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Grasso G, Rotunno S, Debruyne R, Bittner L, Miozzi L, Marmeisse R, Bianciotto V. Identification of DNA Viruses in Ancient DNA from Herbarium Samples. Methods Mol Biol 2024; 2732:221-234. [PMID: 38060128 DOI: 10.1007/978-1-0716-3515-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Herbaria encompass millions of plant specimens, mostly collected in the nineteenth and twentieth centuries that can represent a key resource for investigating the history and evolution of phytopathogens. In the last years, the application of high-throughput sequencing technologies for the analysis of ancient nucleic acids has revolutionized the study of ancient pathogens including viruses, allowing the reconstruction of historical genomic viral sequences, improving phylogenetic based molecular dating, and providing essential insight into plant virus ecology. In this chapter, we describe a protocol to reconstruct ancient plant and soil viral sequences starting from highly fragmented ancient DNA extracted from herbarium plants and their associated rhizospheric soil. Following Illumina high-throughput sequencing, sequence data are de novo assembled, and DNA viral sequences are selected, according to their similarity with known viruses.
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Affiliation(s)
- Gianluca Grasso
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi of Turin, Turin, Italy
- Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy
| | - Silvia Rotunno
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy
| | - Régis Debruyne
- Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE: UMR 7209 CNRS-MNHN), Paris, France
| | - Lucie Bittner
- Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France
- Institut Universitaire de France, Paris, France
| | - Laura Miozzi
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy
| | - Roland Marmeisse
- Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France.
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy.
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy.
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2
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Bradshaw MJ, Carey J, Liu M, Bartholomew HP, Jurick WM, Hambleton S, Hendricks D, Schnittler M, Scholler M. Genetic time traveling: sequencing old herbarium specimens, including the oldest herbarium specimen sequenced from kingdom Fungi, reveals the population structure of an agriculturally significant rust. THE NEW PHYTOLOGIST 2023; 237:1463-1473. [PMID: 36385249 DOI: 10.1111/nph.18622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera. We then obtained sequences from an economically important biological control agent, Puccinia suaveolens, to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range. Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial-temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi. In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant-microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.
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Affiliation(s)
- Michael J Bradshaw
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Julie Carey
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Miao Liu
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Holly P Bartholomew
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Wayne M Jurick
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sarah Hambleton
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Dylan Hendricks
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, 17487, Greifswald, Germany
| | - Markus Scholler
- Staatliches Museum für Naturkunde, Abteilung Biowissenschaften, D-76133, Karlsruhe, Germany
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3
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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4
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Campos PE, Groot Crego C, Boyer K, Gaudeul M, Baider C, Richard D, Pruvost O, Roumagnac P, Szurek B, Becker N, Gagnevin L, Rieux A. First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence. PLoS Pathog 2021; 17:e1009714. [PMID: 34324594 PMCID: PMC8320980 DOI: 10.1371/journal.ppat.1009714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.
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Affiliation(s)
- Paola E. Campos
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
- Herbier national (P), Muséum national d’Histoire naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound), Agricultural Services, Réduit, Mauritius
| | | | | | - Philippe Roumagnac
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
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5
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. THE NEW PHYTOLOGIST 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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6
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Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Ma WJ, Hood ME, Giraud T. Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence. Mol Biol Evol 2020; 37:668-682. [PMID: 31651949 PMCID: PMC7038665 DOI: 10.1093/molbev/msz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Wen-Juan Ma
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Michael E Hood
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
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7
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Ristaino JB. The Importance of Mycological and Plant Herbaria in Tracking Plant Killers. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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8
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Yost JM, Pearson KD, Alexander J, Gilbert E, Hains LA, Barry T, Bencie R, Bowler P, Carter B, Crowe RE, Dean E, Der J, Fisher A, Fisher K, Flores-Renteria L, Guilliams CM, Hatfield C, Hendrickson L, Huggins T, Janeway L, Lay C, Litt A, Markos S, Mazer SJ, McCamish D, McDade L, Mesler M, Mishler B, Nazaire M, Rebman J, Rosengreen L, Rundel PW, Potter D, Sanders A, Seltmann KC, Simpson MG, Wahlert GA, Waselkov K, Williams K, Wilson PS. THE CALIFORNIA PHENOLOGY COLLECTIONS NETWORK: USING DIGITAL IMAGES TO INVESTIGATE PHENOLOGICAL CHANGE IN A BIODIVERSITY HOTSPOT. ACTA ACUST UNITED AC 2020. [DOI: 10.3120/0024-9637-66.4.130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jenn M. Yost
- Robert F. Hoover Herbarium, Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407-0401
| | - Katelin D. Pearson
- Robert F. Hoover Herbarium, Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407-0401
| | - Jason Alexander
- University and Jepson Herbaria, University of California, Berkeley, CA 94720
| | - Edward Gilbert
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | | | - Teri Barry
- UC Davis Center for Plant Diversity, Plant Sciences M.S. 7, One Shields Ave., Davis, CA 95616
| | - Robin Bencie
- Vascular Plant Herbarium, Humboldt State University, Arcata, CA 95521
| | - Peter Bowler
- UCI Arboretum and Herbarium, University of California, Irvine, CA 92697
| | - Benjamin Carter
- Carl W. Sharsmith Herbarium and Department of Biological Sciences, San Jose State University, San Jose, CA 95192
| | - Rebecca E. Crowe
- UCI Arboretum and Herbarium, University of California, Irvine, CA 92697
| | - Ellen Dean
- UC Davis Center for Plant Diversity, Plant Sciences M.S. 7, One Shields Ave., Davis, CA 95616
| | - Joshua Der
- Department of Biological Science, California State University, Fullerton, CA 92834
| | - Amanda Fisher
- Department of Biological Sciences, Long Beach State University, Long Beach, CA 90840
| | - Kirsten Fisher
- CSLA Herbarium, California State University, Los Angeles, Los Angeles, CA 90032
| | | | - C. Matt Guilliams
- Clifton Smith Herbarium, Santa Barbara Botanic Garden, Santa Barbara, CA 93105
| | - Colleen Hatfield
- Chico State Herbarium, Department of Biological Sciences, California State University, Chico, CA 95929
| | - Larry Hendrickson
- Colorado Desert District, California Department of Parks and Recreation, Borrego Springs, CA 92004
| | - Tom Huggins
- UCLA Herbarium, University of California, Los Angeles, CA 90095
| | - Lawrence Janeway
- Chico State Herbarium, Department of Biological Sciences, California State University, Chico, CA 95929
| | - Christopher Lay
- Norris Center for Natural History, University of California, Santa Cruz, CA 95064
| | - Amy Litt
- Department of Botany & Plant Sciences, University of California, Riverside, CA 92521
| | - Staci Markos
- University and Jepson Herbaria, University of California, Berkeley, CA 94720
| | - Susan J. Mazer
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106
| | - Danny McCamish
- Colorado Desert District, California Department of Parks and Recreation, Borrego Springs, CA 92004
| | | | - Michael Mesler
- Vascular Plant Herbarium, Humboldt State University, Arcata, CA 95521
| | - Brent Mishler
- University and Jepson Herbaria, University of California, Berkeley, CA 94720
| | - Mare Nazaire
- Rancho Santa Ana Botanic Garden, Claremont, CA 91711
| | - Jon Rebman
- SD Herbarium, San Diego Natural History Museum, San Diego, CA 92101
| | - Lars Rosengreen
- Carl W. Sharsmith Herbarium and Department of Biological Sciences, San Jose State University, San Jose, CA 95192
| | - Philip W. Rundel
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Dan Potter
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Andrew Sanders
- Herbarium, Department of Botany & Plant Sciences, University of California Riverside, CA 92521
| | - Katja C. Seltmann
- Cheadle Center for Biodiversity and Ecological Restoration, University of California, Santa Barbara, CA 93106
| | | | - Gregory A. Wahlert
- Cheadle Center for Biodiversity and Ecological Restoration, University of California, Santa Barbara, CA 93106
| | | | - Kimberlyn Williams
- Biology Department, California State University San Bernardino, San Bernardino, CA 92407
| | - Paul S. Wilson
- Department of Biology, California State University, Northridge, CA 91330
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9
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Kido A, Hood ME. Mining new sources of natural history observations for disease interactions. AMERICAN JOURNAL OF BOTANY 2020; 107:3-11. [PMID: 31885083 PMCID: PMC6980919 DOI: 10.1002/ajb2.1409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Allyson Kido
- Department of BiologyAmherst CollegeAmherstMassachusettsUSA
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10
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Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T. Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:431-457. [PMID: 31337277 DOI: 10.1146/annurev-phyto-082718-095947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anther-smut fungi provide a powerful system to study host-pathogen specialization and coevolution, with hundreds of Microbotryum species specialized on diverse Caryophyllaceae plants, castrating their hosts through manipulation of the hosts' reproductive organs to facilitate disease transmission. Microbotryum fungi have exceptional genomic characteristics, including dimorphic mating-type chromosomes, that make this genus anexcellent model for studying the evolution of mating systems and their influence on population genetics structure and adaptive potential. Important insights into adaptation, coevolution, host specialization, and mating system evolution have been gained using anther-smut fungi, with new insights made possible by the recent advent of genomic approaches. We illustrate with Microbotryum case studies how using a combination of comparative genomics, population genomics, and transcriptomics approaches enables the integration of different evolutionary perspectives across different timescales. We also highlight current challenges and suggest future studies that will contribute to advancing our understanding of the mechanisms underlying adaptive processes in populations of fungal pathogens.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | | | - Fantin Carpentier
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | - Pierre Gladieux
- UMR BGPI, Univ. Montpellier, INRA, CIRAD, Montpellier SupAgro, 34398 Montpellier, France
| | - Amandine Cornille
- Génétique Quantitative et Evolution-Le Moulon, INRA; Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, Massachusetts 01002-5000, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
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11
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Burdon JJ. Lessons from a Life in Time and Space. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:1-13. [PMID: 31082308 DOI: 10.1146/annurev-phyto-082718-095938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A research career investigating epidemiological and evolutionary patterns in both natural and crop host-pathogen systems emphasizes the need for flexibility in thinking and a willingness to adopt ideas from a wide diversity of subdisciplines. Here, I reflect on the pivotal issues, research areas, and interactions, including the role of science management, that shaped my career in the hope of demonstrating that career paths and collaborations in science can be as diverse and unpredictable as the natural world in which we study our organisms of choice.
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12
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Schrieber K, Wolf S, Wypior C, Höhlig D, Keller SR, Hensen I, Lachmuth S. Release from natural enemies mitigates inbreeding depression in native and invasive Silene latifolia populations. Ecol Evol 2019; 9:3564-3576. [PMID: 30962911 PMCID: PMC6434559 DOI: 10.1002/ece3.4990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/12/2019] [Accepted: 01/26/2019] [Indexed: 01/01/2023] Open
Abstract
Inbreeding and enemy infestation are common in plants and can synergistically reduce their performance. This inbreeding ×environment (I × E) interaction may be of particular importance for the success of plant invasions if introduced populations experience a release from attack by natural enemies relative to their native conspecifics. Here, we investigate whether inbreeding affects plant infestation damage, whether inbreeding depression in growth and reproduction is mitigated by enemy release, and whether this effect is more pronounced in invasive than native plant populations. We used the invader Silene latifolia and its natural enemies as a study system. We performed two generations of experimental out- and inbreeding within eight native (European) and eight invasive (North American) populations under controlled conditions using field-collected seeds. Subsequently, we exposed the offspring to an enemy exclusion and inclusion treatment in a common garden in the species' native range to assess the interactive effects of population origin (range), breeding treatment, and enemy treatment on infestation damage, growth, and reproduction. Inbreeding increased flower and leaf infestation damage in plants from both ranges, but had opposing effects on fruit damage in native versus invasive plants. Inbreeding significantly reduced plant fitness; whereby, inbreeding depression in fruit number was higher in enemy inclusions than exclusions. This effect was equally pronounced in populations from both distribution ranges. Moreover, the magnitude of inbreeding depression in fruit number was lower in invasive than native populations. These results support that inbreeding has the potential to reduce plant defenses in S. latifolia, which magnifies inbreeding depression in the presence of enemies. However, future studies are necessary to further explore whether enemy release in the invaded habitat has actually decreased inbreeding depression and thus facilitated the persistence of inbred founder populations and invasion success.
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Affiliation(s)
- Karin Schrieber
- Department of Chemical Ecology, Faculty of BiologyBielefeld UniversityBielefeldGermany
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Sabrina Wolf
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Catherina Wypior
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Diana Höhlig
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | | | - Isabell Hensen
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Susanne Lachmuth
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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Meineke EK, Davies TJ. Museum specimens provide novel insights into changing plant-herbivore interactions. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170393. [PMID: 30455211 PMCID: PMC6282078 DOI: 10.1098/rstb.2017.0393] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/16/2022] Open
Abstract
Mounting evidence shows that species interactions may mediate how individual species respond to climate change. However, long-term anthropogenic effects on species interactions are poorly characterized owing to a lack of data. Insect herbivory is a major ecological process that represents the interaction between insect herbivores and their host plants, but historical data on insect damage to plants is particularly sparse. Here, we suggest that museum collections of insects and plants can fill key gaps in our knowledge on changing trophic interactions, including proximate mechanisms and the net outcomes of multiple global change drivers across diverse insect herbivore-plant associations. We outline theory on how global change may affect herbivores and their host plants and highlight the unique data that could be extracted from museum specimens to explore their shifting interactions. We aim to provide a framework for using museum specimens to explore how some of the most diverse co-evolved relationships are responding to climate and land use change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - T Jonathan Davies
- Departments of Botany, Forest, and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2006, South Africa
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Meineke EK, Davies TJ, Daru BH, Davis CC. Biological collections for understanding biodiversity in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0386. [PMID: 30455204 DOI: 10.1098/rstb.2017.0386] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as discussed in the accompanying collection of papers within this theme issue. As these unparalleled resources are under threat owing to budget cuts and other institutional pressures, we aim to shed light on the unique discoveries that are possible in museums and, thus, the singular value of natural history collections in a period of rapid change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - T Jonathan Davies
- Department of Ecology and Evolutionary Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4.,African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2006, South Africa
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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15
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Andrew C, Diez J, James TY, Kauserud H. Fungarium specimens: a largely untapped source in global change biology and beyond. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170392. [PMID: 30455210 PMCID: PMC6282084 DOI: 10.1098/rstb.2017.0392] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 11/12/2022] Open
Abstract
For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Carrie Andrew
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Jeffrey Diez
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
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16
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Meineke EK, Davis CC, Davies TJ. The unrealized potential of herbaria for global change biology. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1307] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Emily K. Meineke
- Department of Organismic and Evolutionary Biology; Harvard University Herbaria; 22 Divinity Avenue Cambridge Massachusetts 02138 USA
- Department of Biology; McGill University; 1205 Dr. Penfield Avenue Montreal Quebec H3A 1B1 Canada
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology; Harvard University Herbaria; 22 Divinity Avenue Cambridge Massachusetts 02138 USA
| | - T. Jonathan Davies
- Department of Biology; McGill University; 1205 Dr. Penfield Avenue Montreal Quebec H3A 1B1 Canada
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17
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18
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Schrieber K, Wolf S, Wypior C, Höhlig D, Hensen I, Lachmuth S. Adaptive and non-adaptive evolution of trait means and genetic trait correlations for herbivory resistance and performance in an invasive plant. OIKOS 2016. [DOI: 10.1111/oik.03781] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Karin Schrieber
- Inst. of Biology; Geobotany and Botanical Garden, Martin Luther Univ. Halle-Wittenberg; Halle (Saale) Germany
- Faculty of Biology, Dept. of Chemical Ecology; Univ. Bielefeld; Bielefeld Germany
| | - Sabrina Wolf
- Inst. of Biology; Geobotany and Botanical Garden, Martin Luther Univ. Halle-Wittenberg; Halle (Saale) Germany
| | - Catherina Wypior
- Inst. of Biology; Geobotany and Botanical Garden, Martin Luther Univ. Halle-Wittenberg; Halle (Saale) Germany
| | - Diana Höhlig
- Inst. of Biology; Geobotany and Botanical Garden, Martin Luther Univ. Halle-Wittenberg; Halle (Saale) Germany
| | - Isabell Hensen
- Inst. of Biology; Geobotany and Botanical Garden, Martin Luther Univ. Halle-Wittenberg; Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Susanne Lachmuth
- Inst. of Biology; Geobotany and Botanical Garden, Martin Luther Univ. Halle-Wittenberg; Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
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Bueker B, Eberlein C, Gladieux P, Schaefer A, Snirc A, Bennett DJ, Begerow D, Hood ME, Giraud T. Distribution and population structure of the anther smut Microbotryum silenes-acaulis parasitizing an arctic-alpine plant. Mol Ecol 2016; 25:811-24. [PMID: 26671732 DOI: 10.1111/mec.13512] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/02/2015] [Accepted: 11/26/2015] [Indexed: 12/18/2022]
Abstract
Cold-adapted organisms with current arctic-alpine distributions have persisted during the last glaciation in multiple ice-free refugia, leaving footprints in their population structure that contrast with temperate plants and animals. However, pathogens that live within hosts having arctic-alpine distributions have been little studied. Here, we therefore investigated the geographical range and population structure of a fungus parasitizing an arctic-alpine plant. A total of 1437 herbarium specimens of the plant Silene acaulis were examined, and the anther smut pathogen Microbotryum silenes-acaulis was present throughout the host's geographical range. There was significantly greater incidence of anther smut disease in more northern latitudes and where the host locations were less dense, indicating a major influence of environmental factors and/or host demographic structure on the pathogen distribution. Genetic analyses with seven microsatellite markers on recent collections of 195 M. silenes-acaulis individuals revealed three main genetic clusters, in North America, northern Europe and southern Europe, likely corresponding to differentiation in distinct refugia during the last glaciation. The lower genetic diversity in northern Europe indicates postglacial recolonization northwards from southern refugia. This study combining herbarium surveys and population genetics thus uniquely reveals the effects of climate and environmental factors on a plant pathogen species with an arctic-alpine distribution.
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Affiliation(s)
- Britta Bueker
- Lehrstuhl für Evolution und Biodiversität der Pflanzen, AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.,Department of Biology, Amherst College, 220 South Pleasant Street, Amherst, MA, 01002, USA
| | - Chris Eberlein
- Lehrstuhl für Evolution und Biodiversität der Pflanzen, AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.,Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médicine, Quebec City, Quebec, Canada, G1V 0A6
| | - Pierre Gladieux
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.,INRA, UMR BGPI, Bâtiment K, Campus International de Baillarguet, F-34398, Montpellier, France.,CIRAD, F-34398, Montpellier, France
| | - Angela Schaefer
- Lehrstuhl für Evolution und Biodiversität der Pflanzen, AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Dominic J Bennett
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Dominik Begerow
- Lehrstuhl für Evolution und Biodiversität der Pflanzen, AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Michael E Hood
- Department of Biology, Amherst College, 220 South Pleasant Street, Amherst, MA, 01002, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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20
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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21
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Fontaine MC, Gladieux P, Hood ME, Giraud T. History of the invasion of the anther smut pathogen on Silene latifolia in North America. THE NEW PHYTOLOGIST 2013; 198:946-956. [PMID: 23406496 DOI: 10.1111/nph.12177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/09/2013] [Indexed: 06/01/2023]
Abstract
Understanding the routes of pathogen introduction contributes greatly to efforts to protect against future disease emergence. Here, we investigated the history of the invasion in North America by the fungal pathogen Microbotryum lychnidis-dioicae, which causes the anther smut disease on the white campion Silene latifolia. This system is a well-studied model in evolutionary biology and ecology of infectious disease in natural systems. Analyses based on microsatellite markers show that the introduced American M. lychnidis-dioicae probably came from Scotland, from a single population, and thus suffered from a drastic bottleneck compared with genetic diversity in the native European range. The pattern in M. lychnidis-dioicae contrasts with that found by previous studies in its host plant species S. latifolia, also introduced in North America. In the plant, several European lineages have been introduced from across Europe. The smaller number of introductions for M. lychnidis-dioicae probably relates to its life history traits, as it is an obligate, specialized pathogen that is neither transmitted by the seeds nor persistent in the environment. The results show that even a nonagricultural, biotrophic, and insect-vectored pathogen suffering from a very strong bottleneck can successfully establish populations on its introduced host.
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Affiliation(s)
- Michael C Fontaine
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR8079, Orsay Cedex, F-91405, France
- CNRS, UMR 8079, Orsay Cedex, F-91405, France
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Pierre Gladieux
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR8079, Orsay Cedex, F-91405, France
- CNRS, UMR 8079, Orsay Cedex, F-91405, France
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | - Tatiana Giraud
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR8079, Orsay Cedex, F-91405, France
- CNRS, UMR 8079, Orsay Cedex, F-91405, France
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Keller SR, Gilbert KJ, Fields PD, Taylor DR. Bayesian inference of a complex invasion history revealed by nuclear and chloroplast genetic diversity in the colonizing plant, Silene latifolia. Mol Ecol 2012; 21:4721-34. [PMID: 22943057 DOI: 10.1111/j.1365-294x.2012.05751.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 06/12/2012] [Accepted: 06/20/2012] [Indexed: 01/07/2023]
Abstract
Species invading new ranges are subject to a series of demographic events that can strongly shape genetic diversity. Describing this demographic history is important for understanding where invasive species come from and how they spread, and is critical to testing hypotheses of postinvasion adaptation. Here, we analyse nuclear and chloroplast genetic diversity to study the invasion history of the widespread colonizing weed, Silene latifolia (Caryophyllaceae). Bayesian clustering and PCA revealed strong population structure in the native range of Europe, and although genotypes from multiple native sources were present in the introduced range of North America, the spatial distribution of genetic variance was dramatically reorganized. Using approximate Bayesian computation (ABC), we compared support for different invasion scenarios, including the number and size of independent introduction events and the amount of admixture occurring between sources of introduced genotypes. Our results supported independent introductions into eastern and western North America, with the latter forming a bridgehead for a secondary invasion into the Great Lakes region of central North America. Despite small estimated founder population sizes, the duration of the demographic bottleneck after the initial introduction appeared extremely short-lived. This pattern of repeated colonization and rapid expansion has effectively eroded the strong population structure and cytonuclear associations present in Europe, but has retained overall high genetic diversity since invasion. Our results highlight the flexibility of the ABC approach for constructing a narrative of the demographic history of species invasions and provide baseline for future studies of evolutionary changes in introduced S. latifolia populations.
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Affiliation(s)
- Stephen R Keller
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD 21532, USA.
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23
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Fabre B, Ioos R, Piou D, Marçais B. Is the emergence of Dothistroma needle blight of pine in France caused by the cryptic species Dothistroma pini? PHYTOPATHOLOGY 2012; 102:47-54. [PMID: 22165983 DOI: 10.1094/phyto-02-11-0036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Dothistroma needle blight (DNB) emerged in France in the past 15 years. This disease is induced by two closely related species: Dothistroma septosporum and D. pini. Although both species are currently present in France, only D. septosporum was reported in the past. We investigated whether a recent arrival of D. pini in France could be a cause of the DNB emergence. We analyzed herbarium specimens of pine needles with DNB symptoms using polymerase chain reaction techniques to study the past frequency of D. pini in France. We also determined the present distribution within the country of D. septosporum and D. pini and compared it with the spatial pattern of DNB reported in the Département de la Santé des Forêts (DSF; French forest health monitoring agency) database. Although D. pini was detected on herbarium specimens from 1907 and 1965, it was not frequent in France in the past. Today, it is frequent, although not present throughout the country, being absent from the north and the east. There is no relationship between the D. pini distribution in France and the spatial pattern of DNB reported in the DSF database. Thus, the emergence of DNB in France cannot be explained by a recent arrival of D. pini.
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Affiliation(s)
- B Fabre
- INRA Nancy, INRA/UHP, Champenoux, France
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24
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Piątek M, Lutz M, Ronikier A, Kemler M, Świderska-Burek U. Microbotryum heliospermae, a new anther smut fungus parasitic on Heliosperma pusillum in the mountains of the European Alpine System. Fungal Biol 2011; 116:185-95. [PMID: 22289764 DOI: 10.1016/j.funbio.2011.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 10/10/2011] [Accepted: 10/26/2011] [Indexed: 10/15/2022]
Abstract
The members of the smut genus Microbotryum are pathogens of a wide range of host plant species from nine dicotyledonous families. Within the genus, the species sporulating in anthers of Caryophyllaceae form a monophyletic group that in recent years attracted much interest in various biological studies. The phylogenetic framework developed for species delimitation within Microbotryum revealed that high level host-specificity is a major feature of most caryophyllaceous anther smuts. However, the great number of anther smut specimens on diverse host plant species reported worldwide has still not been included in phylogenetic analyses due to the inaccessibility of recently collected specimens, and thus many species remain still undiscovered. In this study, anther smut specimens on Heliosperma pusillum originating from all main mountain ranges of the European Alpine System were examined using partial rDNA sequence and/or morphological analyses. The investigation revealed that all specimens are morphologically uniform and phylogenetically represent a monophyletic lineage, sister to Microbotryum lagerheimii complex on Atocion rupestre/Silene lacera/Silene vulgaris/Viscaria vulgaris. This lineage cannot be attributed to any of the previously described species, and therefore the smut in anthers of H. pusillum is described and illustrated here as a new species, Microbotryum heliospermae. The species is known from subalpine zone of the Alps, the Carpathians, the Dinaric Alps, and the Pyrenees, inhabiting host plants growing in open spring communities or semihumid mountain meadows.
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Affiliation(s)
- Marcin Piątek
- Department of Mycology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland.
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Antonovics J, Edwards M. Spatio-temporal dynamics of bumblebee nest parasites (Bombus subgenus Psythirus ssp.) and their hosts (Bombus spp.). J Anim Ecol 2011; 80:999-1011. [PMID: 21644977 DOI: 10.1111/j.1365-2656.2011.01846.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1. A 39-year bumblebee data base was used to study the codistribution of six cuckoo bumblebees in the subgenus Psythirus of Bombus (hereafter called Psythirus) and their free-living bumblebee hosts in the British Isles. 2. A model of nest parasitism predicted host threshold densities and stable deterministic dynamics, with fluctuations only emerging as a result of environmental or demographic stochasticity. 3. Standardized transects indicated that variation in total number of records could be largely attributed to variation in observer effort; analyses were therefore carried out using relative abundance. 4. Spatially, parasite-free zones were evident in areas of low host abundance, but the host threshold for parasite presence differed among species and locations. 5. Temporally, the relative numbers of the parasite and host species remained relatively constant, except that the nest parasite P. campestris declined significantly since 1990. 6. There were consistent negative effects of the parasitic species on the numbers of hosts in the following year, and this pattern was seen over large geographic areas. 7. The spatio-temporal patterns confirmed a high degree of host specificity, except that P. campestris may be parasitizing not only B. pascuorum but also other species in the subgenus Thoracobombus.
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Affiliation(s)
- Janis Antonovics
- Biology Department, University of Virginia, Charlottesville, VA 22904, USA.
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Vercken E, Fontaine MC, Gladieux P, Hood ME, Jonot O, Giraud T. Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica. PLoS Pathog 2010; 6:e1001229. [PMID: 21187901 PMCID: PMC3002987 DOI: 10.1371/journal.ppat.1001229] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 11/15/2010] [Indexed: 11/18/2022] Open
Abstract
Climate warming is predicted to increase the frequency of invasions by pathogens and to cause the large-scale redistribution of native host species, with dramatic consequences on the health of domesticated and wild populations of plants and animals. The study of historic range shifts in response to climate change, such as during interglacial cycles, can help in the prediction of the routes and dynamics of infectious diseases during the impending ecosystem changes. Here we studied the population structure in Europe of two Microbotryum species causing anther smut disease on the plants Silene latifolia and Silene dioica. Clustering analyses revealed the existence of genetically distinct groups for the pathogen on S. latifolia, providing a clear-cut example of European phylogeography reflecting recolonization from southern refugia after glaciation. The pathogen genetic structure was congruent with the genetic structure of its host species S. latifolia, suggesting dependence of the migration pathway of the anther smut fungus on its host. The fungus, however, appeared to have persisted in more numerous and smaller refugia than its host and to have experienced fewer events of large-scale dispersal. The anther smut pathogen on S. dioica also showed a strong phylogeographic structure that might be related to more northern glacial refugia. Differences in host ecology probably played a role in these differences in the pathogen population structure. Very high selfing rates were inferred in both fungal species, explaining the low levels of admixture between the genetic clusters. The systems studied here indicate that migration patterns caused by climate change can be expected to include pathogen invasions that follow the redistribution of their host species at continental scales, but also that the recolonization by pathogens is not simply a mirror of their hosts, even for obligate biotrophs, and that the ecology of hosts and pathogen mating systems likely affects recolonization patterns.
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Affiliation(s)
- Elodie Vercken
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR 8079, Orsay, France.
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Hood ME, Mena-Alí JI, Gibson AK, Oxelman B, Giraud T, Yockteng R, Arroyo MTK, Conti F, Pedersen AB, Gladieux P, Antonovics J. Distribution of the anther-smut pathogen Microbotryum on species of the Caryophyllaceae. THE NEW PHYTOLOGIST 2010; 187:217-229. [PMID: 20406409 PMCID: PMC3487183 DOI: 10.1111/j.1469-8137.2010.03268.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 03/02/2010] [Indexed: 05/29/2023]
Abstract
*Understanding disease distributions is of fundamental and applied importance, yet few studies benefit from integrating broad sampling with ecological and phylogenetic data. Here, anther-smut disease, caused by the fungus Microbotryum, was assessed using herbarium specimens of Silene and allied genera of the Caryophyllaceae. *A total of 42,000 herbarium specimens were examined, and plant geographical distributions and morphological and life history characteristics were tested as correlates of disease occurrence. Phylogenetic comparative methods were used to determine the association between disease and plant life-span. *Disease was found on 391 herbarium specimens from 114 species and all continents with native Silene. Anther smut occurred exclusively on perennial plants, consistent with the pathogen requiring living hosts to overwinter. The disease was estimated to occur in 80% of perennial species of Silene and allied genera. The correlation between plant life-span and disease was highly significant while controlling for the plant phylogeny, but the disease was not correlated with differences in floral morphology. *Using resources available in natural history collections, this study illustrates how disease distribution can be determined, not by restriction to a clade of susceptible hosts or to a limited geographical region, but by association with host life-span, a trait that has undergone frequent evolutionary transitions.
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Affiliation(s)
- Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | | | | | - Bengt Oxelman
- Department of Plant and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91405 Orsay Cedex, France
| | - Roxana Yockteng
- MNHN, Département Systématique et Evolution, 16 rue Buffon CP 39, 75005 Paris, France
| | - Mary T K Arroyo
- Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias, University of Chile, Casilla 653, Santiago, Chile
| | - Fabio Conti
- Dipartimento di Scienze Ambientali, Università di Camerino - Centro Ricerche Floristiche dell'Appennino, Barisciano (L'Aquila), Italy
| | - Amy B Pedersen
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Pierre Gladieux
- Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91405 Orsay Cedex, France
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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Alexander HM. Disease in Natural Plant Populations, Communities, and Ecosystems: Insights into Ecological and Evolutionary Processes. PLANT DISEASE 2010; 94:492-503. [PMID: 30754479 DOI: 10.1094/pdis-94-5-0492] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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Biological collections and ecological/environmental research: a review, some observations and a look to the future. Biol Rev Camb Philos Soc 2009; 85:247-66. [PMID: 19961469 DOI: 10.1111/j.1469-185x.2009.00098.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Housed worldwide, mostly in museums and herbaria, is a vast collection of biological specimens developed over centuries. These biological collections, and associated taxonomic and systematic research, have received considerable long-term public support. The work remaining in systematics has been expanding as the estimated total number of species of organisms on Earth has risen over recent decades, as have estimated numbers of undescribed species. Despite this increasing task, support for taxonomic and systematic research, and biological collections upon which such research is based, has declined over the last 30-40 years, while other areas of biological research have grown considerably, especially those that focus on environmental issues. Reflecting increases in research that deals with ecological questions (e.g. what determines species distribution and abundance) or environmental issues (e.g. toxic pollution), the level of research attempting to use biological collections in museums or herbaria in an ecological/environmental context has risen dramatically during about the last 20 years. The perceived relevance of biological collections, and hence the support they receive, should be enhanced if this trend continues and they are used prominently regarding such environmental issues as anthropogenic loss of biodiversity and associated ecosystem function, global climate change, and decay of the epidemiological environment. It is unclear, however, how best to use biological collections in the context of such ecological/environmental issues or how best to manage collections to facilitate such use. We demonstrate considerable and increasingly realized potential for research based on biological collections to contribute to ecological/environmental understanding. However, because biological collections were not originally intended for use regarding such issues and have inherent biases and limitations, they are proving more useful in some contexts than in others. Biological collections have, for example, been particularly useful as sources of information regarding variation in attributes of individuals (e.g. morphology, chemical composition) in relation to environmental variables, and provided important information in relation to species' distributions, but less useful in the contexts of habitat associations and population sizes. Changes to policies, strategies and procedures associated with biological collections could mitigate these biases and limitations, and hence make such collections more useful in the context of ecological/environmental issues. Haphazard and opportunistic collecting could be replaced with strategies for adding to existing collections that prioritize projects that use biological collections and include, besides taxonomy and systematics, a focus on significant environmental/ecological issues. Other potential changes include increased recording of the nature and extent of collecting effort and information associated with each specimen such as nearby habitat and other individuals observed but not collected. Such changes have begun to occur within some institutions. Institutions that house biological collections should, we think, pursue a mission of 'understanding the life of the planet to inform its stewardship' (Krishtalka & Humphrey, 2000), as such a mission would facilitate increased use of biological collections in an ecological/environmental context and hence lead to increased appreciation, encouragement and support from the public for these collections, their associated research, and the institutions that house them.
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Reynolds RJ, Westbrook MJ, Rohde AS, Cridland JM, Fenster CB, Dudash MR. Pollinator specialization and pollination syndromes of three related North AmericanSilene. Ecology 2009; 90:2077-87. [DOI: 10.1890/08-1141.1] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Antonovics J. The effect of sterilizing diseases on host abundance and distribution along environmental gradients. Proc Biol Sci 2009; 276:1443-8. [PMID: 19324815 DOI: 10.1098/rspb.2008.1256] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study analyses the effect of host-specific pathogens on range restriction of their hosts across environmental gradients at population margins. Sterilizing diseases can limit host range by causing large reductions in population size in what would otherwise be the central area of a species range. Diseases showing frequency-dependent transmission can also pull back a population from its disease-free margin. A wide range of disease prevalence versus abundance patterns emerge which often differ from the classical expectation of increasing prevalence with increasing abundance. Surprisingly, very few empirical studies have investigated the dynamics of disease across environmental gradients or at range limits.
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Affiliation(s)
- Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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Brooks C, Antonovics J, Keitt T. Spatial and Temporal Heterogeneity Explain Disease Dynamics in a Spatially Explicit Network Model. Am Nat 2008; 172:149-59. [DOI: 10.1086/589451] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Steets JA, Wolf DE, Auld JR, Ashman TL. The role of natural enemies in the expression and evolution of mixed mating in hermaphroditic plants and animals. Evolution 2007; 61:2043-55. [PMID: 17767581 DOI: 10.1111/j.1558-5646.2007.00184.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although a large portion of plant and animal species exhibit intermediate levels of outcrossing, the factors that maintain this wealth of variation are not well understood. Natural enemies are one relatively understudied ecological factor that may influence the evolutionary stability of mixed mating. In this paper, we aim for a conceptual unification of the role of enemies in mating system expression and evolution in both hermaphroditic animals and plants. We review current theory and detail the potential effects of enemies on fundamental mating system parameters. In doing so, we identify situations in which consideration of enemies alters expectations about the stability of mixed mating. Generally, we find that inclusion of the enemy dimension may broaden conditions in which mixed mating systems are evolutionarily stable. Finally, we highlight avenues ripe for future theoretical and empirical work that will advance our understanding of enemies in the expression and evolution of mixed mating in their hosts/victims, including examination of feedback cycles between victims and enemies and quantification of mating system-related parameters in victim populations in the presence and absence of enemies.
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Affiliation(s)
- Janette A Steets
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA.
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Taylor DR, Keller SR. Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion. Evolution 2007; 61:334-45. [PMID: 17348944 DOI: 10.1111/j.1558-5646.2007.00037.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.
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Affiliation(s)
- Douglas R Taylor
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904-4328, USA.
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