism between countries and regions of origin. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Metakovsky EV, Melnik VA, Redaelli R, Rodriguez-Quijano M. Comparison of Alleles at Gli-2 Loci of Common Wheat by Means of Two-Dimensional Electrophoresis of Gliadin. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718020068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chromosomal structural changes and microsatellite variations in newly synthesized hexaploid wheat mediated by unreduced gametes. J Genet 2017; 95:819-830. [PMID: 27994180 DOI: 10.1007/s12041-016-0704-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate chromosome level variation and microsatellite level variation of newly synthesized hexaploid wheat have been rarely reported. Here, unreduced gametes were applied to develop synthesized hexaploid wheat, NA0928, population by crossing T. turgidum ssp. dicoccum MY3478 and Ae. tauschii SY41, and further S0-S3 generations of NA0928 were assayed by sequential cytological and microsatellite techniques. We demonstrated that plentiful chromosomal structural changes and microsatellite variations emerged in the early generations of newly synthesized hexaploid wheat population NA0928, including aneuploidy with whole-chromosome loss or gain, aneuploidy with telosome formation, chromosome-specific repeated sequence elimination (indicated by fluorescence in situ hybridization) and microsatellite sequence elimination (indicated by sequencing), and many kinds of variations have not been previously reported. Additionally, we reported a new germplasm, T. turgidum accession MY3478 with excellent unreduced gametes trait, and then succeeded to transfer powdery mildew resistance from Ae. tauschii SY41 to synthesized allohexaploid wheat population NA0928, which would be valuable resistance resources for wheat improvement.
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Hoareau TB. Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics. Syst Biol 2015; 65:449-64. [PMID: 26683588 DOI: 10.1093/sysbio/syv120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/10/2015] [Indexed: 12/18/2022] Open
Abstract
The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.
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Affiliation(s)
- Thierry B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private bag X20, Hatfield, Pretoria 0028, South Africa
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Volis S, Ormanbekova D, Yermekbayev K, Song M, Shulgina I. The Conservation Value of Peripheral Populations and a Relationship Between Quantitative Trait and Molecular Variation. Evol Biol 2015. [DOI: 10.1007/s11692-015-9346-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Iefimenko TS, Fedak YG, Antonyuk MZ, Ternovska TK. Microsatellite analysis of chromosomes from the fifth homoeologous group in the introgressive Triticum aestivum/Amblyopyrum muticum wheat lines. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715030056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dussert Y, Snirc A, Robert T. Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet. Mol Ecol 2015; 24:1387-402. [PMID: 25705965 DOI: 10.1111/mec.13119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/04/2023]
Abstract
Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.
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Affiliation(s)
- Y Dussert
- Ecologie, Systématique et Evolution, UMR 8079 CNRS, Université Paris-Sud, 91405, Orsay, France; Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
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Thépot S, Restoux G, Goldringer I, Hospital F, Gouache D, Mackay I, Enjalbert J. Efficiently tracking selection in a multiparental population: the case of earliness in wheat. Genetics 2015; 199:609-23. [PMID: 25406468 PMCID: PMC4317666 DOI: 10.1534/genetics.114.169995] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/11/2014] [Indexed: 11/18/2022] Open
Abstract
Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations.
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Affiliation(s)
- Stéphanie Thépot
- Université Paris-Sud, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Gwendal Restoux
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8079, Université Paris-Sud, Orsay, France
| | - Isabelle Goldringer
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Frédéric Hospital
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, F-78352 Jouy en Josas, France
| | - David Gouache
- Arvalis, Institut du Végétal, Station Expérimentale, F-91720 Boigneville, France
| | - Ian Mackay
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, United Kingdom
| | - Jérôme Enjalbert
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 0320/Unité Mixte de Recherche 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France
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Luo J, Hao M, Zhang L, Chen J, Zhang L, Yuan Z, Yan Z, Zheng Y, Zhang H, Yen Y, Liu D. Microsatellite mutation rate during allohexaploidization of newly resynthesized wheat. Int J Mol Sci 2012. [PMID: 23202911 PMCID: PMC3497285 DOI: 10.3390/ijms131012533] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F(1 )haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S(1) generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S(1) generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10-6. This mutation most likely occurred in the respective F(1) hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate.
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Affiliation(s)
- Jiangtao Luo
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Li Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Jixiang Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
| | - Huaigang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, the Chinese Academy of Sciences, Xining 810001, China; E-Mail:
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; E-Mail:
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; E-Mails: (J.L.); (M.H.); (L.Z.); (J.C.); (L.Z.); (Z.Y.); (Z.Y.); (Y.Z.)
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, the Chinese Academy of Sciences, Xining 810001, China; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-28-8265-0312; Fax: +86-28-8265-0350
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Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Time-dependent rates of molecular evolution. Mol Ecol 2011; 20:3087-101. [PMID: 21740474 DOI: 10.1111/j.1365-294x.2011.05178.x] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.
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Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Negri V, Tiranti B. Effectiveness of in situ and ex situ conservation of crop diversity. What a Phaseolus vulgaris L. landrace case study can tell us. Genetica 2010; 138:985-98. [PMID: 20835753 DOI: 10.1007/s10709-010-9485-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
Abstract
The effectiveness of in situ (on-farm) and ex situ conservation strategies to maintain total genetic diversity was assessed in a threatened Phaseolus vulgaris L. landrace. Farmer seed lots (subpopulations) were sampled initially and then after in situ and ex situ multiplication (two locations). The number of plants used in the ex situ multiplications (120) was much larger than that normally used in germplasm bank procedures and the farmer seed lots were kept separate. In situ, the landrace was multiplied by each farmer with the usual population size. Eighty plants from the initial population, the in situ and the two ex situ multiplications were individually tested using 26 microsatellite markers. Most of the genetic parameters showed a consistent decline in the ex situ populations compared with the in situ population, with a notable loss of less frequent alleles. The differentiation among the farmer subpopulations increased when the multiplication took place outside of the adaptation area. Although 120 plants were multiplied in each ex situ cycle, a bottleneck effect was present. In addition, tests for neutrality detected three loci that are involved in pathogen response and are potentially under selective effects. The diversity conservation and the management practices of autogamous landrace crops are discussed.
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Affiliation(s)
- Valeria Negri
- Dipartimento di Biologia Applicata, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy.
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Depaulis F, Orlando L, Hänni C. Using classical population genetics tools with heterochroneous data: time matters! PLoS One 2009; 4:e5541. [PMID: 19440242 PMCID: PMC2678253 DOI: 10.1371/journal.pone.0005541] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 04/15/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. METHODOLOGY/PRINCIPAL FINDINGS We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)). CONCLUSIONS/SIGNIFICANCE Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.
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Affiliation(s)
- Frantz Depaulis
- Laboratoire d'Ecologie et Evolution, CNRS UMR 7625, UPMC Paris Universitas, Ecole Normale Supérieure, Paris, France
| | - Ludovic Orlando
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Catherine Hänni
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France
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