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Zeitler L, Gilbert KJ. Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates. Genome Biol Evol 2024; 16:evae139. [PMID: 38935434 PMCID: PMC11245710 DOI: 10.1093/gbe/evae139] [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: 02/27/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data.
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Affiliation(s)
- Leo Zeitler
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
| | - Kimberly J Gilbert
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
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2
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Mishra P, Roggen A, Ljung K, Albani MC, Vayssières A. Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials. FRONTIERS IN PLANT SCIENCE 2024; 15:1352830. [PMID: 38693930 PMCID: PMC11062184 DOI: 10.3389/fpls.2024.1352830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.
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Affiliation(s)
- Priyanka Mishra
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, India
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Maria C. Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Rijk Zwaan, De Lier, Netherlands
| | - Alice Vayssières
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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3
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Wunder J, Fulgione A, Toräng P, Wötzel S, Herzog M, Obeso JR, Kourmpetis Y, van Ham R, Odong T, Bink M, Kemi U, Ågren J, Coupland G. Adaptation of perennial flowering phenology across the European range of Arabis alpina. Proc Biol Sci 2023; 290:20231401. [PMID: 37989245 PMCID: PMC10688268 DOI: 10.1098/rspb.2023.1401] [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: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
Flowering phenology is important in the adaptation of many plants to their local environment, but its adaptive value has not been extensively studied in herbaceous perennials. We used Arabis alpina as a model system to determine the importance of flowering phenology to fitness of a herbaceous perennial with a wide geographical range. Individual plants representative of local genetic diversity (accessions) were collected across Europe, including in Spain, the Alps and Scandinavia. The flowering behaviour of these accessions was documented in controlled conditions, in common-garden experiments at native sites and in situ in natural populations. Accessions from the Alps and Scandinavia varied in whether they required exposure to cold (vernalization) to induce flowering, and in the timing and duration of flowering. By contrast, all Spanish accessions obligately required vernalization and had a short duration of flowering. Using experimental gardens at native sites, we show that an obligate requirement for vernalization increases survival in Spain. Based on our analyses of genetic diversity and flowering behaviour across Europe, we propose that in the model herbaceous perennial A. alpina, an obligate requirement for vernalization, which is correlated with short duration of flowering, is favoured by selection in Spain where the plants experience a long growing season.
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Affiliation(s)
- Jörg Wunder
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Andrea Fulgione
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Per Toräng
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
| | - Stefan Wötzel
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Michel Herzog
- Laboratoire d’Écologie Alpine, LECA, Université Grenoble Alpes, 38000 Grenoble, France
| | - José Ramón Obeso
- Research Unit of Biodiversity (UO-CSIC-PA), Universidad de Oviedo, Campus de Mieres, 33600 Mieres, Spain
| | - Yiannis Kourmpetis
- Biometris, Wageningen University and Research Centre, 6700 AC Wageningen, The Netherlands
| | - Roeland van Ham
- Laboratory of Bioinformatics, Wageningen University, 6708 PB Wageningen, The Netherlands
- KeyGene, 6708 PW Wageningen, The Netherlands
| | - Thomas Odong
- Biometris, Wageningen University and Research Centre, 6700 AC Wageningen, The Netherlands
| | - Marco Bink
- Biometris, Wageningen University and Research Centre, 6700 AC Wageningen, The Netherlands
| | - Ulla Kemi
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jon Ågren
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
| | - George Coupland
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Rehman S, Bahadur S, Xia W. An overview of floral regulatory genes in annual and perennial plants. Gene 2023; 885:147699. [PMID: 37567454 DOI: 10.1016/j.gene.2023.147699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228 China
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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Zeitler L, Parisod C, Gilbert KJ. Purging due to self-fertilization does not prevent accumulation of expansion load. PLoS Genet 2023; 19:e1010883. [PMID: 37656747 PMCID: PMC10501686 DOI: 10.1371/journal.pgen.1010883] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/14/2023] [Accepted: 07/25/2023] [Indexed: 09/03/2023] Open
Abstract
As species expand their geographic ranges, colonizing populations face novel ecological conditions, such as new environments and limited mates, and suffer from evolutionary consequences of demographic change through bottlenecks and mutation load accumulation. Self-fertilization is often observed at species range edges and, in addition to countering the lack of mates, is hypothesized as an evolutionary advantage against load accumulation through increased homozygosity and purging. We study how selfing impacts the accumulation of genetic load during range expansion via purging and/or speed of colonization. Using simulations, we disentangle inbreeding effects due to demography versus due to selfing and find that selfers expand faster, but still accumulate load, regardless of mating system. The severity of variants contributing to this load, however, differs across mating system: higher selfing rates purge large-effect recessive variants leaving a burden of smaller-effect alleles. We compare these predictions to the mixed-mating plant Arabis alpina, using whole-genome sequences from refugial outcrossing populations versus expanded selfing populations. Empirical results indicate accumulation of expansion load along with evidence of purging in selfing populations, concordant with our simulations, suggesting that while purging is a benefit of selfing evolving during range expansions, it is not sufficient to prevent load accumulation due to range expansion.
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Affiliation(s)
- Leo Zeitler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Christian Parisod
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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Gutiérrez-Valencia J, Fracassetti M, Horvath R, Laenen B, Désamore A, Drouzas AD, Friberg M, Kolář F, Slotte T. Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina. Mol Biol Evol 2021; 39:6456311. [PMID: 34878144 PMCID: PMC8788238 DOI: 10.1093/molbev/msab349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Robert Horvath
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aurélie Désamore
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Magne Friberg
- Department of Biology, Lund University, Lund, Sweden
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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7
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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Luizzi VJ, Friberg M, Petrén H. Phenotypic plasticity in floral scent in response to nutrient, but not water, availability in the perennial plant
Arabis alpina. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victoria J. Luizzi
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Department of Biology Lund University Lund Sweden
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Petrén H, Toräng P, Ågren J, Friberg M. Evolution of floral scent in relation to self-incompatibility and capacity for autonomous self-pollination in the perennial herb Arabis alpina. ANNALS OF BOTANY 2021; 127:737-747. [PMID: 33555338 PMCID: PMC8103803 DOI: 10.1093/aob/mcab007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The transition from outcrossing to selfing is a frequent evolutionary shift in flowering plants and is predicted to result in reduced allocation to pollinator attraction if plants can self-pollinate autonomously. The evolution of selfing is associated with reduced visual floral signalling in many systems, but effects on floral scent have received less attention. We compared multiple populations of the arctic-alpine herb Arabis alpina (Brassicaceae), and asked whether the transition from self-incompatibility to self-compatibility has been associated with reduced visual and chemical floral signalling. We further examined whether floral signalling differ between self-compatible populations with low and high capacity for autonomous self-pollination, as would be expected if benefits of signalling decrease with reduced dependence on pollinators for pollen transfer. METHODS In a common garden we documented flower size and floral scent emission rate and composition in eight self-compatible and nine self-incompatible A. alpina populations. These included self-compatible Scandinavian populations with high capacity for autonomous self-pollination, self-compatible populations with low capacity for autonomous self-pollination from France and Spain, and self-incompatible populations from Italy and Greece. KEY RESULTS The self-compatible populations produced smaller and less scented flowers than the self-incompatible populations. However, flower size and scent emission rate did not differ between self-compatible populations with high and low capacity for autonomous self-pollination. Floral scent composition differed between self-compatible and self-incompatible populations, but also varied substantially among populations within the two categories. CONCLUSIONS Our study demonstrates extensive variation in floral scent among populations of a geographically widespread species. Contrary to expectation, floral signalling did not differ between self-compatible populations with high and low capacity for autonomous self-pollination, indicating that dependence on pollinator attraction can only partly explain variation in floral signalling. Additional variation may reflect adaptation to other aspects of local environments, genetic drift, or a combination of these processes.
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Affiliation(s)
- Hampus Petrén
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Per Toräng
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
- SLU Swedish Species Information Centre, Box 7007, SE-750 07 Uppsala, Sweden
| | - Jon Ågren
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Magne Friberg
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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Mishra P, Roggen A, Ljung K, Albani MC. Natural Variation in Adventitious Rooting in the Alpine Perennial Arabis alpina. PLANTS 2020; 9:plants9020184. [PMID: 32028613 PMCID: PMC7076489 DOI: 10.3390/plants9020184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 11/16/2022]
Abstract
Arctic alpine species follow a mixed clonal-sexual reproductive strategy based on the environmental conditions at flowering. Here, we explored the natural variation for adventitious root formation among genotypes of the alpine perennial Arabis alpina that show differences in flowering habit. We scored the presence of adventitious roots on the hypocotyl, main stem and axillary branches on plants growing in a long-day greenhouse. We also assessed natural variation for adventitious rooting in response to foliar auxin spray. In both experimental approaches, we did not detect a correlation between adventitious rooting and flowering habit. In the greenhouse, and without the application of synthetic auxin, the accession Wca showed higher propensity to produce adventitious roots on the main stem compared to the other accessions. The transcript accumulation of the A. alpina homologue of the auxin inducible GH3.3 gene (AaGH3.3) on stems correlated with the adventitious rooting phenotype of Wca. Synthetic auxin, 1-Naphthaleneacetic acid (1-NAA), enhanced the number of plants with adventitious roots on the main stem and axillary branches. A. alpina plants showed an age-, dosage- and genotype-dependent response to 1-NAA. Among the genotypes tested, the accession Dor was insensitive to auxin and Wca responded to auxin on axillary branches.
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Affiliation(s)
- Priyanka Mishra
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47B, 50674 Cologne, Germany (A.R.)
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences “From Complex Traits towards Synthetic Modules”, 40225 Düsseldorf, Germany
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47B, 50674 Cologne, Germany (A.R.)
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90736 Umeå, Sweden;
| | - Maria C. Albani
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47B, 50674 Cologne, Germany (A.R.)
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences “From Complex Traits towards Synthetic Modules”, 40225 Düsseldorf, Germany
- Correspondence: or
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11
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Carbognani M, Piotti A, Leonardi S, Pasini L, Spanu I, Vendramin GG, Tomaselli M, Petraglia A. Reproductive and genetic consequences of extreme isolation in Salix herbacea L. at the rear edge of its distribution. ANNALS OF BOTANY 2019; 124:849-860. [PMID: 31361802 PMCID: PMC6868362 DOI: 10.1093/aob/mcz129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS At the rear edge of the distribution of species, extreme isolation and small population size influence the genetic diversity and differentiation of plant populations. This may be particularly true for Arctic-alpine species in mid-latitude mountains, but exactly how peripherality has shaped their genetic and reproductive characteristics is poorly investigated. The present study, focused on Salix herbacea, aims at providing new insights into the causes behind ongoing demographic dynamics and their consequences for peripheral populations of Arctic-alpine species. METHODS We performed a whole-population, highly detailed sampling of the only two S. herbacea populations in the northern Apennines, comparing their clonal and genetic diversity, sex ratio and spatial genetic structure with a reference population from the Alps. After inspecting ~1800 grid intersections in the three populations, 563 ramets were genotyped at 11 nuclear microsatellite markers (nSSRs). Past demography and mating patterns of Apennine populations were investigated to elucidate the possible causes of altered reproductive dynamics. KEY RESULTS Apennine populations, which experienced a Holocene bottleneck and are highly differentiated (FST = 0.15), had lower clonal and genetic diversity compared with the alpine population (RMLG = 1 and HE = 0.71), with the smaller population exhibiting the lowest diversity (RMLG = 0.03 and HE = 0.24). An unbalanced sex ratio was found in the larger (63 F:37 M) and the smaller (99 F:1 M) Apennine population. Both were characterized by the presence of extremely large clones (up to 2500 m2), which, however, did not play a dominant role in local reproductive dynamics. CONCLUSIONS Under conditions of extreme isolation and progressive size reduction, S. herbacea has experienced an alteration of genetic characteristics produced by the prevalence of clonal growth over sexual reproduction. However, our results showed that the larger Apennine population has maintained levels of sexual reproduction enough to counteract a dramatic loss of genetic and clonal diversity.
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Affiliation(s)
- M Carbognani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - A Piotti
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Sesto Fiorentino (Firenze), Italy
| | - S Leonardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - L Pasini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - I Spanu
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Sesto Fiorentino (Firenze), Italy
| | - G G Vendramin
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Sesto Fiorentino (Firenze), Italy
| | - M Tomaselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - A Petraglia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Winkler DE, Chapin KJ, François O, Garmon JD, Gaut BS, Huxman TE. Multiple introductions and population structure during the rapid expansion of the invasive Sahara mustard ( Brassica tournefortii). Ecol Evol 2019; 9:7928-7941. [PMID: 31380061 PMCID: PMC6662425 DOI: 10.1002/ece3.5239] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 12/23/2022] Open
Abstract
The specific mechanisms that result in the success of any species invasion case are difficult to document. Reproductive strategies are often cited as a primary driver of invasive success, with human activities further facilitating invasions by, for example, acting as seed vectors for dispersal via road, train, air, and marine traffic, and by producing efficient corridors for movement including canals, drainages, and roadways. Sahara mustard (Brassica tournefortii) is a facultative autogamous annual native to Eurasia that has rapidly invaded the southwestern United States within the past century, displacing natives, and altering water-limited landscapes in the southwest. We used a genotyping-by-sequencing approach to study the population structure and spatial geography of Sahara mustard from 744 individuals from 52 sites across the range of the species' invasion. We also used herbaria records to model range expansion since its initial introduction in the 1920s. We found that Sahara mustard occurs as three populations in the United States unstructured by geography, identified three introduction sites, and combined herbaria records with genomic analyses to map the spread of the species. Low genetic diversity and linkage disequilibrium are consistent with self-fertilization, which likely promoted rapid invasive spread. Overall, we found that Sahara mustard experienced atypical expansion patterns, with a relatively constant rate of expansion and without the lag phase that is typical of many invasive species.
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Affiliation(s)
- Daniel E. Winkler
- Department of Ecology and Evolutionary BiologyUniversity of California, IrvineIrvineCalifornia
- U.S. Geological SurveySouthwest Biological Science CenterMoabUtah
| | - Kenneth J. Chapin
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona
| | | | | | - Brandon S. Gaut
- Department of Ecology and Evolutionary BiologyUniversity of California, IrvineIrvineCalifornia
| | - Travis E. Huxman
- Department of Ecology and Evolutionary BiologyUniversity of California, IrvineIrvineCalifornia
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Rogivue A, Choudhury RR, Zoller S, Joost S, Felber F, Kasser M, Parisod C, Gugerli F. Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae). Mol Ecol Resour 2019; 19:773-787. [PMID: 30636378 DOI: 10.1111/1755-0998.12991] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 02/01/2023]
Abstract
Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population-specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.
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Affiliation(s)
- Aude Rogivue
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Rimjhim R Choudhury
- University of Neuchâtel, Neuchâtel, Switzerland.,Institute of Plant Sciences, University of Berne, Bern, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre, ETH Zürich, Zürich, Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - François Felber
- University of Neuchâtel, Neuchâtel, Switzerland.,Musée et Jardins botaniques cantonaux, Lausanne, Switzerland
| | | | | | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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14
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Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing. Int J Mol Sci 2018; 19:ijms19020602. [PMID: 29463014 PMCID: PMC5855824 DOI: 10.3390/ijms19020602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 02/01/2023] Open
Abstract
Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species.
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15
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Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina. Proc Natl Acad Sci U S A 2018; 115:816-821. [PMID: 29301967 DOI: 10.1073/pnas.1707492115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.
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Graf W, Vitecek S. A new species of Limnephilidae (Insecta: Trichoptera) from the Western Alps (Insecta: Trichoptera). Zootaxa 2016; 4085:431-437. [PMID: 27069351 DOI: 10.11646/zootaxa.4085.3.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
A new species of the alpine caddisfly genus Consorophylax (Trichoptera, Limnephilidae, Stenophylacini) and the female of the recently described C. vinconi Graf & Malicky 2015 are described. The new species C. lepontiorumsp. nov. is a microendemic of the South-Western Alps and differs from its congeners in the shape of the superior and inferior appendages and the unique setation of the aedeagus, absent in all other Consorophylax species. The female of C. vinconi is characterized by the unique formation of the anal tube. Potential effects of alpine orogenesis, phenology and climatic oscillation on speciation of aquatic insects inhabiting high-altitude habitats are discussed. The description of C. lepontiorumsp. nov. accentuates the significance of the Western Alps as harbours of aquatic insect biodiversity, and demonstrates the necessity of faunal and taxonomic studies in Europe - a supposedly well-explored region.
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Affiliation(s)
- Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Applied Life Sciences, Max Emanuel-Strasse 17, A-1180 Vienna, Austria
| | - Simon Vitecek
- Department of Limnology & Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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17
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Tedder A, Carleial S, Gołębiewska M, Kappel C, Shimizu KK, Stift M. Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae). PLoS One 2015; 10:e0126618. [PMID: 26039362 PMCID: PMC4454584 DOI: 10.1371/journal.pone.0126618] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 04/04/2015] [Indexed: 12/03/2022] Open
Abstract
Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution.
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Affiliation(s)
- Andrew Tedder
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
| | - Samuel Carleial
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martyna Gołębiewska
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam-Golm, Germany
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
- * E-mail: (KKS); (MS)
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
- * E-mail: (KKS); (MS)
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18
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Toräng P, Wunder J, Obeso JR, Herzog M, Coupland G, Ågren J. Large-scale adaptive differentiation in the alpine perennial herb Arabis alpina. THE NEW PHYTOLOGIST 2015; 206:459-470. [PMID: 25422098 DOI: 10.1111/nph.13176] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Information about the incidence and magnitude of local adaptation can help to predict the response of natural populations to a changing environment, and should be of particular interest in arctic and alpine environments where the effects of climate change are expected to be severe. To quantify adaptive differentiation in the arctic-alpine perennial herb Arabis alpina, we conducted reciprocal transplant experiments for 3 yr between Spanish and Scandinavian populations. At the sites of one Spanish and one Scandinavian population, we planted seedlings representing two Spanish and four Scandinavian populations, and recorded survival, flowering propensity and fecundity. The experiment was replicated in two subsequent years. The results demonstrate strong adaptive differentiation between A. alpina populations from the two regions. At the field site in Spain, survival and fruit production of Spanish populations were higher than those of Scandinavian populations, while the opposite was true at the site in Scandinavia, and these differences were consistent across years. By comparison, fitness varied little among populations from the same region. The results suggest that the magnitude and geographical scale of local adaptation need to be considered in predictions of the effects of global change on the dynamics of arctic and alpine plant populations.
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Affiliation(s)
- Per Toräng
- Department of Plant Ecology and Evolution, EBC, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Jörg Wunder
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Cologne, Germany
| | - José Ramón Obeso
- Research Unit of Biodivesity (UO-CSIC-PA), Universidad de Oviedo, Campus de Mieres, 33600, Mieres, Spain
| | - Michel Herzog
- LECA, Université Grenoble Alpes, F-38000, Grenoble, France
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829, Cologne, Germany
| | - Jon Ågren
- Department of Plant Ecology and Evolution, EBC, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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Buehler D, Holderegger R, Brodbeck S, Schnyder E, Gugerli F. Validation of outlier loci through replication in independent data sets: a test on Arabis alpina. Ecol Evol 2014; 4:4296-306. [PMID: 25540691 PMCID: PMC4267868 DOI: 10.1002/ece3.1300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/11/2014] [Accepted: 10/01/2014] [Indexed: 12/25/2022] Open
Abstract
Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.
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Affiliation(s)
- Dominique Buehler
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Sabine Brodbeck
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Elvira Schnyder
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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20
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Kim DH, Sung S. Genetic and epigenetic mechanisms underlying vernalization. THE ARABIDOPSIS BOOK 2014; 12:e0171. [PMID: 24653667 PMCID: PMC3952384 DOI: 10.1199/tab.0171] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants have evolved a number of monitoring systems to sense their surroundings and to coordinate their growth and development accordingly. Vernalization is one example, in which flowering is promoted after plants have been exposed to a long-term cold temperature (i.e. winter). Vernalization results in the repression of floral repressor genes that inhibit the floral transition in many plant species. Here, we describe recent advances in our understanding of the vernalization-mediated promotion of flowering in Arabidopsis and other flowering plants. In Arabidopsis, the vernalization response includes the recruitment of chromatin-modifying complexes to floral repressors and thus results in the enrichment of repressive histone marks that ensure the stable repression of floral repressor genes. Changes in histone modifications at floral repressor loci are stably maintained after cold exposure, establishing the competence to flower the following spring. We also discuss similarities and differences in regulatory circuits in vernalization responses among Arabidopsis and other plants.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Sibum Sung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712
- Address correspondence to
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Lobréaux S, Manel S, Melodelima C. Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery. Mol Ecol Resour 2013; 14:411-8. [PMID: 24128264 DOI: 10.1111/1755-0998.12189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/28/2022]
Abstract
The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next-generation sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127,041 single-nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.
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Affiliation(s)
- Stéphane Lobréaux
- Laboratoire d'Ecologie Alpine, Université Joseph Fourier, UMR-CNRS 5553, BP53 38041, Grenoble, France
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22
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Melodelima C, Lobréaux S. Complete Arabis alpina chloroplast genome sequence and insight into its polymorphism. Meta Gene 2013; 1:65-75. [PMID: 25606376 PMCID: PMC4205033 DOI: 10.1016/j.mgene.2013.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 11/29/2022] Open
Abstract
The alpine plant Arabis alpina (alpine rock-cress) is a thoroughly studied species in the fields of perennial plant flowering regulation, phylogeography, and adaptation to harsh alpine climatic conditions. We report the complete A. alpina chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The A. alpina cp circular genome is 152,866 bp in length and built of two inverted repeats of 26,933 bp separated by unique regions: a large single copy of 82,338 bp and a small single copy of 17,938 bp. The genome contains 131 genes, some of them being duplicated in the inverted repeats. Seventy-nine unique protein-coding genes were annotated, together with 29 tRNA genes and 4 ribosomal RNA genes. Sequencing and mapping of 23 additional A. alpina DNA samples enabled to gain insight into the intraspecies polymorphism of the sequenced cp genome. Genetic variability among genomes was detected as 44 indels, most of them being located in noncoding regions, and 130 single-nucleotide polymorphisms, 37 of them corresponding to mutations in coding regions. A. alpina chloroplast genome sequence will be helpful in population studies or investigations of chloroplast functions of this alpine plant species. We report the complete A. alpina chloroplast genome sequence through de novo assembly. Arabis alpina plastome is 152,866 in length and harbors 131 genes. Intraspecies polymorphism analysis was investigated among 24 samples. We detected 44 indels and 130 single nucleotide polymorphisms.
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Affiliation(s)
- Christelle Melodelima
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, BP53, 38041 Grenoble, France
| | - Stéphane Lobréaux
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, BP53, 38041 Grenoble, France
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Karl R, Koch MA. A world-wide perspective on crucifer speciation and evolution: phylogenetics, biogeography and trait evolution in tribe Arabideae. ANNALS OF BOTANY 2013; 112:983-1001. [PMID: 23904444 PMCID: PMC3783230 DOI: 10.1093/aob/mct165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/29/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Tribe Arabideae are the most species-rich monophyletic lineage in Brassicaceae. More than 500 species are distributed in the majority of mountain and alpine regions worldwide. This study provides the first comprehensive phylogenetic analysis for the species assemblage and tests for association of trait and characters, providing the first explanations for the enormous species radiation since the mid Miocene. METHODS Phylogenetic analyses of DNA sequence variation of nuclear encoded loci and plastid DNA are used to unravel a reliable phylogenetic tree. Trait and ancestral area reconstructions were performed and lineage-specific diversification rates were calculated to explain various radiations in the last 15 Myr in space and time. KEY RESULTS A well-resolved phylogenetic tree demonstrates the paraphyly of the genus Arabis and a new systematic concept is established. Initially, multiple radiations involved a split between lowland annuals and mountain/alpine perennial sister species. Subsequently, increased speciation rates occur in the perennial lineages. The centre of origin of tribe Arabideae is most likely the Irano-Turanian region from which the various clades colonized the temperate mountain and alpine regions of the world. CONCLUSIONS Mid Miocene early diversification started with increased speciation rates due to the emergence of various annual lineages. Subsequent radiations were mostly driven by diversification within perennial species during the Pliocene, but increased speciation rates also occurred during that epoch. Taxonomic concepts in Arabis are still in need of a major taxonomic revision to define monophyletic groups.
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Affiliation(s)
| | - Marcus A. Koch
- Department of Plant Systematics and Biodiversity, Center for Organismal Studies (COS Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
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Moore AJ, Merges D, Kadereit JW. The origin of the serpentine endemicMinuartia laricifoliasubsp.ophioliticaby vicariance and competitive exclusion. Mol Ecol 2013; 22:2218-31. [DOI: 10.1111/mec.12266] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Abigail J. Moore
- Institut für Spezielle Botanik und Botanischer Garten; Johannes Gutenberg-Universität Mainz; Anselm-Franz-von-Bentzelweg 9a D-55099 Mainz Germany
| | - Dominik Merges
- Institut für Spezielle Botanik und Botanischer Garten; Johannes Gutenberg-Universität Mainz; Anselm-Franz-von-Bentzelweg 9a D-55099 Mainz Germany
| | - Joachim W. Kadereit
- Institut für Spezielle Botanik und Botanischer Garten; Johannes Gutenberg-Universität Mainz; Anselm-Franz-von-Bentzelweg 9a D-55099 Mainz Germany
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Zulliger D, Schnyder E, Gugerli F. Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species. Mol Ecol 2013; 22:1626-39. [PMID: 23398479 DOI: 10.1111/mec.12199] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 11/22/2012] [Accepted: 11/22/2012] [Indexed: 11/27/2022]
Abstract
Local adaptation is one possible response of organisms to survive in a changing environment. However, the genetic basis of adaptation is not well understood, especially in nonmodel species. To infer recurrent patterns of local adaptation, we investigated whether the same putative adaptive loci reoccur in related species. We performed genome scans using amplified fragment length polymorphism (AFLP) markers on populations of five Alpine Brassicaceae species sampled across a wide range of environmental conditions. To identify markers potentially under directional selection, we performed outlier and environmental association analyses using a set of topo-climatic variables available as GIS layers. Several AFLP loci showed signatures of adaptation, of which one, found in Cardamine resedifolia (Cre_P1_212.5), was associated with precipitation. We sequence-characterized this candidate locus and genotyped single nucleotide polymorphisms (SNPs) found within this locus for all species. Testing for environmental associations of SNPs revealed the same association of this locus in Arabis alpina but not in other study species. Cumulative statistical evidence indicates that locus Cre_P1_212.5 is environmentally relevant or is linked to a gene under selection in our study range. Furthermore, the locus shows an association to the same potentially selective factor in at least one other related species. These findings help to identify trends in plant adaptation in Alpine ecosystems in response to particular environmental parameters.
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Affiliation(s)
- Deborah Zulliger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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Schoebel CN, Brodbeck S, Buehler D, Cornejo C, Gajurel J, Hartikainen H, Keller D, Leys M, Ríčanová S, Segelbacher G, Werth S, Csencsics D. Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing. J Evol Biol 2013; 26:600-11. [PMID: 23331991 DOI: 10.1111/jeb.12077] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 11/19/2012] [Indexed: 11/28/2022]
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way of microsatellite development from 454 pyrosequencing data and analyse data sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a mammal) for microsatellite repeats and flanking regions suitable for primer development. We then compare the numbers of successfully lab-tested microsatellite markers for the various species and furthermore describe diverse challenges that might arise in different study species, for example, large genome size or nonpure extraction of genomic DNA. Successful primer identification was feasible for all species. We found that in species for which large repeat numbers are uncommon, such as fungi, polymorphic markers can nevertheless be developed from 454 pyrosequencing reads containing small repeat numbers (five to six repeats). Furthermore, the development of microsatellite markers for species with large genomes was also with Next Generation Sequencing techniques more cost and time-consuming than for species with smaller genomes. In this study, we showed that depending on the species, a different amount of 454 pyrosequencing data might be required for successful identification of a sufficient number of microsatellite markers for ecological genetic studies.
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Affiliation(s)
- C N Schoebel
- Biodiversity & Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland.
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An outlier locus relevant in habitat-mediated selection in an alpine plant across independent regional replicates. Evol Ecol 2012. [DOI: 10.1007/s10682-012-9597-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Buehler D, Graf R, Holderegger R, Gugerli F. Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape. ANNALS OF BOTANY 2012; 109:1359-67. [PMID: 22492332 PMCID: PMC3359921 DOI: 10.1093/aob/mcs066] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/20/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Gene flow is important in counteracting the divergence of populations but also in spreading genes among populations. However, contemporary gene flow is not well understood across alpine landscapes. The aim of this study was to estimate contemporary gene flow through pollen and to examine the realized mating system in the alpine perennial plant, Arabis alpina (Brassicaceae). METHODS An entire sub-alpine to alpine landscape of 2 km(2) was exhaustively sampled in the Swiss Alps. Eighteen nuclear microsatellite loci were used to genotype 595 individuals and 499 offspring from 49 maternal plants. Contemporary gene flow by pollen was estimated from paternity analysis, matching the genotypes of maternal plants and offspring to the pool of likely father plants. Realized mating patterns and genetic structure were also estimated. KEY RESULTS Paternity analysis revealed several long-distance gene flow events (≤1 km). However, most outcrossing pollen was dispersed close to the mother plants, and 84 % of all offspring were selfed. Individuals that were spatially close were more related than by chance and were also more likely to be connected by pollen dispersal. CONCLUSIONS In the alpine landscape studied, genetic structure occurred on small spatial scales as expected for alpine plants. However, gene flow also covered large distances. This makes it plausible for alpine plants to spread beneficial alleles at least via pollen across landscapes at a short time scale. Thus, gene flow potentially facilitates rapid adaptation in A. alpina likely to be required under ongoing climate change.
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Affiliation(s)
- D. Buehler
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
- ETH Zürich, Institute of Integrative Biology, Universitätsstrasse 16, CH-8092 Zürich, Switzerland
| | - R. Graf
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - R. Holderegger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
- ETH Zürich, Institute of Integrative Biology, Universitätsstrasse 16, CH-8092 Zürich, Switzerland
| | - F. Gugerli
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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Karl R, Kiefer C, Ansell SW, Koch MA. Systematics and evolution of Arctic-Alpine Arabis alpina (Brassicaceae) and its closest relatives in the eastern Mediterranean. AMERICAN JOURNAL OF BOTANY 2012; 99:778-794. [PMID: 22454383 DOI: 10.3732/ajb.1100447] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The high mountains in southern Anatolia and the eastern Mediterranean are assumed to play a major role as a primary center of genetic diversity and species richness in Eurasia. We tested this hypothesis by focusing on the widespread perennial arctic-alpine Arabis alpina and its sympatrically distributed closest relatives in the eastern Mediterranean. METHODS Plastid (trnL intron, trnL-F intergenic spacer) and nuclear (ITS) DNA sequence analysis was used for phylogenetic reconstruction. Broad-scale plastid haplotype analyses were conducted to infer ancestral biogeographic patterns. KEY RESULTS Five Arabis species, identified from the eastern Mediterranean (Turkey mainland and Cyprus), evolved directly and independently from A. alpina, leaving Arabis alpina as a paraphyletic taxon. These species are not affected by hybridization or introgression, and species divergence took place at the diploid level during the Pleistocene. CONCLUSIONS Pleistocene climate fluctuations produced local altitudinal range-shifts among mountain glacial survival areas, resulting not only in the accumulation of intraspecific genotype diversity but also in the formation of five local species. We also show that the closest sister group of Arabis alpina consists exclusively of annuals/winter annuals and diverged prior to Pleistocene climatic fluctuations during the colonization of the lowland Mediterranean landscape. These findings highlight that Anatolia is not only a center of species richness but also a center for life-history diversification.
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Affiliation(s)
- Robert Karl
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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Španiel S, Marhold K, Passalacqua NG, Zozomová-Lihová J. Intricate variation patterns in the diploid-polyploid complex of Alyssum montanum-A. repens (Brassicaceae) in the Apennine Peninsula: evidence for long-term persistence and diversification. AMERICAN JOURNAL OF BOTANY 2011; 98:1887-904. [PMID: 22052961 DOI: 10.3732/ajb.1100147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The Apennine Peninsula, one of the three peninsulas of the European Mediterranean, is an important hotspot of genetic and species diversity, but studies devoted to plant evolution are still very scarce in this region. We studied the diploid-polyploid complex of Alyssum montanum-A. repens, focusing on Apennine and adjacent southwestern Alpine populations from southeastern France, with the aim of examining their taxonomic position and evolutionary patterns. METHODS We employed AFLP markers and cpDNA sequences, along with cytotype determination using flow cytometry, and a multivariate morphometric approach. KEY RESULTS The Italian and French populations formed two well-delimited groupings within the studied complex that were, in contrast to previous taxonomic treatments, clearly distinct from A. montanum. Populations from southeastern France represent A. orophilum, a previously described but abandoned species. Those from central and southern Italy correspond to A. diffusum, exhibiting high, geographically structured variation (central Apennines, Gargano, and southern Apennines/Calabria). This pattern coincides with hotspot refugial regions, in congruence with the "refugia-within-refugia" hypothesis, and is reflected here in the recognition of three subspecies within A. diffusum. CONCLUSIONS We provide evidence for the presence of Mediterranean refugia for the studied Alyssum montanum-A. repens complex located in central and southern Italy, which, however, did not contribute to the postglacial colonization of Central Europe. Past extinctions, genetic bottlenecks, and recent expansion were inferred in Central Europe, while long-term accumulation of diversity as well as polyploidization occurred in the Apennines.
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Affiliation(s)
- Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic.
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31
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Zecca G, Casazza G, Minuto L, Labra M, Grassi F. Allopatric divergence and secondary contacts in Euphorbia spinosa L: Influence of climatic changes on the split of the species. ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0063-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tedder A, Ansell SW, Lao X, Vogel JC, Mable BK. Sporophytic self-incompatibility genes and mating system variation in Arabis alpina. ANNALS OF BOTANY 2011; 108:699-713. [PMID: 21821832 PMCID: PMC3170156 DOI: 10.1093/aob/mcr157] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Sporophytic self-incompatibility (SI) prevents inbreeding in many members of the Brassicaceae, and has been well documented in a variety of high-profile species. Arabis alpina is currently being developed as a model system for studying the ecological genetics of arctic-alpine environments, and is the focus of numerous studies on population structure and alpine phylogeography. Although it is highly inbreeding throughout most of its range, populations in central Italy have been identified that show inbreeding coefficients (F(IS)) more typical of self-incompatible relatives. The purpose of this study was to establish whether this variation is due to a functioning SI system. METHODS Outcrossing rate estimates were calculated based on 16 allozyme loci and self-compatibility assessed based on controlled pollinations for six Italian populations that have previously been shown to vary in F(IS) values. Putative SRK alleles (the gene controlling the female component of SI in other Brassicaceae) amplified from A. alpina were compared with those published for other species. Linkage of putative SRK alleles and SI phenotypes was assessed using a diallel cross. KEY RESULTS Functional avoidance of inbreeding is demonstrated in three populations of A. alpina, corresponding with previous F(IS) values. The presence is described of 15 putative SRK-like alleles, which show high sequence identity to known alleles from Brassica and Arabidopsis and the high levels of synonymous and nonsynonymous variation typical of genes under balancing selection. Also, orthologues of two other members of the S-receptor kinase gene family, Aly8 (ARK3) and Aly9 (AtS1) are identified. Further to this, co-segregation between some of the putative S-alleles and compatibility phenotypes was demonstrated using a full-sibling cross design. CONCLUSIONS The results strongly suggest that, as with other species in the Brassicaceae, A. alpina has a sporophytic SI system but shows variation in the strength of SI within and between populations.
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Affiliation(s)
- A. Tedder
- Division of Ecology and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - S. W. Ansell
- Department of Botany, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - X. Lao
- Nara Institute of Science and Technology, Nara 630-0101, Japan
| | - J. C. Vogel
- Department of Botany, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - B. K. Mable
- Division of Ecology and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK
- For correspondence. E-mail
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Ansell SW, Stenøien HK, Grundmann M, Russell SJ, Koch MA, Schneider H, Vogel JC. The importance of Anatolian mountains as the cradle of global diversity in Arabis alpina, a key arctic-alpine species. ANNALS OF BOTANY 2011; 108:241-52. [PMID: 21712298 PMCID: PMC3143044 DOI: 10.1093/aob/mcr134] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Anatolia is a biologically diverse, but phylogeographically under-explored region. It is described as either a centre of origin and long-term Pleistocene refugium, or as a centre for genetic amalgamation, fed from distinct neighbouring refugia. These contrasting hypotheses are tested through a global phylogeographic analysis of the arctic-alpine herb, Arabis alpina. METHODS Herbarium and field collections were used to sample comprehensively the entire global range, with special focus on Anatolia and Levant. Sequence variation in the chloroplast DNA trnL-trnF region was examined in 483 accessions. A haplotype genealogy was constructed and phylogeographic methods, demographic analysis and divergence time estimations were used to identify the centres of diversity and to infer colonization history. KEY RESULTS Fifty-seven haplotypes were recovered, belonging to three haplogroups with non-overlapping distributions in (1) North America/Europe/northern Africa, (2) the Caucuses/Iranian Plateau/Arabian Peninsula and (3) Ethiopia-eastern Africa. All haplogroups occur within Anatolia, and all intermediate haplotypes linking the three haplogroups are endemic to central Anatolia and Levant, where haplotypic and nucleotide diversities exceeded all other regions. The local pattern of haplotype distribution strongly resembles the global pattern, and the haplotypes began to diverge approx. 2·7 Mya, coinciding with the climate cooling of the early Middle Pleistocene. CONCLUSIONS The phylogeographic structure of Arabis alpina is consistent with Anatolia being the cradle of origin for global genetic diversification. The highly structured landscape in combination with the Pleistocene climate fluctuations has created a network of mountain refugia and the accumulation of spatially arranged genotypes. This local Pleistocene population history has subsequently left a genetic imprint at the global scale, through four range expansions from the Anatolian diversity centre into Europe, the Near East, Arabia and Africa. Hence this study also illustrates the importance of sampling and scaling effects when translating global from local diversity patterns during phylogeographic analyses.
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Affiliation(s)
- Stephen W Ansell
- Department of Botany, The Natural History Museum, London SW7 5BD, UK.
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Evans MEK, Hearn DJ, Theiss KE, Cranston K, Holsinger KE, Donoghue MJ. Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera). THE NEW PHYTOLOGIST 2011; 191:555-563. [PMID: 21449951 DOI: 10.1111/j.1469-8137.2011.03697.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, ecological conditions, and geographical context. Here, we examined two such predictions: that self-compatibility should be associated with the annual life history or extreme climatic conditions. We analyzed data from a clade of plants remarkable for variation in breeding system, life history and climatic conditions (Oenothera, sections Anogra and Kleinia, Onagraceae). We used a phylogenetic comparative approach and Bayesian or hybrid Bayesian tests to account for phylogenetic uncertainty. Geographic information system (GIS)-based climate data and ecological niche modeling allowed us to quantify climatic conditions. Breeding system and reproductive life span are not correlated in Anogra and Kleinia. Instead, self-compatibility is associated with the extremes of temperature in the coldest part of the year and precipitation in the driest part of the year. In the 60 yr since this pattern was anticipated, this is the first demonstration of a relationship between the evolution of self-compatibility and climatic extremes. We discuss possible explanations for this pattern and possible implications with respect to anthropogenic climate change.
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Affiliation(s)
- Margaret E K Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Present address: Origin, Structure, and Evolution of Biodiversity, UMR 7205, Museum National d'Histoire Naturelle, 16 rue Buffon, 75231 Paris, Cedex 05, France
| | - David J Hearn
- Department of Biological Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
| | - Kathryn E Theiss
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269, USA
| | - Karen Cranston
- National Evolutionary Synthesis Center, 2024 W. Main Street, A200, Durham, NC 27705, USA
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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Meirmans PG, Goudet J, Gaggiotti OE. Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Mol Ecol 2011; 20:3144-55. [PMID: 21689194 DOI: 10.1111/j.1365-294x.2011.05164.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.
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Affiliation(s)
- Patrick G Meirmans
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble, France.
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Franzke A, Lysak MA, Al-Shehbaz IA, Koch MA, Mummenhoff K. Cabbage family affairs: the evolutionary history of Brassicaceae. TRENDS IN PLANT SCIENCE 2011; 16:108-16. [PMID: 21177137 DOI: 10.1016/j.tplants.2010.11.005] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 11/12/2010] [Accepted: 11/17/2010] [Indexed: 05/03/2023]
Abstract
Life without the mustard family (Brassicaceae) would be a world without many crop species and the model organism Arabidopsis (Arabidopsis thaliana) that has revolutionized our knowledge in almost every field of modern plant biology. Despite this importance, research breakthroughs in understanding family-wide evolutionary patterns and processes within this flowering plant family were not achieved until the past few years. In this review, we examine recent outcomes from diverse botanical disciplines (taxonomy, systematics, genomics, paleobotany and other fields) to synthesize for the first time a holistic view on the evolutionary history of the mustard family.
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Affiliation(s)
- Andreas Franzke
- Heidelberg Botanic Garden, Centre for Organismal Studies Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
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Vila M, Marí-Mena N, Guerrero A, Schmitt T. Some butterflies do not care much about topography: a single genetic lineage of Erebia euryale (Nymphalidae) along the northern Iberian mountains. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00587.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Agnarsson I, Maddison WP, Avilés L. Complete separation along matrilines in a social spider metapopulation inferred from hypervariable mitochondrial DNA region. Mol Ecol 2010; 19:3052-63. [PMID: 20598078 DOI: 10.1111/j.1365-294x.2010.04681.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distribution and quantity of genetic diversity may be profoundly influenced by the emergence and dynamics of social groups. Permanent social living in spiders has resulted in the subdivision of their populations in more or less isolated colony lineages that grow, proliferate and become extinct without mixing with one another. A newly discovered hypervariable mitochondrial DNA region allowed us to examine the fine scale metapopulation structure in the social Anelosimus eximius. We sampled 39 colonies in Ecuador and French Guiana and identified 25 haplotypes. The majority of colonies contained one haplotype. Additional haplotypes occurred in approximately 15% of the colonies, and were always closely related to the common colony haplotype. Our findings confirm that colonies consist of single matrilines, with within-colony variation explained by mutations within the matriline. We thus found no evidence of mixing of matrilines. Likewise, colonies in a cluster often shared a haplotype, implying common colony ancestry. In few cases, however, haplotypes were shared between more distant colonies, providing evidence for occasional longer distance dispersal and/or widespread colony lineages. The geographical localities of colonies were incongruent with phylogenetic trees and haplotype networks, showing that some areas contained two or more matrilines. Hence, females do not migrate into foreign colonies, but faithfully remain within their own colony lineage, even when they disperse into new areas. These results indicate that the fine scale metapopulation structure of pure matrilines is maintained over the long term and that colony turnover is not extensive or radical enough to homogenize entire geographical areas. Genetic diversity is thus preserved to some extent at the metapopulation level.
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Affiliation(s)
- I Agnarsson
- Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, PO Box 306, SI-1001 Ljubljana, Slovenia.
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Wubs ERJ, de Groot GA, During HJ, Vogel JC, Grundmann M, Bremer P, Schneider H. Mixed mating system in the fern Asplenium scolopendrium: implications for colonization potential. ANNALS OF BOTANY 2010; 106:583-90. [PMID: 20682575 PMCID: PMC2944980 DOI: 10.1093/aob/mcq157] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Human-mediated environmental change is increasing selection pressure for the capacity in plants to colonize new areas. Habitat fragmentation combined with climate change, in general, forces species to colonize areas over longer distances. Mating systems and genetic load are important determinants of the establishment and long-term survival of new populations. Here, the mating system of Asplenium scolopendrium, a diploid homosporous fern species, is examined in relation to colonization processes. METHODS A common environment experiment was conducted with 13 pairs of sporophytes, each from a different site. Together they constitute at least nine distinct genotypes, representing an estimated approx. 95 % of the non-private intraspecific genetic variation in Europe. Sporophyte production was recorded for gametophytes derived from each parent sporophyte. Gametophytes were grown in vitro in three different ways: (I) in isolation, (II) with a gametophyte from a different sporophyte within the same site or (III) with a partner from a different site. KEY RESULTS Sporophyte production was highest in among-site crosses (III), intermediate in within-site crosses (II) and was lowest in isolated gametophytes (I), strongly indicating inbreeding depression. However, intragametophytic selfing was observed in most of the genotypes tested (eight out of nine). CONCLUSIONS The results imply a mixed mating system in A. scolopendrium, with outcrossing when possible and occasional selfing when needed. Occasional intragametophytic selfing facilitates the successful colonization of new sites from a single spore. The resulting sporophyte, which will be completely homozygous, will shed large amounts of spores over time. Each year this creates a bed of gametophytes in the vicinity of the parent. Any unrelated spore which arrives is then selectively favoured to reproduce and contribute its genes to the new population. Thus, while selfing facilitates initial colonization success, inbreeding depression promotes genetically diverse populations through outcrossing. The results provide further evidence against the overly simple dichotomous distinction of fern species as either selfing or outcrossing.
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Affiliation(s)
- E. R. Jasper Wubs
- Ecology and Biodiversity group, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - G. Arjen de Groot
- Ecology and Biodiversity group, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- For correspondence. E-mail
| | - Heinjo J. During
- Ecology and Biodiversity group, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Johannes C. Vogel
- Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Michael Grundmann
- Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Piet Bremer
- Nature Conservation and Plant Ecology group, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
| | - Harald Schneider
- Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Manel S, Poncet BN, Legendre P, Gugerli F, Holderegger R. Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina. Mol Ecol 2010; 19:3824-35. [PMID: 20723057 DOI: 10.1111/j.1365-294x.2010.04716.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A major challenges facing landscape geneticists studying adaptive variation is to include all the environmental variables that might be correlated with allele frequencies across the genome. One way of identifying loci that are possibly under selection is to see which ones are associated with environmental gradient or heterogeneity. Since it is difficult to measure all environmental variables, one may take advantage of the spatial nature of environmental filters to incorporate the effect of unaccounted environmental variables in the analysis. Assuming that the spatial signature of these variables is broad-scaled, broad-scale Moran's eigenvector maps (MEM) can be included as explanatory variables in the analysis as proxies for unmeasured environmental variables. We applied this approach to two data sets of the alpine plant Arabis alpina. The first consisted of 140 AFLP loci sampled at 130 sites across the European Alps (large scale). The second one consisted of 712 AFLP loci sampled at 93 sites (regional scale) in three mountain massifs (local scale) of the French Alps. For each scale, we regressed the frequencies of each AFLP allele on a set of eco-climatic and MEM variables as predictors. Twelve (large scale) and 11% (regional scale) of all loci were detected as significantly correlated to at least one of the predictors ( > 0.5), and, except for one massif, 17% at the local scale. After accounting for spatial effects, temperature and precipitation were the two major determinants of allele distributions. Our study shows how MEM models can account for unmeasured environmental variation in landscape genetics models.
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Affiliation(s)
- Stéphanie Manel
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, 38041 Grenoble Cedex 09, France.
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Poncet BN, Herrmann D, Gugerli F, Taberlet P, Holderegger R, Gielly L, Rioux D, Thuiller W, Aubert S, Manel S. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 2010; 19:2896-907. [PMID: 20609082 DOI: 10.1111/j.1365-294x.2010.04696.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.
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Affiliation(s)
- Bénédicte N Poncet
- Laboratoire d'Ecologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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Pedall I, Fritz U, Stuckas H, Valdeón A, Wink M. Gene flow across secondary contact zones of the Emys orbicularis complex in the Western Mediterranean and evidence for extinction and re-introduction of pond turtles on Corsica and Sardinia (Testudines: Emydidae). J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00572.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Herrmann D, Poncet BN, Manel S, Rioux D, Gielly L, Taberlet P, Gugerli F. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome 2010; 53:302-10. [DOI: 10.1139/g10-006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.
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Affiliation(s)
- Doris Herrmann
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Bénédicte N. Poncet
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Stéphanie Manel
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Delphine Rioux
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Ludovic Gielly
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Pierre Taberlet
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
| | - Felix Gugerli
- Ecological Genetics and Evolution, WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Laboratoire d’Ecologie Alpine (LECA), CNRS UMR 5553, Université Joseph Fourier, BP 53, 2233 rue de la Piscine, 38041 Grenoble CEDEX 9, France
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Ansell SW, Stenøien HK, Grundmann M, Schneider H, Hemp A, Bauer N, Russell SJ, Vogel JC. Population structure and historical biogeography of European Arabidopsis lyrata. Heredity (Edinb) 2010; 105:543-53. [PMID: 20160758 DOI: 10.1038/hdy.2010.10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Understanding the natural history of model organisms is important for the effective use of their genomic resources. Arabidopsis lyrata has emerged as a useful plant for studying ecological and evolutionary genetics, based on its extensive natural variation, sequenced genome and close relationship to A. thaliana. We studied genetic diversity across the entire range of European Arabidopsis lyrata ssp. petraea, in order to explore how population history has influenced population structure. We sampled multiple populations from each region, using nuclear and chloroplast genome markers, and combined population genetic and phylogeographic approaches. Within-population diversity is substantial for nuclear allozyme markers (mean P=0.610, A(e)=1.580, H(e)=0.277) and significantly partitioned among populations (F(ST)=0.271). The Northern populations have modestly increased inbreeding (F(IS)=0.163 verses F(IS)=0.093), but retain comparable diversity to central European populations. Bottlenecks are common among central and northern Europe populations, indicating recent demographic history as a dominant factor in structuring the European diversity. Although the genetic structure was detected at all geographic scales, two clear differentiated units covering northern and central European areas (F(CT) =0.155) were identified by Bayesian analysis and supported by regional pairwise F(CT) calculations. A highly similar geographic pattern was observed from the distribution of chloroplast haplotypes, with the dominant northern haplotypes absent from central Europe. We conclude A. l. petraea's cold-tolerance and preference for disturbed habitats enabled glacial survival between the alpine and Nordic glaciers in central Europe and an additional cryptic refugium. While German populations are probable peri-glacial leftovers, Eastern Austrian populations have diversity patterns possibly compatible with longer-term survival.
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Affiliation(s)
- S W Ansell
- Department of Botany, Natural History Museum, Cromwell Road, London, UK.
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Grassi F, Minuto L, Casazza G, Labra M, Sala F. Haplotype richness in refugial areas: phylogeographical structure of Saxifraga callosa. JOURNAL OF PLANT RESEARCH 2009; 122:377-387. [PMID: 19363647 DOI: 10.1007/s10265-009-0230-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 03/01/2009] [Indexed: 05/27/2023]
Abstract
This paper illustrates the phylogeographical structure of Saxifraga callosa in order to describe its genetic richness in refugial areas and to reconstruct its glacial history. S. callosa is a species spread throughout south-east France and Italy with a high distribution in the Maritime Alps. Four chloroplast microsatellite and AFLP markers were analyzed in populations of S. callosa. The size variants of all tested loci amount to 11 different haplotypes. Intrapopulational haplotype variation was found in two of the populations analyzed: on the Mt. Toraggio in the Maritime Alps, and in the Apuan Alps. On the other hand, no intrapopulational variation was found in 25 populations, most of which were sampled from isolated areas. Analysis of the haplotype distribution showed that population subdivision across all populations was high (G (ST) = 0.899). Moreover, its genetic structure was studied using AMOVA and STRUCTURE analysis. The study legitimated inferred conclusions about the phylogeographical structure of the species and identified centers of diversity. Considerations concerning genetic structure and divergence among three major clades (Maritime Alps, Apuan Alps and Apennines), the patchy distribution of haplotypes, and the high number of private haplotypes support the proposal that S. callosa survived in some refugia within the Italian Peninsula refugium, and that mainly northern populations of refugia were involved in postglacial recolonization.
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Affiliation(s)
- F Grassi
- Botanical Garden, Department of Biology, University of Milan, 20133 Milan, Italy.
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PEP1 regulates perennial flowering in Arabis alpina. Nature 2009; 459:423-7. [PMID: 19369938 DOI: 10.1038/nature07988] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 03/12/2009] [Indexed: 12/21/2022]
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