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Bastias CC, Estarague A, Vile D, Gaignon E, Lee CR, Exposito-Alonso M, Violle C, Vasseur F. Ecological trade-offs drive phenotypic and genetic differentiation of Arabidopsis thaliana in Europe. Nat Commun 2024; 15:5185. [PMID: 38890286 PMCID: PMC11189578 DOI: 10.1038/s41467-024-49267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Plant diversity is shaped by trade-offs between traits related to competitive ability, propagule dispersal, and stress resistance. However, we still lack a clear understanding of how these trade-offs influence species distribution and population dynamics. In Arabidopsis thaliana, recent genetic analyses revealed a group of cosmopolitan genotypes that successfully recolonized Europe from its center after the last glaciation, excluding older (relict) lineages from the distribution except for their north and south margins. Here, we tested the hypothesis that cosmopolitans expanded due to higher colonization ability, while relicts persisted at the margins due to higher tolerance to competition and/or stress. We compared the phenotypic and genetic differentiation between 71 European genotypes originating from the center, and the south and north margins. We showed that a trade-off between plant fecundity and seed mass shapes the differentiation of A. thaliana in Europe, suggesting that the success of the cosmopolitan groups could be explained by their high dispersal ability. However, at both north and south margins, we found evidence of selection for alleles conferring low dispersal but highly competitive and stress-resistance abilities. This study sheds light on the role of ecological trade-offs as evolutionary drivers of the distribution and dynamics of plant populations.
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Affiliation(s)
- Cristina C Bastias
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
- Área de Ecología, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Córdoba, Spain.
| | - Aurélien Estarague
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Elza Gaignon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology & Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | | | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Buysse SF, Pérez SG, Puzey JR, Garrison A, Bradburd GS, Oakley CG, Tonsor SJ, Picó FX, Josephs EB, Conner JK. The Roles of Drift and Selection on Short Stamen Loss in Arabidopsis thaliana along an Elevational Gradient in the Spanish Pyrenees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598645. [PMID: 38915635 PMCID: PMC11195200 DOI: 10.1101/2024.06.12.598645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Traits that have lost function sometimes persist through evolutionary time. These traits may be maintained by a lack of standing genetic variation for the trait, if selection against the trait is weak relative to drift, or if they have a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in the Spanish Pyrenees. We found a cline in short stamen number from retention of short stamens in high elevation populations to incomplete loss in low elevation populations. We did not find evidence that limited genetic variation constrains the loss of short stamens at high elevations nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in the Spanish Pyrenees that are different from loci associated with variation in short stamen number across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms maintaining an elevational cline in short stamen number but did identify different genetic loci underlying the variation in short stamen along similar phenotypic clines. Teaser text The evolutionary mechanisms underlying loss or retention of traits that have lost function are poorly understood. Short stamens in Arabidopsis thaliana provide a compelling system to investigate the roles of genetic drift and selection in trait loss across latitudinal and elevational clines. This study investigates the role of drift and selection in short stamen loss in 16 populations of A. thaliana along an elevational gradient in the Spanish Pyrenees. An investigation of the genetic loci underlying variation in short stamen number suggests mutations in different genes may cause trait loss in similar phenotypic clines within a species.
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3
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Kishino H, Nakamichi R, Kitada S. Genetic adaptations in the population history of Arabidopsis thaliana. G3 (BETHESDA, MD.) 2023; 13:jkad218. [PMID: 37748020 PMCID: PMC10700115 DOI: 10.1093/g3journal/jkad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 05/26/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana, we constructed a database of phenotypic adaptations (p-adaptations) and gene expression (e-adaptations) adaptations in the population. Through the enrichment analysis of the identified adaptations, we inferred a likely scenario of adaptation that is consistent with the biological evidence from experimental work. We analyzed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes and identified 650 p-adaptations and 3,925 e-adaptations [false discovery rate (FDR) = 0.05]. The population underwent large-scale p-adaptations and e-adaptations along 4 lineages. Extremely cold winters and short summers prolonged seed dormancy and expanded the root system architecture. Low temperatures prolonged the growing season, and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected alleles for lower heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The p-adaptations are directly interpretable, while the coadapted gene expressions reflect the physiological requirements for the adaptation. The integration of this information characterizes when and where the population has experienced environmental stress and how the population responded at the molecular level.
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Affiliation(s)
- Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Research and Development Initiative, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Reiichiro Nakamichi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Shuichi Kitada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
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Novikova PY, Kolesnikova UK, Scott AD. Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae. PLANT REPRODUCTION 2023; 36:125-138. [PMID: 36282331 PMCID: PMC9957919 DOI: 10.1007/s00497-022-00451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 05/15/2023]
Abstract
Self-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits in diploid plants, for polyploids who often face a scarcity of mating partners, self-incompatibility can thwart reproduction. In contrast, self-compatibility provides an immediate advantage: a route to reproductive viability. Thus, diploid selfing lineages may facilitate the formation of new allopolyploid species. Here, we describe the mechanism of establishment of at least four allopolyploid species in Brassicaceae (Arabidopsis suecica, Arabidopsis kamchatica, Capsella bursa-pastoris, and Brassica napus), in a manner dependent on the prior loss of the self-incompatibility mechanism in one of the ancestors. In each case, the degraded S-locus from one parental lineage was dominant over the functional S-locus of the outcrossing parental lineage. Such dominant loss-of-function mutations promote an immediate transition to selfing in allopolyploids and may facilitate their establishment.
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Affiliation(s)
- Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.
| | - Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
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5
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Christenhusz MJ, Twyford AD, Hudson A. The genome sequence of thale cress, Arabidopsis thaliana (Heynh., 1842). Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18665.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We present a genome assembly of an Arabidopsis thaliana specimen (thale cress; Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence spans 138 megabases. Most of the assembly (98.76%) is scaffolded into five chromosomal pseudomolecules. The mitochondrial and plastid genomes were also assembled and are 368.8 and 154.5 kilobases in length respectively.
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Fournier-Level A, Taylor MA, Paril JF, Martínez-Berdeja A, Stitzer MC, Cooper MD, Roe JL, Wilczek AM, Schmitt J. Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 234:719-734. [PMID: 35090191 DOI: 10.1111/nph.17999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.
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Affiliation(s)
| | - Mark A Taylor
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
| | - Jefferson F Paril
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | | | - Michelle C Stitzer
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
| | - Martha D Cooper
- Department of Ecology and Evolution, Brown University, Providence, RI, 02912, USA
| | - Judith L Roe
- College of Arts and Sciences, Biology, Agricultural Science & Agribusiness, University of Maine at Presque Isle, Presque Isle, ME, 04769, USA
| | | | - Johanna Schmitt
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
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7
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Bi J, Shen W, Zhu W. Random Forest Adjustment for Approximate Bayesian Computation. J Comput Graph Stat 2021. [DOI: 10.1080/10618600.2021.1981341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jiefeng Bi
- Wang Yanan Institute for Studies in Economics (WISE), Xiamen University, Xiamen, China
| | - Weining Shen
- Department of Statistics, University of California, Irvine, CA
| | - Weixuan Zhu
- Wang Yanan Institute for Studies in Economics (WISE), Department of Statistics and Data Science, School of Economics, Xiamen University, Xiamen, China
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8
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Larsson DJ, Pan D, Schneeweiss GM. Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling. ALPINE BOTANY 2021; 132:5-19. [PMID: 35368907 PMCID: PMC8933363 DOI: 10.1007/s00035-021-00263-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/05/2021] [Indexed: 06/14/2023]
Abstract
Phylogeographic studies of alpine plants have evolved considerably in the last two decades from ad hoc interpretations of genetic data to statistical model-based approaches. In this review we outline the developments in alpine plant phylogeography focusing on the recent approach of integrative distributional, demographic and coalescent (iDDC) modeling. By integrating distributional data with spatially explicit demographic modeling and subsequent coalescent simulations, the history of alpine species can be inferred and long-standing hypotheses, such as species-specific responses to climate change or survival on nunataks during the last glacial maximum, can be efficiently tested as exemplified by available case studies. We also discuss future prospects and improvements of iDDC.
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Affiliation(s)
- Dennis J. Larsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V. Population genomic evidence of Plasmodium vivax Southeast Asian origin. SCIENCE ADVANCES 2021; 7:7/18/eabc3713. [PMID: 33910900 PMCID: PMC8081369 DOI: 10.1126/sciadv.abc3713] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/10/2021] [Indexed: 05/15/2023]
Abstract
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, 46 rue H. Huchard, 75877 Paris Cedex 18, France
| | - Celine Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Christine Sidobre
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
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Hagenblad J, Morales J. An Evolutionary Approach to the History of Barley ( Hordeum vulgare) Cultivation in the Canary Islands. THE AFRICAN ARCHAEOLOGICAL REVIEW 2020; 37:579-595. [PMID: 33268912 PMCID: PMC7677147 DOI: 10.1007/s10437-020-09415-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
The Canary Islands are an archipelago that lies about 100 km west of North Africa. Barley (Hordeum vulgare) has been continuously cultivated since the colonization of the islands. To investigate the agricultural history of the islands, the DNA from multiple individuals of six extant landraces of barley was sequenced, and the resulting data were analyzed with ABC modeling. Estimates of separation times of barley populations on the different islands and the mainland were congruent with archaeological dating of the earliest settlements on the islands. The results of the genetic analyses were consistent with the continuous cultivation of barley on Lanzarote island since it was first colonized, but suggested cultivation was carried out at a smaller scale than on Gran Canaria and Tenerife. Contrary to archaeological evidence and early written historical sources, the genetic analyses suggest that barley was cultivated on a larger scale on Tenerife than on Gran Canaria. The genetic analysis of contemporary barley added support to the dating of the colonization of the islands and pointed to the need for more archaeological data concerning barley cultivation on Tenerife.
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Affiliation(s)
- Jenny Hagenblad
- IFM Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Jacob Morales
- Department of Historical Sciences, University of Las Palmas de Gran Canaria, Pérez del Toro 1, 35003 Las Palmas de Gran Canaria, Spain
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Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics 2020; 35:4480-4483. [PMID: 31077292 PMCID: PMC6821363 DOI: 10.1093/bioinformatics/btz311] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
SUMMARY SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework. The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a large variety of DNA mutation models. These implementations have been applied independently to various studies, but grouped together in the current version. AVAILABILITY AND IMPLEMENTATION SPLATCHE3 is written in C++ and is freely available for non-commercial use from the website http://www.splatche.com/splatche3. It includes console versions for Linux, MacOs and Windows and a user-friendly GUI for Windows, as well as detailed documentation and ready-to-use examples.
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Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva 1211, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, Vigo 36310, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Claudio S Quilodràn
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Nicolas Ray
- Institute of Global Health, GeoHealth Group, University of Geneva, Geneva 1205, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva 1205, Switzerland
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12
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Nardi FD, Hülber K, Moser D, Alonso‐Marcos H, Tribsch A, Dobeš C. Occurrence of apomictic conspecifics and ecological preferences rather than colonization history govern the geographic distribution of sexual Potentilla puberula. Ecol Evol 2020; 10:7306-7319. [PMID: 32760530 PMCID: PMC7391561 DOI: 10.1002/ece3.6455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 11/24/2022] Open
Abstract
The geographic distribution of sexual-apomictic taxa (i.e., comprising individuals usually reproducing either sexually or asexually via seeds) is traditionally thought to be driven by their ecological preferences and colonization histories. Where sexuals and apomicts get into contact with each other, competitive and reproductive interactions can interfere with these factors, an aspect which hitherto received little attention in biogeographic studies. We disentangled and quantified the relative effects of the three factors on the distribution of tetraploid sexuals in Potentilla puberula in a latitudinal transect through the Eastern European Alps, in which they are codistributed with penta-, hepta-, and octoploid apomictic conspecifics. Effects were explored by means of binomial generalized linear regression models combining a single with a multiple predictor approach. Postglacial colonization history was inferred from population genetic variation (AFLPs and cpDNA) and quantified using a cost distance metric. The study was based on 235 populations, which were purely sexual, purely apomictic, or of mixed reproductive mode. The occurrence of apomicts explained most of the variation in the distribution of sexuals (31%). Specifically, the presence of sexual tetraploids was negatively related to the presence of each of the three apomictic cytotypes. Effects of ecological preferences were substantial too (7% and 12% of the total variation explained by ecological preferences alone, or jointly with apomicts' occurrence, respectively). In contrast, colonization history had negligible effects on the occurrence of sexuals. Taken together, our results highlight the potentially high impact of reproductive interactions on the geographic distribution of sexual and apomictic conspecifics and that resultant mutual exclusion interrelates to ecological differentiation, a situation potentially promoting their local coexistence.
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Affiliation(s)
- Flavia Domizia Nardi
- Department of Forest GeneticsAustrian Research Centre for ForestsViennaAustria
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Karl Hülber
- Department of Conservation Biology, Vegetation Ecology and Landscape EcologyUniversity of ViennaViennaAustria
| | - Dietmar Moser
- Department of Conservation Biology, Vegetation Ecology and Landscape EcologyUniversity of ViennaViennaAustria
| | - Henar Alonso‐Marcos
- Department of Forest GeneticsAustrian Research Centre for ForestsViennaAustria
- Department of Conservation Biology, Vegetation Ecology and Landscape EcologyUniversity of ViennaViennaAustria
| | - Andreas Tribsch
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Christoph Dobeš
- Department of Forest GeneticsAustrian Research Centre for ForestsViennaAustria
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13
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Negin B, Moshelion M. Remember where you came from: ABA insensitivity is epigenetically inherited in mesophyll, but not seeds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110455. [PMID: 32534619 DOI: 10.1016/j.plantsci.2020.110455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/10/2020] [Accepted: 02/16/2020] [Indexed: 05/11/2023]
Abstract
Plants transmit their experiences of environmental conditions to their progeny through epigenetic inheritance, improving their progeny's fitness under prevailing conditions. Though ABA is known to regulate epigenetic-modification genes, no strong phenotypic link between those genes and intergenerational "memory" has been shown. Previously, we demonstrated that mesophyll insensitivity to ABA (FBPase::abi1-1{fa} transgenic plants) results in a range of developmental phenotypes, including early growth vigor and early flowering (i.e., stress-escape behavior). Here, we show that null plants, used as controls (segregates of FBPase::abi1 that are homozygote descendants of a heterozygous transgenic plant, but do not contain the transformed abi1-1 gene) phenotypically resembled their FBPase::abi1-1 parents. However, in germination and early seedling development assays, null segregants resembled WT plants. These FBPase::abi1-1 null segregants mesophyll-related phenotypes were reproducible and stable for at least three generations. These results suggest that the heritability of stress response is linked to ABA's epigenetic regulatory effect through ABI1 and mesophyll-related traits. The discrepancy between the epigenetic heritability of seed and mesophyll-related traits is an example of the complexity of epigenetic regulation, which is both gene and process-specific, and may be attributed to the fine-tuning of tradeoffs between flowering time, growth rate and levels of risk that allow annual plants to optimize their fitness in uncertain environments.
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Affiliation(s)
- Boaz Negin
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel.
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14
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You M, Ke F, You S, Wu Z, Liu Q, He W, Baxter SW, Yuchi Z, Vasseur L, Gurr GM, Ward CM, Cerda H, Yang G, Peng L, Jin Y, Xie M, Cai L, Douglas CJ, Isman MB, Goettel MS, Song Q, Fan Q, Wang-Pruski G, Lees DC, Yue Z, Bai J, Liu T, Lin L, Zheng Y, Zeng Z, Lin S, Wang Y, Zhao Q, Xia X, Chen W, Chen L, Zou M, Liao J, Gao Q, Fang X, Yin Y, Yang H, Wang J, Han L, Lin Y, Lu Y, Zhuang M. Variation among 532 genomes unveils the origin and evolutionary history of a global insect herbivore. Nat Commun 2020; 11:2321. [PMID: 32385305 PMCID: PMC7211002 DOI: 10.1038/s41467-020-16178-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/15/2020] [Indexed: 12/30/2022] Open
Abstract
The diamondback moth, Plutella xylostella is a cosmopolitan pest that has evolved resistance to all classes of insecticide, and costs the world economy an estimated US $4-5 billion annually. We analyse patterns of variation among 532 P. xylostella genomes, representing a worldwide sample of 114 populations. We find evidence that suggests South America is the geographical area of origin of this species, challenging earlier hypotheses of an Old-World origin. Our analysis indicates that Plutella xylostella has experienced three major expansions across the world, mainly facilitated by European colonization and global trade. We identify genomic signatures of selection in genes related to metabolic and signaling pathways that could be evidence of environmental adaptation. This evolutionary history of P. xylostella provides insights into transoceanic movements that have enabled it to become a worldwide pest.
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Affiliation(s)
- Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.
| | - Fushi Ke
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Zhangyan Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qingfeng Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Simon W Baxter
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Zhiguang Yuchi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada.
| | - Geoff M Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,Graham Centre, Charles Sturt University, Orange, NSW, 2800, Australia.
| | - Christopher M Ward
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Hugo Cerda
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Instituto Superior de Formación Docente Salomé Ureña (ISFODOSU), Recinto Lus Napoleón Núñez Molina, Carretera Duarte, Km 10 1/2, Municipio de Licey Al Medio, Provincia de Santiago, República Dominicana
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Lu Peng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Yuanchun Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Miao Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Lijun Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Carl J Douglas
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Murray B Isman
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Mark S Goettel
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Qisheng Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Qinghai Fan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Plant Health & Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealand
| | - Gefu Wang-Pruski
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.,Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, PO Box 550, Truro, NS, B2N 5E3, Canada
| | - David C Lees
- Natural History Museum, Cromwell Road, South Kensington, SW7 5BD, London, UK
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Jianlin Bai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Tiansheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Lianyun Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yunkai Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Zhaohua Zeng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Sheng Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Yue Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Qian Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Xiaofeng Xia
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Wenbin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Lilin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Mingmin Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Jinying Liao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jian Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Liwei Han
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Yingjun Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Yanping Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Mousheng Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
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15
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Smith AL, Hodkinson TR, Villellas J, Catford JA, Csergő AM, Blomberg SP, Crone EE, Ehrlén J, Garcia MB, Laine AL, Roach DA, Salguero-Gómez R, Wardle GM, Childs DZ, Elderd BD, Finn A, Munné-Bosch S, Baudraz MEA, Bódis J, Brearley FQ, Bucharova A, Caruso CM, Duncan RP, Dwyer JM, Gooden B, Groenteman R, Hamre LN, Helm A, Kelly R, Laanisto L, Lonati M, Moore JL, Morales M, Olsen SL, Pärtel M, Petry WK, Ramula S, Rasmussen PU, Enri SR, Roeder A, Roscher C, Saastamoinen M, Tack AJM, Töpper JP, Vose GE, Wandrag EM, Wingler A, Buckley YM. Global gene flow releases invasive plants from environmental constraints on genetic diversity. Proc Natl Acad Sci U S A 2020; 117:4218-4227. [PMID: 32034102 PMCID: PMC7049112 DOI: 10.1073/pnas.1915848117] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a globally distributed demographic research network comprising 35 native and 18 nonnative populations of Plantago lanceolata Species-specific simulation experiments showed that dispersal would dilute demographic influences on genetic diversity at local scales. Populations in the native European range had strong spatial genetic structure associated with geographic distance and precipitation seasonality. In contrast, nonnative populations had weaker spatial genetic structure that was not associated with environmental gradients but with higher within-population genetic diversity. Our findings show that dispersal caused by repeated, long-distance, human-mediated introductions has allowed invasive plant populations to overcome environmental constraints on genetic diversity, even without strong demographic changes. The impact of invasive plants may, therefore, increase with repeated introductions, highlighting the need to constrain future introductions of species even if they already exist in an area.
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Affiliation(s)
- Annabel L Smith
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland;
- School of Agriculture and Food Science, University of Queensland, Gatton, 4343, Australia
| | - Trevor R Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Jesus Villellas
- Departamento Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales-Consejo Superior de Investigaciones Científicas (MNCN-CSIC), E-28006 Madrid, Spain
| | - Jane A Catford
- Department of Geography, King's College London, WC2B 4BG London, United Kingdom
| | - Anna Mária Csergő
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
- Department of Botany, Faculty of Horticultural Science, Szent István University, 1118 Budapest, Hungary
- Soroksár Botanical Garden, Faculty of Horticultural Science, Szent István University, 1118 Budapest, Hungary
| | - Simone P Blomberg
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Johan Ehrlén
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Maria B Garcia
- Pyrenean Institute of Ecology, CSIC, 50059 Zaragoza, Spain
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Deborah A Roach
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | | | - Glenda M Wardle
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dylan Z Childs
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, United Kingdom
| | - Bret D Elderd
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Alain Finn
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat, University of Barcelona, 08028 Barcelona, Spain
| | - Maude E A Baudraz
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Judit Bódis
- Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Hungary
| | - Francis Q Brearley
- Department of Natural Sciences, Manchester Metropolitan University, M1 5GD Manchester, United Kingdom
| | - Anna Bucharova
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, 72074 Tübingen, Germany
- Ecosystem and Biodiversity Research Group, Institute of Landscape Ecology, University of Münster, 48149 Münster, Germany
| | - Christina M Caruso
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
| | - John M Dwyer
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
- CSIRO Land & Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD 4102, Australia
| | - Ben Gooden
- CSIRO Health & Biosecurity, CSIRO, Black Mountain, ACT 2601, Australia
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | | | - Liv Norunn Hamre
- Department of Environmental Sciences, Western Norway University of Applied Sciences, N-6856 Sogndal, Norway
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia
| | - Ruth Kelly
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Lauri Laanisto
- Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Michele Lonati
- Department of Agricultural, Forest and Food Science, University of Torino, 10015 Grugliasco, Italy
| | - Joslin L Moore
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Melanie Morales
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- Research Group of Plant Biology under Mediterranean Conditions, Faculty of Biology, University of Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Siri Lie Olsen
- Norwegian Institute for Nature Research, N-0349 Oslo, Norway
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia
| | - William K Petry
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Satu Ramula
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Pil U Rasmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
- The National Research Centre for the Working Environment, 2100 København Ø, Denmark
| | - Simone Ravetto Enri
- Department of Agricultural, Forest and Food Science, University of Torino, 10015 Grugliasco, Italy
| | - Anna Roeder
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), 04318 Leipzig, Germany
| | - Christiane Roscher
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), 04318 Leipzig, Germany
| | - Marjo Saastamoinen
- Helsinki Institute of Life Science, University of Helsinki, 00100 Helsinki, Finland
- Organismal and Evolutionary Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | - Gregory E Vose
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Elizabeth M Wandrag
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Astrid Wingler
- School of Biological, Earth & Environmental Sciences and Environmental Research Institute, University College Cork, Cork T23 N73K, Ireland
| | - Yvonne M Buckley
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
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16
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Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:2526-2534. [PMID: 31964817 PMCID: PMC7007534 DOI: 10.1073/pnas.1912451117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The seasonal timing of seed germination is critical for plant fitness in different climates. To germinate at the right time of year, seeds respond to seasonal environmental cues, such as cold temperatures. We characterized genetic variation in seed dormancy responses to cold across the geographic range of a widespread annual plant. Induction of secondary seed dormancy during winter conditions (which restricts germination to autumn) was positively correlated with flowering time, constructing winter and spring seasonal life-history strategies. Variation in seed chilling responses was strongly associated with functional variants of a known dormancy gene. These variants showed evidence of ancient diversification associated with Pleistocene glacial cycles, and were associated with climate gradients across the species’ geographical range. The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.
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17
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Mattila TM, Laenen B, Slotte T. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems. Methods Mol Biol 2020; 2090:269-287. [PMID: 31975171 DOI: 10.1007/978-1-0716-0199-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
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18
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Mattingsdal M, Jorde PE, Knutsen H, Jentoft S, Stenseth NC, Sodeland M, Robalo JI, Hansen MM, André C, Blanco Gonzalez E. Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe. Mol Ecol 2019; 29:160-171. [DOI: 10.1111/mec.15310] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Morten Mattingsdal
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
| | | | - Halvor Knutsen
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
- Institute of Marine Research Flødevigen Norway
| | - Sissel Jentoft
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Nils Christian Stenseth
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Marte Sodeland
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
| | - Joana I. Robalo
- Marine and Environmental Sciences Centre ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida Lisboa Portugal
| | | | - Carl André
- Department of Marine Sciences‐Tjärnö Göteborg University Strömstad Sweden
| | - Enrique Blanco Gonzalez
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
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19
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Greenbaum G, Rubin A, Templeton AR, Rosenberg NA. Network-based hierarchical population structure analysis for large genomic data sets. Genome Res 2019; 29:2020-2033. [PMID: 31694865 PMCID: PMC6886512 DOI: 10.1101/gr.250092.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/01/2019] [Indexed: 01/24/2023]
Abstract
Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.
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Affiliation(s)
- Gili Greenbaum
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Amir Rubin
- Department of Computer Science, Ben-Gurion University of the Negev, Be'er-Sheva, 8410501, Israel
| | - Alan R Templeton
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa, 31905, Israel
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, California 94305, USA
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Matsuoka S, Iwasaki T, Sugiyama Y, Kawaguchi E, Doi H, Osono T. Biogeographic Patterns of Ectomycorrhizal Fungal Communities Associated With Castanopsis sieboldii Across the Japanese Archipelago. Front Microbiol 2019; 10:2656. [PMID: 31798567 PMCID: PMC6868053 DOI: 10.3389/fmicb.2019.02656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/31/2019] [Indexed: 11/13/2022] Open
Abstract
Biogeographic patterns in ectomycorrhizal (ECM) fungal communities and their drivers have been elucidated, including effects of host tree species and abiotic (climatic and edaphic) conditions. At these geographic scales, genotypic diversity and composition of single host tree species change with spatial and environmental gradients, reflecting their historical dispersal events. However, whether the host genotypes can be associated with the biogeographic patterns of ECM communities remains unclear. We investigated the biogeographic pattern of ECM fungal community associated with the single host species Castanopsis sieboldii (Fagaceae), whose genotypic diversity and composition across the Japanese archipelago has already been evaluated. ECM communities were investigated in 12 mature Castanopsis-dominated forests covering almost the entire distribution range of C. sieboldii, and we quantified the effect of host genotypes on the biogeographic pattern of ECM fungal communities. Richness and community composition of ECM fungi changed with latitude and longitude; these biogeographic changes of ECM community were significantly correlated with host genotypic variables. Quantitative analyses showed a higher relative explanatory power of climatic and spatial variables than that of host genotypic variables for the biogeographic patterns in the ECM community. Our results suggest historical events of host dispersal can affect the biogeographic patterns of the ECM fungal community, while their explanation power was lower than that for climatic filtering and/or fungal dispersal.
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Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Takaya Iwasaki
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eri Kawaguchi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Takashi Osono
- Department of Environmental Systems Science, Faculty of Science and Engineering, Doshisha University, Kyoto, Japan
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21
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Khokhar W, Hassan MA, Reddy ASN, Chaudhary S, Jabre I, Byrne LJ, Syed NH. Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1160. [PMID: 31632417 PMCID: PMC6785726 DOI: 10.3389/fpls.2019.01160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/26/2019] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans-sQTL (trans-sQTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties.
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Affiliation(s)
- Waqas Khokhar
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Musa A. Hassan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Saurabh Chaudhary
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Ibtissam Jabre
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Lee J. Byrne
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Naeem H. Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
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22
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Prentice MB, Bowman J, Murray DL, Klütsch CFC, Khidas K, Wilson PJ. Evaluating evolutionary history and adaptive differentiation to identify conservation units of Canada lynx (Lynx canadensis). Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00708] [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] Open
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23
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Hu K, Xu K, Wen J, Yi B, Shen J, Ma C, Fu T, Ouyang Y, Tu J. Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species. BMC Bioinformatics 2019; 20:354. [PMID: 31234777 PMCID: PMC6591975 DOI: 10.1186/s12859-019-2945-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/11/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated. RESULTS We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes. CONCLUSION EAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis.
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Affiliation(s)
- Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Kai Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Hsu CW, Lo CY, Lee CR. On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East. THE NEW PHYTOLOGIST 2019; 222:1447-1457. [PMID: 30636325 DOI: 10.1111/nph.15682] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/07/2019] [Indexed: 05/28/2023]
Abstract
With more sequenced genomes, our understanding of the demographic history of Arabidopsis thaliana is rapidly expanding. However, no-one has yet compiled previous data to investigate patterns of genetic variation across Eurasia. While sub-Saharan accessions have been reported to be the most divergent group, in the nuclear genome we found accessions from Yunnan, China to be genetically closest to the sub-Saharan group. In chloroplast, several deeply diverged haplogroups exist only in Eurasia, and African populations have lower variation in many haplogroups that they share with the Eurasian populations. These patterns cannot be easily explained by a single out-of-Africa event suggested previously. For more recent demographic history, we dated the nonrelict expansion to 10 ka. In the Chinese Yangtze nonrelicts, we found clear traces of gene flow with local relicts, and genes under strong selection were enriched for traces of relict introgression, especially those related to biotic and immune responses. The results suggest the ability of nonrelicts to obtain locally adaptive alleles through admixture with relicts is important for the expansion across environmental gradients of Eurasia. Our re-analyses provide another model for the early history as well as elucidating factors contributing to the recent demographic turnover event of this species.
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Affiliation(s)
- Che-Wei Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei, 10617, Taiwan ROC
| | - Cheng-Yu Lo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei, 10617, Taiwan ROC
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei, 10617, Taiwan ROC
- Institute of Plant Biology, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei, 10617, Taiwan ROC
- Genome and Systems Biology Degree Program, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei, 10617, Taiwan ROC
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25
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De Lorenzis G, Mercati F, Bergamini C, Cardone MF, Lupini A, Mauceri A, Caputo AR, Abbate L, Barbagallo MG, Antonacci D, Sunseri F, Brancadoro L. SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination. BMC PLANT BIOLOGY 2019; 19:7. [PMID: 30612542 PMCID: PMC6322315 DOI: 10.1186/s12870-018-1576-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/27/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Magna Graecia is the ancient name for the modern geopolitical region of South Italy extensively populated by Greek colonizers, shown by archeological and historical evidence to be the oldest wine growing region of Italy, crucial for the spread of specialized viticulture around Mediterranean shores. Here, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in grapevine propagation around the Mediterranean basin was underlined. RESULTS A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia to the Iberian Peninsula using the 18 K SNP array. A high level of genetic diversity of the analyzed germplasm was determined; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South Italy and the Eastern Mediterranean (Greece). Gene flow from east (Georgia) to west (Iberian Peninsula) was identified throughout the large number of detected admixed samples. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved. CONCLUSIONS This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes, as well as, by the availability of different thermal resources for cultivars growing in such different winegrowing areas. The uniqueness of this ampelographic platform was mainly an outcome of complex natural or human-driven crosses involving elite cultivars.
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Affiliation(s)
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR, Corso Calatafimi 414, 90120 Palermo, Italy
| | - Carlo Bergamini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Maria Francesca Cardone
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Antonio Lupini
- Dipartimento AGRARIA, località Feo di Vito snc, 89121 Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento AGRARIA, località Feo di Vito snc, 89121 Reggio Calabria, Italy
| | - Angelo Raffaele Caputo
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Loredana Abbate
- Istituto di Bioscienze e Biorisorse CNR, Corso Calatafimi 414, 90120 Palermo, Italy
| | | | - Donato Antonacci
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Viticoltura ed Enologia, CREA-VE, via Casamassima 148, 70010 Turi, Bari Italy
| | - Francesco Sunseri
- Dipartimento AGRARIA, località Feo di Vito snc, 89121 Reggio Calabria, Italy
| | - Lucio Brancadoro
- Dipartimento di Scienze Agrarie ed Ambientali, via Celoria 2, 20133 Milan, Italy
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26
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Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus). Heredity (Edinb) 2018; 122:759-769. [PMID: 30459340 DOI: 10.1038/s41437-018-0164-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of species is a dynamic process as they modify, expand, and contract their spatial distributions over time. Range expansions (REs) occur through a series of founder events that are followed by migration among neighboring demes. The process usually results in structured metapopulations and leaves a distinct signature in the genetic variability of species. Explicitly modeling the consequences of complex demographic events such as REs is computationally very intensive. Here we propose an an alternative approach that requires less computational effort than a comprehensive RE model, but that can recover the demography of species undergoing a RE, by combining spatially explicit modelling with simplified but realistic metapopulation models. We examine the demographic and colonization history of Carcharhinus melanopterus, an abundant reef-associated shark, as a test case. We first used a population genomics approach to statistically confirm the occurrence of a RE in C. melanopterus, and identify its origin in the Indo-Australian Archipelago. Spatial genetic modelling identified two waves of stepping-stone colonization: an eastward wave moving through the Pacific and a westward one moving through the Indian Ocean. We show that metapopulation models best describe the demographic history of this species and that not accounting for this may lead to incorrectly interpreting the observed genetic variation as signals of widespread population bottlenecks. Our study highlights insights that can be gained about demography by coupling metapopulation models with spatial modeling and underscores the need for cautious interpretation of population genetic data when advancing conservation priorities.
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27
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Fulgione A, Hancock AM. Archaic lineages broaden our view on the history of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 219:1194-1198. [PMID: 29862511 DOI: 10.1111/nph.15244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/25/2018] [Indexed: 05/15/2023]
Abstract
Contents Summary 1194 I. Introduction 1194 II. Origin of the A. thaliana species 1194 III. The classic model of the history of A. thaliana 1195 IV. New genomic data from outside Eurasia challenge our view of A. thaliana history 1195 V. Conclusions 1197 Acknowledgements 1197 References 1197 SUMMARY: Natural variation in Arabidopsis thaliana has contributed to discoveries in diverse areas of plant biology. While A. thaliana has typically been considered a weed associated primarily with human-mediated environments, including agricultural and urban sites and railways, it has recently been shown that it is also native in remote natural areas, including high altitude sites in Eurasia and Africa, from the Atlas mountains in Morocco to the afro-alpine regions in Eastern and South Africa to Yunnan in China, the Himalayas and the Tibetan Plateau. This finding suggests that while A. thaliana has been extensively studied in Europe and Western Asia there are still many open questions about its population history, genotype-phenotype relationships and mechanisms of adaptation.
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Affiliation(s)
- Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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28
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Koc J, Androsiuk P, Chwedorzewska KJ, Cuba-Díaz M, Górecki R, Giełwanowska I. Range-wide pattern of genetic variation in Colobanthus quitensis. Polar Biol 2018. [DOI: 10.1007/s00300-018-2383-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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No distinct barrier effects of highways and a wide river on the genetic structure of the Alpine newt (Ichthyosaura alpestris) in densely settled landscapes. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1046-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Theodoridis S, Randin C, Szövényi P, Boucher FC, Patsiou TS, Conti E. How Do Cold-Adapted Plants Respond to Climatic Cycles? Interglacial Expansion Explains Current Distribution and Genomic Diversity in Primula farinosa L. Syst Biol 2018; 66:715-736. [PMID: 28334079 DOI: 10.1093/sysbio/syw114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in $P$. farinosa through the Late Quaternary. Our results support the interglacial expansion of $P$. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes.
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Affiliation(s)
- Spyros Theodoridis
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland
| | - Christophe Randin
- Institute of Botany, University of Basel, CH-4056 Basel, Switzerland.,Department of Ecology & Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Peter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland
| | - Florian C Boucher
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Department of Botany and Zoology, University of Stellenbosch, 7602 Matieland, South Africa
| | - Theofania S Patsiou
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland.,Institute of Botany, University of Basel, CH-4056 Basel, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland.,Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland
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31
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Günther T, Malmström H, Svensson EM, Omrak A, Sánchez-Quinto F, Kılınç GM, Krzewińska M, Eriksson G, Fraser M, Edlund H, Munters AR, Coutinho A, Simões LG, Vicente M, Sjölander A, Jansen Sellevold B, Jørgensen R, Claes P, Shriver MD, Valdiosera C, Netea MG, Apel J, Lidén K, Skar B, Storå J, Götherström A, Jakobsson M. Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS Biol 2018; 16:e2003703. [PMID: 29315301 PMCID: PMC5760011 DOI: 10.1371/journal.pbio.2003703] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500–6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east–west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans. The Scandinavian peninsula was the last part of Europe to be colonized after the Last Glacial Maximum. The migration routes, cultural networks, and the genetic makeup of the first Scandinavians remain elusive and several hypotheses exist based on archaeology, climate modeling, and genetics. By analyzing the genomes of early Scandinavian hunter-gatherers, we show that their migrations followed two routes: one from the south and another from the northeast along the ice-free Norwegian Atlantic coast. These groups met and mixed in Scandinavia, creating a population more diverse than contemporaneous central and western European hunter-gatherers. As northern Europe is associated with cold and low light conditions, we investigated genomic patterns of adaptation to these conditions and genes known to be involved in skin pigmentation. We demonstrate that Mesolithic Scandinavians had higher levels of light pigmentation variants compared to the respective source populations of the migrations, suggesting adaptation to low light levels and a surprising signal of genetic continuity in TMEM131, a gene that may be involved in long-term adaptation to the cold.
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Affiliation(s)
- Torsten Günther
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Helena Malmström
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Emma M. Svensson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Gülşah M. Kılınç
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Gunilla Eriksson
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Magdalena Fraser
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University-Campus Gotland, Visby, Sweden
| | - Hanna Edlund
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | | | - Luciana G. Simões
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mário Vicente
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Anders Sjölander
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jørgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Peter Claes
- Department of Electrical Engineering, Center for Processing Speech and Images, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mark D. Shriver
- Department of Anthropology, Penn State University, State College, Pennsylvania, United States of America
| | - Cristina Valdiosera
- Department of Archaeology and History, La Trobe University, Melbourne, Australia
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jan Apel
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, Norwegian University of Science and Technology University Museum, Trondheim, Norway
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- SciLifeLab, Uppsala and Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala and Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
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32
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Singh A, Roy S. High altitude population of Arabidopsis thaliana is more plastic and adaptive under common garden than controlled condition. BMC Ecol 2017; 17:39. [PMID: 29237449 PMCID: PMC5729231 DOI: 10.1186/s12898-017-0149-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Population differentiation and their adaptation to a particular environment depend on their ability to respond to a new environment. This, in turn is governed to an extent, by the degree of phenotypic plasticity exhibited by the populations. The populations of same species inhabiting different climatic conditions may differ in their phenotypic plasticity. Himalayan populations of Arabidopsis thaliana originating from a steep altitude are exposed to different climatic conditions ranging from sub-tropical to temperate. Thus they might have experienced different selection pressures during evolution and may respond differently under common environmental condition. RESULTS Phenotypic plasticity and differentiation of natural populations of A. thaliana grown under common garden and controlled conditions were determined. A total of seventeen morphological traits, their plasticity, association between traits and environment were performed using 45 accessions from three populations. Plants from different altitudes differed in phenotypes, their selection and fitness under two conditions. Under both the conditions lower altitude population was characterized by higher leaf count and larger silique than higher and middle altitude population. Flowering time of high altitude population increased while that of low and medium altitude decreased under controlled condition compared to open field. An increase in seed weight and germination was observed for all the population under open field than controlled. Rosette area was under divergent selection in both the condition. The heritability of lower altitude population was the highest under both the conditions, where as it was the least for higher altitude population further indicating that the high altitude populations are more responsive towards phenotypic changes under new environmental conditions. Ninety-nine percent of variability in traits and their plasticity co-varied with the altitude of their origin. The population of high altitude was more plastic and differentiated as compared to the lower altitude one. CONCLUSIONS Arabidopsis thaliana population native to different altitudes of the west Himalaya responds differently when grown under common environments. The success of high altitude population is more in common garden than the controlled conditions. The significant variability in phenotype and its association with altitude of origin predicts for non-random genetic differentiation among the populations.
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Affiliation(s)
- Akanksha Singh
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
| | - Sribash Roy
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
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33
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Plötner B, Nurmi M, Fischer A, Watanabe M, Schneeberger K, Holm S, Vaid N, Schöttler MA, Walther D, Hoefgen R, Weigel D, Laitinen RAE. Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:251-262. [PMID: 28378460 DOI: 10.1111/tpj.13560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 05/28/2023]
Abstract
Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.
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Affiliation(s)
- Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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34
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African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:5213-5218. [PMID: 28473417 DOI: 10.1073/pnas.1616736114] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa. Moreover, we show that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Our results also reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral A. thaliana population began to split by 120-90 kya, during the last interglacial and Abbassia pluvial, and Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for diverse species, including humans, implying a key role for climatic events during interglacial and pluvial periods in shaping the histories and current distributions of a wide range of species.
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35
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Lee CR, Svardal H, Farlow A, Exposito-Alonso M, Ding W, Novikova P, Alonso-Blanco C, Weigel D, Nordborg M. On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Commun 2017; 8:14458. [PMID: 28181519 PMCID: PMC5309843 DOI: 10.1038/ncomms14458] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/03/2017] [Indexed: 02/03/2023] Open
Abstract
Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts of other groups can be found in local populations along the Mediterranean Sea. Here we provide evidence that these 'relicts' occupied post-glacial Eurasia first and were later replaced by the invading 'non-relicts', which expanded through the east-west axis of Eurasia, leaving traces of admixture in the north and south of the species range. The non-relict expansion was likely associated with human activity and led to a demographic replacement similar to what occurred in humans. Introgressed genomic regions from relicts are associated with flowering time and enriched for genes associated with environmental conditions, such as root cap development or metal ion trans-membrane transport, which suggest that admixture with locally adapted relicts helped the non-relicts colonize new habitats.
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Affiliation(s)
- Cheng-Ruei Lee
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Institute of Ecology and Evolutionary Biology & Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Rd, 10617 Taipei, Taiwan
| | - Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Moises Exposito-Alonso
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Wei Ding
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Polina Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
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36
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Gonneau C, Noret N, Godé C, Frérot H, Sirguey C, Sterckeman T, Pauwels M. Demographic history of the trace metal hyperaccumulator Noccaea caerulescens (J. Presl and C. Presl) F. K. Mey. in Western Europe. Mol Ecol 2016; 26:904-922. [PMID: 27914207 DOI: 10.1111/mec.13942] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/27/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
Abstract
Noccaea caerulescens (Brassicaceae) is a major pseudometallophyte model for the investigation of the genetics and evolution of metal hyperaccumulation in plants. We studied the population genetics and demographic history of this species to advance the understanding of among-population differences in metal hyperaccumulation and tolerance abilities. Sampling of seven to 30 plants was carried out in 62 sites in Western Europe. Genotyping was carried out using a combination of new chloroplast and nuclear neutral markers. A strong genetic structure was detected, allowing the definition of three genetic subunits. Subunits showed a good geographic coherence. Accordingly, distant metallicolous populations generally belonged to distinct subunits. Approximate Bayesian computation analysis of demographic scenarios among subunits further supported a primary isolation of populations from the southern Massif Central prior to last glacial maximum, whereas northern populations may have derived during postglacial recolonization events. Estimated divergence times among subunits were rather recent in comparison with the species history, but certainly before the establishment of anthropogenic metalliferous sites. Our results suggest that the large-scale genetic structure of N. caerulescens populations pre-existed to the local adaptation to metalliferous sites. The population structure of quantitative variation for metal-related adaptive traits must have established independently in isolated gene pools. However, features of the most divergent genetic unit (e.g. extreme levels of Cd accumulation observed in previous studies) question the putative relationships between adaptive evolution of metal-related traits and subunits isolation. Finally, admixture signals among distant metallicolous populations suggest a putative role of human activities in facilitating long-distance genetic exchanges.
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Affiliation(s)
- Cédric Gonneau
- Laboratoire Sols et Environnement UMR1120, Université de Lorraine, TSA 40602, Vandœuvre-lès-Nancy Cedex, F-54518, France.,Laboratoire Sols et Environnement UMR1120, INRA, Vandœuvre-lès-Nancy Cedex, F-54518, France
| | - Nausicaa Noret
- Laboratoire d'Écologie Végétale et Biogéochimie, Université libre de Bruxelles, Campus de la Plaine - CP244, Boulevard du Triomphe, B-1050, Ixelles, Belgium
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Hélène Frérot
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Catherine Sirguey
- Laboratoire Sols et Environnement UMR1120, Université de Lorraine, TSA 40602, Vandœuvre-lès-Nancy Cedex, F-54518, France.,Laboratoire Sols et Environnement UMR1120, INRA, Vandœuvre-lès-Nancy Cedex, F-54518, France
| | - Thibault Sterckeman
- Laboratoire Sols et Environnement UMR1120, Université de Lorraine, TSA 40602, Vandœuvre-lès-Nancy Cedex, F-54518, France.,Laboratoire Sols et Environnement UMR1120, INRA, Vandœuvre-lès-Nancy Cedex, F-54518, France
| | - Maxime Pauwels
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
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37
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Günther T, Jakobsson M. Genes mirror migrations and cultures in prehistoric Europe — a population genomic perspective. Curr Opin Genet Dev 2016; 41:115-123. [DOI: 10.1016/j.gde.2016.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023]
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38
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Maisano Delser P, Corrigan S, Hale M, Li C, Veuille M, Planes S, Naylor G, Mona S. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Sci Rep 2016; 6:33753. [PMID: 27651217 PMCID: PMC5030670 DOI: 10.1038/srep33753] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/19/2016] [Indexed: 01/23/2023] Open
Abstract
Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Shannon Corrigan
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
| | - Matthew Hale
- Medical University of South Carolina, College of Graduate Studies, Charleston 29403, SC, USA
| | - Chenhong Li
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Serge Planes
- CRIOBE-USR 3278, CNRS-EPHE-UPVD, Laboratoire d’Excellence ‘CORAIL’, 58 Avenue Paul Alduy, 66860 Perpignan, France
| | - Gavin Naylor
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
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39
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Martins H, Caye K, Luu K, Blum MGB, François O. Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. Mol Ecol 2016; 25:5029-5042. [DOI: 10.1111/mec.13822] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/18/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Helena Martins
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Kevin Caye
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Keurcien Luu
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Michael G. B. Blum
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Olivier François
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
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40
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Mona S. On the role played by the carrying capacity and the ancestral population size during a range expansion. Heredity (Edinb) 2016; 118:143-153. [PMID: 27599574 DOI: 10.1038/hdy.2016.73] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 01/05/2023] Open
Abstract
Most species are structured and various population genetics models have been proposed to investigate their history. For mathematical tractability, most of these models make the simplifying assumption of equilibrium. Here we focus on the properties of a nonequilibrium spatial explicit model, range expansions (REs). Despite their abundance, many details of their genetic consequences need yet to be fully investigated. The model we studied is characterized by four main parameters: the effective population size of each deme (N), the migration rate per generation per deme (m), the time of the expansion (Texp) and the effective size of the deme from which the expansion started (Nanc). By means of extensive coalescent simulations, we focused on two aspects of range expansions for fixed Nm: (1) the separate influence of N and m and (2) the role of Nanc. We compared our results with an equilibrium stepping stone model and found two main features typical of REs: an excess of rare variants for larger N and a complex interaction between N, Texp and Nanc in shaping the degree of population differentiation (which depends only on Nm in the stepping stone model). Finally, we developed an approximate Bayesian computation approach to jointly estimate N and m and to infer Nanc. When applied to pseudo-observed data sets, we could correctly recover both N and m (but not Nanc), provided a large number of demes were sampled. These findings highlight how it will be possible to estimate the dispersal rate in nonequilibrium metapopulations by using population genetics approaches.
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Affiliation(s)
- S Mona
- EPHE, PSL Research University, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
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41
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Sebasky ME, Keller SR, Taylor DR. Investigating past range dynamics for a weed of cultivation, Silene vulgaris. Ecol Evol 2016; 6:4800-11. [PMID: 27547314 PMCID: PMC4979708 DOI: 10.1002/ece3.2250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/10/2016] [Accepted: 05/16/2016] [Indexed: 11/05/2022] Open
Abstract
Since the last glacial maximum (LGM), many plant and animal taxa have expanded their ranges by migration from glacial refugia. Weeds of cultivation may have followed this trend or spread globally following the expansion of agriculture or ruderal habitats associated with human‐mediated disturbance. We tested whether the range expansion of the weed Silene vulgaris across Europe fit the classical model of postglacial expansion from southern refugia, or followed known routes of the expansion of human agricultural practices. We used species distribution modeling to predict spatial patterns of postglacial expansion and contrasted these with the patterns of human agricultural expansion. A population genetic analysis using microsatellite loci was then used to test which scenario was better supported by spatial patterns of genetic diversity and structure. Genetic diversity was highest in southern Europe and declined with increasing latitude. Locations of ancestral demes from genetic cluster analysis were consistent with areas of predicted refugia. Species distribution models showed the most suitable habitat in the LGM on the southern coasts of Europe. These results support the typical postglacial northward colonization from southern refugia while refuting the east‐to‐west agricultural spread as the main mode of expansion for S. vulgaris. We know that S. vulgaris has recently colonized many regions (including North America and other continents) through human‐mediated dispersal, but there is no evidence for a direct link between the Neolithic expansion of agriculture and current patterns of genetic diversity of S. vulgaris in Europe. Therefore, the history of range expansion of S. vulgaris likely began with postglacial expansion after the LGM, followed by more recent global dispersal by humans.
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Affiliation(s)
- Megan E Sebasky
- Department of Biology University of Virginia Charlottesville Virginia
| | - Stephen R Keller
- Department of Plant Biology University of Vermont Burlington Vermont
| | - Douglas R Taylor
- Department of Biology University of Virginia Charlottesville Virginia
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42
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Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock AM, Henz SR, Holm S, Horton M, Jarsulic M, Kerstetter RA, Korte A, Korte P, Lanz C, Lee CR, Meng D, Michael TP, Mott R, Muliyati NW, Nägele T, Nagler M, Nizhynska V, Nordborg M, Novikova PY, Picó FX, Platzer A, Rabanal FA, Rodriguez A, Rowan BA, Salomé PA, Schmid KJ, Schmitz RJ, Seren Ü, Sperone FG, Sudkamp M, Svardal H, Tanzer MM, Todd D, Volchenboum SL, Wang C, Wang G, Wang X, Weckwerth W, Weigel D, Zhou X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016; 166:481-491. [PMID: 27293186 PMCID: PMC4949382 DOI: 10.1016/j.cell.2016.05.063] [Citation(s) in RCA: 723] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/30/2022]
Abstract
Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
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43
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Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen RA, Jeddeloh JA, Colot V. The Arabidopsis thaliana mobilome and its impact at the species level. eLife 2016; 5. [PMID: 27258693 PMCID: PMC4917339 DOI: 10.7554/elife.15716] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/01/2016] [Indexed: 01/07/2023] Open
Abstract
Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles.
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Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale Supérieure, Paris, France
| | - Amanda Bortolini Silveira
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale Supérieure, Paris, France
| | | | - Chantal LeBlanc
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Robert A Martienssen
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Palo Alto, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale Supérieure, Paris, France
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Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright SI, Lascoux M. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Mol Ecol 2016; 25:616-29. [PMID: 26607306 DOI: 10.1111/mec.13491] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/29/2022]
Abstract
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
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Affiliation(s)
- A Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - A Salcedo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - D Kryvokhyzha
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - K Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - M Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
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45
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Atanasov KE, Barboza-Barquero L, Tiburcio AF, Alcázar R. Genome Wide Association Mapping for the Tolerance to the Polyamine Oxidase Inhibitor Guazatine in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:401. [PMID: 27092150 PMCID: PMC4820465 DOI: 10.3389/fpls.2016.00401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/14/2016] [Indexed: 05/09/2023]
Abstract
Guazatine is a potent inhibitor of polyamine oxidase (PAO) activity. In agriculture, guazatine is used as non-systemic contact fungicide efficient in the protection of cereals and citrus fruits against disease. The composition of guazatine is complex, mainly constituted by a mixture of synthetic guanidated polyamines (polyaminoguanidines). Here, we have studied the effects from exposure to guazatine in the weed Arabidopsis thaliana. We report that micromolar concentrations of guazatine are sufficient to inhibit growth of Arabidopsis seedlings and induce chlorosis, whereas germination is barely affected. We observed the occurrence of quantitative variation in the response to guazatine between 107 randomly chosen Arabidopsis accessions. This enabled us to undertake genome-wide association (GWA) mapping that identified a locus on chromosome one associated with guazatine tolerance. CHLOROPHYLLASE 1 (CLH1) within this locus was studied as candidate gene, together with its paralog (CLH2). The analysis of independent clh1-2, clh1-3, clh2-3, clh2-2, and double clh1-2 clh2-3 mutant alleles indicated that CLH1 and/or CLH2 loss-of-function or expression down-regulation promote guazatine tolerance in Arabidopsis. We report a natural mechanism by which Arabidopsis populations can overcome toxicity by the fungicide guazatine.
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Affiliation(s)
- Kostadin E. Atanasov
- Laboratory of Plant Physiology, Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of BarcelonaBarcelona, Spain
| | - Luis Barboza-Barquero
- Centro para Investigaciones en Granos y Semillas, Universidad de Costa RicaSan José, Costa Rica
| | - Antonio F. Tiburcio
- Laboratory of Plant Physiology, Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of BarcelonaBarcelona, Spain
| | - Rubén Alcázar
- Laboratory of Plant Physiology, Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of BarcelonaBarcelona, Spain
- *Correspondence: Rubén Alcázar
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46
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Tabib A, Vishwanathan S, Seleznev A, McKeown PC, Downing T, Dent C, Sanchez-Bermejo E, Colling L, Spillane C, Balasubramanian S. A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1311. [PMID: 27630650 PMCID: PMC5006647 DOI: 10.3389/fpls.2016.01311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/16/2016] [Indexed: 05/15/2023]
Abstract
Triplet repeat expansions underlie several human genetic diseases such as Huntington's disease and Friedreich's ataxia. Although such mutations are primarily known from humans, a triplet expansion associated genetic defect has also been reported at the IIL1 locus in the Bur-0 accession of the model plant Arabidopsis thaliana. The IIL1 triplet expansion is an example of cryptic genetic variation as its phenotypic effects are seen only under genetic or environmental perturbation, with high temperatures resulting in a growth defect. Here we demonstrate that the IIL1 triplet expansion associated growth defect is not a general stress response and is specific to particular environmental perturbations. We also confirm and map genetic modifiers that suppress the effect of IIL1 triplet repeat expansion. By collecting and analyzing accessions from the island of Ireland, we recover the repeat expansion in wild populations suggesting that the repeat expansion has persisted at least 60 years in Ireland. Through genome-wide genotyping, we show that the repeat expansion is present in diverse Irish populations. Our findings indicate that even deleterious alleles can persist in populations if their effect is conditional. Our study demonstrates that analysis of groups of wild populations is a powerful tool for understanding the dynamics of cryptic genetic variation.
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Affiliation(s)
- Amanda Tabib
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Andrei Seleznev
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Tim Downing
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
- School of Biotechnology, Dublin City UniversityDublin, Ireland
| | - Craig Dent
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Luana Colling
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Sureshkumar Balasubramanian
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
- *Correspondence: Sureshkumar Balasubramanian
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47
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Mayol M, Riba M, González-Martínez SC, Bagnoli F, de Beaulieu JL, Berganzo E, Burgarella C, Dubreuil M, Krajmerová D, Paule L, Romšáková I, Vettori C, Vincenot L, Vendramin GG. Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata). THE NEW PHYTOLOGIST 2015; 208:973-986. [PMID: 26096330 DOI: 10.1111/nph.13496] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/30/2015] [Indexed: 06/04/2023]
Abstract
Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, 08193, Spain
- Univ Autonòma Barcelona, Cerdanyola del Vallès, 08193, Spain
| | | | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | | | - Concetta Burgarella
- Université Montpellier 2, CNRS UMR, Institut de Sciences de l'Evolution de Montpellier, Montpellier, 5554, France
| | | | - Diana Krajmerová
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ladislav Paule
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ivana Romšáková
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
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48
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Caye K, Deist TM, Martins H, Michel O, François O. TESS3: fast inference of spatial population structure and genome scans for selection. Mol Ecol Resour 2015; 16:540-8. [PMID: 26417651 DOI: 10.1111/1755-0998.12471] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/04/2015] [Accepted: 09/16/2015] [Indexed: 11/28/2022]
Abstract
Geography and landscape are important determinants of genetic variation in natural populations, and several ancestry estimation methods have been proposed to investigate population structure using genetic and geographic data simultaneously. Those approaches are often based on computer-intensive stochastic simulations and do not scale with the dimensions of the data sets generated by high-throughput sequencing technologies. There is a growing demand for faster algorithms able to analyse genomewide patterns of population genetic variation in their geographic context. In this study, we present TESS3, a major update of the spatial ancestry estimation program TESS. By combining matrix factorization and spatial statistical methods, TESS3 provides estimates of ancestry coefficients with accuracy comparable to TESS and with run-times much faster than the Bayesian version. In addition, the TESS3 program can be used to perform genome scans for selection, and separate adaptive from nonadaptive genetic variation using ancestral allele frequency differentiation tests. The main features of TESS3 are illustrated using simulated data and analysing genomic data from European lines of the plant species Arabidopsis thaliana.
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Affiliation(s)
- Kevin Caye
- Centre National de la Recherche Scientifique, Université Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, 38042, France
| | - Timo M Deist
- Centre National de la Recherche Scientifique, Université Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, 38042, France
| | - Helena Martins
- Centre National de la Recherche Scientifique, Université Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, 38042, France
| | - Olivier Michel
- Centre National de la Recherche Scientifique, Université Grenoble-Alpes, GIPSA-lab UMR 5216, Grenoble, 38042, France
| | - Olivier François
- Centre National de la Recherche Scientifique, Université Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, 38042, France
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49
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Wang Y, Shahid MQ, Ghouri F, Baloch FS, Wang Y, Huang H. Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci: For conservation of soybean germplasm. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Pierce AA, Zalucki MP, Bangura M, Udawatta M, Kronforst MR, Altizer S, Haeger JF, de Roode JC. Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies. Proc Biol Sci 2015; 281:rspb.2014.2230. [PMID: 25377462 DOI: 10.1098/rspb.2014.2230] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs (Danaus plexippus) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel only short distances. Here, we used microsatellite markers to assess genetic differentiation among 18 monarch populations and to determine worldwide colonization routes. Our results indicate that North American monarch populations connected by land show limited differentiation, probably because of the monarch's ability to migrate long distances. Conversely, we found high genetic differentiation between populations separated by large bodies of water. Moreover, we show evidence for serial founder effects across the Pacific, suggesting stepwise dispersal from a North American origin. These findings demonstrate that genetic drift played a major role in shaping allele frequencies and created genetic differentiation among newly formed populations. Thus, range expansion can give rise to genetic differentiation and declines in genetic diversity, even in highly mobile species.
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Affiliation(s)
- Amanda A Pierce
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Myron P Zalucki
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Marie Bangura
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Milan Udawatta
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Marcus R Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Sonia Altizer
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
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