1
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Hülsmann L, Chisholm RA, Comita L, Visser MD, de Souza Leite M, Aguilar S, Anderson-Teixeira KJ, Bourg NA, Brockelman WY, Bunyavejchewin S, Castaño N, Chang-Yang CH, Chuyong GB, Clay K, Davies SJ, Duque A, Ediriweera S, Ewango C, Gilbert GS, Holík J, Howe RW, Hubbell SP, Itoh A, Johnson DJ, Kenfack D, Král K, Larson AJ, Lutz JA, Makana JR, Malhi Y, McMahon SM, McShea WJ, Mohamad M, Nasardin M, Nathalang A, Norden N, Oliveira AA, Parmigiani R, Perez R, Phillips RP, Pongpattananurak N, Sun IF, Swanson ME, Tan S, Thomas D, Thompson J, Uriarte M, Wolf AT, Yao TL, Zimmerman JK, Zuleta D, Hartig F. Latitudinal patterns in stabilizing density dependence of forest communities. Nature 2024; 627:564-571. [PMID: 38418889 PMCID: PMC10954553 DOI: 10.1038/s41586-024-07118-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10-12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizing CNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.
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Affiliation(s)
- Lisa Hülsmann
- Ecosystem Analysis and Simulation (EASI) Lab, University of Bayreuth, Bayreuth, Germany.
- Theoretical Ecology, University of Regensburg, Regensburg, Germany.
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Liza Comita
- School of the Environment, Yale University, New Haven, CT, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Marco D Visser
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | | | - Salomon Aguilar
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama
| | - Kristina J Anderson-Teixeira
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama
- Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Norman A Bourg
- Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Warren Y Brockelman
- National Biobank of Thailand (NBT), National Science and Technology Development Agency, Bangkok, Thailand
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Sarayudh Bunyavejchewin
- Thai Long Term Forest Ecological Research Project, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Nicolas Castaño
- Instituto Amazónico de Investigaciones Científicas Sinchi, Bogotá, Colombia
| | - Chia-Hao Chang-Yang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | | | - Keith Clay
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Stuart J Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Alvaro Duque
- Departamento de Ciencias Forestales, Universidad Nacional de Colombia Sede Medellín, Medellín, Colombia
| | - Sisira Ediriweera
- Department of Science and Technology, Uva Wellassa University, Badulla, Sri Lanka
| | | | - Gregory S Gilbert
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jan Holík
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | - Robert W Howe
- Cofrin Center for Biodiversity, Department of Biology, University of Wisconsin-Green Bay, Green Bay, WI, USA
| | - Stephen P Hubbell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Akira Itoh
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Daniel J Johnson
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, USA
| | - David Kenfack
- Global Earth Observatory (ForestGEO), Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Kamil Král
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | - Andrew J Larson
- Department of Forest Management, University of Montana, Missoula, MT, USA
- Wilderness Institute, University of Montana, Missoula, MT, USA
| | - James A Lutz
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | | | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Sean M McMahon
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA
- Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - William J McShea
- Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | | | | | - Anuttara Nathalang
- National Biobank of Thailand (NBT), National Science and Technology Development Agency, Bangkok, Thailand
| | - Natalia Norden
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | | | - Renan Parmigiani
- Department of Ecology, University of São Paulo, São Paulo, Brazil
| | - Rolando Perez
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama
| | | | | | - I-Fang Sun
- Department of Natural Resources and Environmental Studies, National Donghwa University, Hualien, Taiwan
| | - Mark E Swanson
- School of the Environment, Washington State University, Pullman, WA, USA
| | | | - Duncan Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jill Thompson
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, UK
| | - Maria Uriarte
- Department of Ecology, Evolution & Environmental Biology, Columbia University, New York, NY, USA
| | - Amy T Wolf
- Department of Biology, University of Wisconsin-Green Bay, Green Bay, WI, USA
| | - Tze Leong Yao
- Forest Research Institute Malaysia, Kepong, Malaysia
| | - Jess K Zimmerman
- Department of Environmental Science, University of Puerto Rico, Rio Piedras, USA
| | - Daniel Zuleta
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany
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2
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Wu Y, Brown A, Ricklefs RE. Host‐specific soil microbes contribute to habitat restriction of closely related oaks (
Quercus
spp.). Ecol Evol 2022; 12:e9614. [PMCID: PMC9745265 DOI: 10.1002/ece3.9614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yingtong Wu
- Department of Biology University of Missouri–St. Louis St. Louis Missouri USA
- Whitney R. Harris World Ecology Center University of Missouri–St. Louis St. Louis Missouri USA
| | - Alicia Brown
- Department of Biology University of Missouri–St. Louis St. Louis Missouri USA
- Whitney R. Harris World Ecology Center University of Missouri–St. Louis St. Louis Missouri USA
| | - Robert E. Ricklefs
- Department of Biology University of Missouri–St. Louis St. Louis Missouri USA
- Whitney R. Harris World Ecology Center University of Missouri–St. Louis St. Louis Missouri USA
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3
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Semchenko M, Barry KE, de Vries FT, Mommer L, Moora M, Maciá-Vicente JG. Deciphering the role of specialist and generalist plant-microbial interactions as drivers of plant-soil feedback. THE NEW PHYTOLOGIST 2022; 234:1929-1944. [PMID: 35338649 DOI: 10.1111/nph.18118] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density-dependence and species co-existence. Such effects are often attributed to the accumulation of host-specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host-specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host-specificity in plant-associated microbes and propose that specific plant-soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant-soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant-microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant-soil feedback and the ways it contributes to plant co-existence.
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Affiliation(s)
- Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kathryn E Barry
- Ecology and Biodiversity, Department of Biology, Institute of Science, Utrecht University, Padualaan 8, Utrecht, the Netherlands
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Liesje Mommer
- Plant Ecology and Nature Conservation, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
| | - Jose G Maciá-Vicente
- Plant Ecology and Nature Conservation, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
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4
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Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nat Commun 2022; 13:2047. [PMID: 35440538 PMCID: PMC9018854 DOI: 10.1038/s41467-022-29584-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA.
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Shawn J Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jesse A Garcia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Steven L Salzberg
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA
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5
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Gibson AK. Genetic diversity and disease: The past, present, and future of an old idea. Evolution 2022; 76:20-36. [PMID: 34796478 PMCID: PMC9064374 DOI: 10.1111/evo.14395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 01/21/2023]
Abstract
Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.
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Affiliation(s)
- Amanda Kyle Gibson
- Department of Biology University of Virginia Charlottesville Virginia 22903
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6
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Stump SM, Song C, Saavedra S, Levine JM, Vasseur DA. Synthesizing the effects of individual‐level variation on coexistence. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Simon Maccracken Stump
- Department of Ecology & Evolutionary Biology Yale University New Haven Connecticut 06511 USA
| | - Chuliang Song
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA
| | - Serguei Saavedra
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA
| | - Jonathan M. Levine
- Department of Ecology & Evolutionary Biology Princeton University Princeton New Jersey 08544 USA
| | - David A. Vasseur
- Department of Ecology & Evolutionary Biology Yale University New Haven Connecticut 06511 USA
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7
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Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021; 22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. RESULTS By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. CONCLUSIONS Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | | | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
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8
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Wills C, Wang B, Fang S, Wang Y, Jin Y, Lutz J, Thompson J, Harms KE, Pulla S, Pasion B, Germain S, Liu H, Smokey J, Su SH, Butt N, Chu C, Chuyong G, Chang-Yang CH, Dattaraja HS, Davies S, Ediriweera S, Esufali S, Fletcher CD, Gunatilleke N, Gunatilleke S, Hsieh CF, He F, Hubbell S, Hao Z, Itoh A, Kenfack D, Li B, Li X, Ma K, Morecroft M, Mi X, Malhi Y, Ong P, Rodriguez LJ, Suresh HS, Sun IF, Sukumar R, Tan S, Thomas D, Uriarte M, Wang X, Wang X, Yao TL, Zimmermann J. Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories. PLoS Comput Biol 2021; 17:e1008853. [PMID: 33914731 PMCID: PMC8084225 DOI: 10.1371/journal.pcbi.1008853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
When Darwin visited the Galapagos archipelago, he observed that, in spite of the islands' physical similarity, members of species that had dispersed to them recently were beginning to diverge from each other. He postulated that these divergences must have resulted primarily from interactions with sets of other species that had also diverged across these otherwise similar islands. By extrapolation, if Darwin is correct, such complex interactions must be driving species divergences across all ecosystems. However, many current general ecological theories that predict observed distributions of species in ecosystems do not take the details of between-species interactions into account. Here we quantify, in sixteen forest diversity plots (FDPs) worldwide, highly significant negative density-dependent (NDD) components of both conspecific and heterospecific between-tree interactions that affect the trees' distributions, growth, recruitment, and mortality. These interactions decline smoothly in significance with increasing physical distance between trees. They also tend to decline in significance with increasing phylogenetic distance between the trees, but each FDP exhibits its own unique pattern of exceptions to this overall decline. Unique patterns of between-species interactions in ecosystems, of the general type that Darwin postulated, are likely to have contributed to the exceptions. We test the power of our null-model method by using a deliberately modified data set, and show that the method easily identifies the modifications. We examine how some of the exceptions, at the Wind River (USA) FDP, reveal new details of a known allelopathic effect of one of the Wind River gymnosperm species. Finally, we explore how similar analyses can be used to investigate details of many types of interactions in these complex ecosystems, and can provide clues to the evolution of these interactions.
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Affiliation(s)
- Christopher Wills
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Bin Wang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin
| | - Shuai Fang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang
| | - Yunquan Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing
| | - Yi Jin
- College of Life Sciences, Zhejiang University, Hangzhou
| | - James Lutz
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Jill Thompson
- Center for Ecology & Hydrology, Penicuik, Midlothian, Scotland
| | - Kyle E. Harms
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Los Angeles, United States of America
| | - Sandeep Pulla
- Divecha Centre for Climate Change, Indian Institute of Science, Bengaluru, India
- National Centre for Biological Sciences, GKVK Campus, Bengaluru, India
| | - Bonifacio Pasion
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan
| | - Sara Germain
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Heming Liu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai
| | - Joseph Smokey
- Department of Biology, Memorial University of Newfoundland, Newfoundland, Canada
| | - Sheng-Hsin Su
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei
| | - Nathalie Butt
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Chengjin Chu
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou
| | - George Chuyong
- Department of Botany and Plant Physiology, University of Buea, Cameroon
| | - Chia-Hao Chang-Yang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung
| | | | - Stuart Davies
- Center for Tropical Forest Science, Smithsonian Institution, Washington, DC, United States of America
| | - Sisira Ediriweera
- Faculty of Science and Technology, Uva Wellassa University, Badulla, Sri Lanka
| | - Shameema Esufali
- Department of Botany, University of Peradeniya, Peradeniya Sri Lanka
| | | | - Nimal Gunatilleke
- Dept. of Botany, Faculty of Science, University of Peradeniya, Peradeniya Sri Lanka
| | - Savi Gunatilleke
- Dept. of Botany, Faculty of Science, University of Peradeniya, Peradeniya Sri Lanka
| | | | - Fangliang He
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou
| | - Stephen Hubbell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Zhanqing Hao
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang
| | - Akira Itoh
- Graduate School of Science, Osaka City University, Sumiyoshi Ku, Osaka, Japan
| | - David Kenfack
- Center for Tropical Forest Science–Forest Global Earth Observatory (CTFS-ForestGEO), Smithsonian Tropical Research Institute, NMNH—MRC, Washington, DC, United States of America
| | - Buhang Li
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou
| | - Xiankun Li
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing
| | | | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing
| | - Yadvinder Malhi
- School of Geography and the Environment, Oxford University Centre for the Environment, University of Oxford, Oxford, United Kingdom
| | - Perry Ong
- Institute of Biology, College of Science, University of the Philippines Diliman, Diliman, Quezon City, Philippines
| | - Lillian Jennifer Rodriguez
- Institute of Biology, College of Science, University of the Philippines Diliman, Diliman, Quezon City, Philippines
| | - H. S. Suresh
- Divecha Centre for Climate Change, Indian Institute of Science, Bengaluru, India
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, India
| | - I Fang Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien
| | - Raman Sukumar
- Divecha Centre for Climate Change, Indian Institute of Science, Bengaluru, India
| | - Sylvester Tan
- Forest Department Sarawak, Bangunan Wisma Sumber Alam, Jalan Stadium, Petra Jaya, Kuching, Sarawak, Malaysia
| | - Duncan Thomas
- Department of Biology, Washington State University, Vancouver, Washington State, United States of America
| | - Maria Uriarte
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York city, New York, United States of America
| | - Xihua Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai
| | - Xugao Wang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang
| | - T. L. Yao
- Forest Research Institute Malaysia, Kepong Selangor, Malaysia
| | - Jess Zimmermann
- Dept of Environmental Sciences, University of Puerto Rico, Rio Piedras, San Juan, PR, United States of America
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9
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Khan AL, Al-Harrasi A, Numan M, AbdulKareem NM, Mabood F, Al-Rawahi A. Spectroscopic and Molecular Methods to Differentiate Gender in Immature Date Palm ( Phoenix dactylifera L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:536. [PMID: 33809251 PMCID: PMC8001243 DOI: 10.3390/plants10030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
Phoenix dactylifera (date palm) is a well-known nutritious and economically important fruit tree found in arid regions of the Middle East and North Africa. Being diploid, it has extremely high divergence in gender, where sex differentiation in immature date palms (Phoenix dactylifera L.) has remained an enigma in recent years. Herein, new robust infrared (near-infrared reflectance spectroscopy (NIRS) and Fourier transform infrared attenuated total reflectance (FTIR/ATR)) and nuclear magnetic resonance (NMR) spectroscopy methods coupled with extensive chemometric analysis were used to identify the sex differentiation in immature date palm leaves. NIRS/FTIR reflectance and 1H-NMR profiling suggested that the signals of monosaccharides (glucose and fructose) and/or disaccharides (maltose and sucrose) play key roles in sex differentiation. The three kinds of spectroscopic data were clearly differentiated among known and unknown male and female leaves via principal component and partial least square discriminant analyses. Furthermore, sex-specific genes and molecular markers obtained from the lower halves of LG12 chromosomes showed enhanced transcript accumulation of mPdIRDP52, mPdIRDP50, and PDK101 in females compared with in males. The phylogeny showed that the mPdIRD033, mPdIRD031, and mPdCIR032 markers formed distinctive clades with more than 70% similarity in gender differentiation. The three robust analyses provide an alternative tool to differentiate sex in date palm trees, which offers a solution to the long-standing challenge of dioecism and could enhance in situ tree propagation programs.
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Affiliation(s)
- Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
| | - Muhammad Numan
- Department of Biology, University of North Carolina, Greensboro, NC 27402-6170, USA;
| | - Noor Mazin AbdulKareem
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
| | - Fazal Mabood
- Institute of Chemical Sciences, University of Swat, Khyber Pakhtunkhwa 19200, Pakistan
| | - Ahmed Al-Rawahi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
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10
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Reinhart KO, Bauer JT, McCarthy‐Neumann S, MacDougall AS, Hierro JL, Chiuffo MC, Mangan SA, Heinze J, Bergmann J, Joshi J, Duncan RP, Diez JM, Kardol P, Rutten G, Fischer M, van der Putten WH, Bezemer TM, Klironomos J. Globally, plant-soil feedbacks are weak predictors of plant abundance. Ecol Evol 2021; 11:1756-1768. [PMID: 33614002 PMCID: PMC7882948 DOI: 10.1002/ece3.7167] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/02/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs estimated from controlled bioassays. We meta-analyzed results from 22 PSF experiments and found an overall positive correlation (0.12 ≤ r ¯ ≤ 0.32) between plant abundance in the field and PSFs across plant functional types (herbaceous and woody plants) but also variation by plant functional type. Thus, our analysis provides quantitative support that plant abundance has a general albeit weak positive relationship with PSFs across ecosystems. Overall, our results suggest that harmful soil biota tend to accumulate around and disproportionately impact species that are rare. However, data for the herbaceous species, which are most common in the literature, had no significant abundance-PSFs relationship. Therefore, we conclude that further work is needed within and across biomes, succession stages and plant types, both under controlled and field conditions, while separating PSF effects from other drivers (e.g., herbivory, competition, disturbance) of plant abundance to tease apart the role of soil biota in causing patterns of plant rarity versus commonness.
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Affiliation(s)
- Kurt O. Reinhart
- Fort Keogh Livestock & Range Research LaboratoryUnited States Department of Agriculture‐ Agricultural Research ServiceMiles CityMTUSA
| | - Jonathan T. Bauer
- Department of BiologyInstitute for the Environment and SustainabilityMiami UniversityOxfordOHUSA
| | | | | | - José L. Hierro
- Laboratorio de EcologíaBiogeografía y Evolución Vegetal (LEByEV)Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)‐Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
- Departamento de BiologíaFacultad de Ciencias Exactas y NaturalesUNLPamSanta RosaArgentina
| | - Mariana C. Chiuffo
- Grupo de Ecología de InvasionesINIBIOMAUniversidad Nacional del ComahueCONICETSan Carlos de BarilocheArgentina
| | - Scott A. Mangan
- Department of Biological SciencesArkansas State UniversityJonesboroARUSA
| | - Johannes Heinze
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
| | - Joana Bergmann
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
- Leibniz Centre for Agricultural Landscape Research (ZALF)MünchebergGermany
- Institut für BiologiePlant EcologyFreie Universität BerlinBerlinGermany
| | - Jasmin Joshi
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
- Institute for Landscape and Open SpaceEastern Switzerland University of Applied SciencesSt. GallenSwitzerland
| | - Richard P. Duncan
- Centre for Conservation Ecology and GeneticsInstitute for Applied EcologyUniversity of CanberraCanberraACTAustralia
| | - Jeff M. Diez
- Institute of Ecology and EvolutionUniversity of OregonEugeneORUSA
| | - Paul Kardol
- Department of Forest Ecology and ManagementSwedish University of Agricultural SciencesUmeåSweden
| | - Gemma Rutten
- Institute of Plant ScienceUniversity of BernBernSwitzerland
- Laboratoire d'Ecologie Alpine (LECA)Université Grenoble AlpesUMR CNRS‐UGA‐USMB 5553GrenobleFrance
| | - Markus Fischer
- Institute of Plant ScienceUniversity of BernBernSwitzerland
| | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of EcologyWageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityWageningenThe Netherlands
| | - Thiemo Martijn Bezemer
- Department of Terrestrial EcologyNetherlands Institute of EcologyWageningenThe Netherlands
- Institute of BiologySection Plant Ecology and PhytochemistryLeiden UniversityLeidenThe Netherlands
| | - John Klironomos
- Department of BiologyUniversity of British ColumbiaKelownaBCCanada
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11
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Song X, Lim JY, Yang J, Luskin MS. When do Janzen-Connell effects matter? A phylogenetic meta-analysis of conspecific negative distance and density dependence experiments. Ecol Lett 2020; 24:608-620. [PMID: 33382527 DOI: 10.1111/ele.13665] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/18/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022]
Abstract
The Janzen-Connell (J-C) hypothesis suggests that specialised natural enemies cause distance- or density-dependent mortality among host plants and is regarded as an important mechanism for species coexistence. However, there remains debate about whether this phenomenon is widespread and how variation is structured across taxa and life stages. We performed the largest meta-analysis of experimental studies conducted under natural settings to date. We found little evidence of distance-dependent or density-dependent mortality when grouping all types of manipulations. Our analysis also reveals very large variation in response among species, with 38.5% of species even showing positive responses to manipulations. However, we found a strong signal of distance-dependent mortality among seedlings but not seed experiments, which we attribute to (a) seedlings sharing susceptible tissues with adults (leaves, wood, roots), (b) seedling enemies having worse dispersal than seed enemies and (c) seedlings having fewer physical and chemical defences than seeds. Both density- and distance-dependent mortality showed large variation within genera and families, suggesting that J-C effects are not strongly phylogenetically conserved. There were no clear trends with latitude, rainfall or study duration. We conclude that J-C effects may not be as pervasive as widely thought. Understanding the variation in J-C effects provides opportunities for new discoveries that will refine our understanding of J-C effects and its role in species coexistence.
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Affiliation(s)
- Xiaoyang Song
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Jun Ying Lim
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jie Yang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Matthew Scott Luskin
- School of Biological Sciences, University of Queensland, Brisbane, Qld., 4072, Australia
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12
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Linan AG, Lowry PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Mol Ecol 2020; 30:4520-4537. [PMID: 33210759 DOI: 10.1111/mec.15736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 12/31/2022]
Abstract
A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.
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Affiliation(s)
- Alexander G Linan
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
| | - Porter P Lowry
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA.,Institut de Systématique, Évolution et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - George E Schatz
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA
| | - Jean-Claude Sevathian
- Botanist, Sustainability Consultant and Landscape Care and Maintenance Service, Beau Bassin-Rose Hill, Mauritius
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
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13
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Stein C, Mangan SA. Soil biota increase the likelihood for coexistence among competing plant species. Ecology 2020; 101:e03147. [PMID: 33460105 DOI: 10.1002/ecy.3147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/01/2020] [Accepted: 06/09/2020] [Indexed: 01/28/2023]
Abstract
Theory predicts that stable species coexistence will occur when population growth rates of competitively dominant species are suppressed when at high conspecific density. Although there is now compelling evidence that plant communities exhibit negative density dependence, the relative importance of the underlying processes leading to these patterns is rarely tested. We coupled reciprocal greenhouse and field experiments with community dynamics modeling to untangle the relative importance of soil biota from competition as stabilizing forces to coexistence. We found that (1) plant-soil biotic interactions compared to competitive interactions were stronger stabilizing forces, (2) only the strength of plant-soil biotic interactions was dependent on plant evolutionary history, and (3) the variation in the strength of plant-soil biotic interactions was correlated with relative abundance patterns in an opposite way than was the variation in the strength of competitive interactions. Collectively, our results demonstrate the fundamental role soil biota have in maintaining plant community diversity.
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Affiliation(s)
- Claudia Stein
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, 7061 Senator's Drive, Montgomery, Alabama, 36117, USA.,Tyson Research Center, Washington University in St. Louis, 6750 Tyson Valley Rd, Eureka, Missouri, 63025, USA
| | - Scott A Mangan
- Tyson Research Center, Washington University in St. Louis, 6750 Tyson Valley Rd, Eureka, Missouri, 63025, USA.,Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, 72467, USA
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14
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Stump SM, Marden JH, Beckman NG, Mangan SA, Comita LS. Resistance Genes Affect How Pathogens Maintain Plant Abundance and Diversity. Am Nat 2020; 196:472-486. [PMID: 32970465 DOI: 10.1086/710486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSpecialized pathogens are thought to maintain plant community diversity; however, most ecological studies treat pathogens as a black box. Here we develop a theoretical model to test how the impact of specialized pathogens changes when plant resistance genes (R-genes) mediate susceptibility. This work synthesizes two major hypotheses: the gene-for-gene model of pathogen resistance and the Janzen-Connell hypothesis of pathogen-mediated coexistence. We examine three scenarios. First, R-genes do not affect seedling survival; in this case, pathogens promote diversity. Second, seedlings are protected from pathogens when their R-gene alleles and susceptibility differ from those of nearby conspecific adults, thereby reducing transmission. If resistance is not costly, pathogens are less able to promote diversity because populations with low R-gene diversity suffer higher mortality, putting those populations at a disadvantage and potentially causing their exclusion. R-gene diversity may also be reduced during population bottlenecks, creating a priority effect. Third, when R-genes affect survival but resistance is costly, populations can avoid extinction by losing resistance alleles, as they cease paying a cost that is unneeded. Thus, the impact pathogens can have on tree diversity depends on the mechanism of plant-pathogen interactions. Future empirical studies should examine which of these scenarios most closely reflects the real world.
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15
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Greenspoon P, Wadhawan K. Colonization limitation of specialized enemies reduces species richness. THEOR ECOL-NETH 2020. [DOI: 10.1007/s12080-020-00474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Phillips P, Livieri TM, Swanson BJ. Genetic signature of disease epizootic and reintroduction history in an endangered carnivore. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
AbstractEmerging infectious diseases have recently increased in wildlife and can result in population declines and the loss of genetic diversity in susceptible populations. As populations of impacted species decline, genetic diversity can be lost, with ramifications including reduced effective population size and increased population structuring. For species of conservation concern, which may already have low genetic diversity, the loss of genetic diversity can be especially important. To investigate the impacts of a novel pathogen on genetic diversity in a genetically depauperate endangered species, we assessed the ramifications of a sylvatic plague-induced bottleneck in black-footed ferrets (Mustela nigripes). Following a plague epizootic, we genotyped 184 ferrets from Conata Basin and Badlands National Park, South Dakota, at seven microsatellite loci. We compared our results to pre-plague studies in the same population. We observed population substructuring into three genetic clusters. These clusters reflect founder effects from ferret reintroduction events followed by genetic drift. Compared to the pre-plague population, we observed losses of allelic diversity in all clusters, as well as significantly reduced heterozygosity in one cluster. These results indicate that disease epizootics may reduce population size and also genetic diversity. Our results suggest the importance of early and sustained management in mitigating disease epizootics in naïve populations for the maintenance of genetic diversity.
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Affiliation(s)
- Payton Phillips
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | | | - Bradley J Swanson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
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17
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La M. The balance of ecological and economic benefits of sea-buckthorn. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-179816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Meixiang La
- College of Economics and Management, Shanxi Agricultural University, Taigu, China
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18
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Schroeder JW, Dobson A, Mangan SA, Petticord DF, Herre EA. Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model. Nat Commun 2020; 11:2204. [PMID: 32371877 PMCID: PMC7200732 DOI: 10.1038/s41467-020-16047-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023] Open
Abstract
Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.
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Affiliation(s)
- John W Schroeder
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama.
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Andrew Dobson
- Princeton University, Princeton, NJ, USA
- Santa Fe Institute, Hyde Park Road, Santa Fe, NM, USA
| | - Scott A Mangan
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
- Washington University, St. Louis, MO, USA
| | - Daniel F Petticord
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
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19
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Lawanprasert A, Guinan CA, Langford EA, Hawkins CE, Sloand JN, Fescemyer HW, Aronson MR, Halle JA, Marden JH, Medina SH. Discovery of antitumor lectins from rainforest tree root transcriptomes. PLoS One 2020; 15:e0229467. [PMID: 32097449 PMCID: PMC7041804 DOI: 10.1371/journal.pone.0229467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/06/2020] [Indexed: 12/16/2022] Open
Abstract
Glycans are multi-branched sugars that are displayed from lipids and proteins. Through their diverse polysaccharide structures they can potentiate a myriad of cellular signaling pathways involved in development, growth, immuno-communication and survival. Not surprisingly, disruption of glycan synthesis is fundamental to various human diseases; including cancer, where aberrant glycosylation drives malignancy. Here, we report the discovery of a novel mannose-binding lectin, ML6, which selectively recognizes and binds to these irregular tumor-specific glycans to elicit potent and rapid cancer cell death. This lectin was engineered from gene models identified in a tropical rainforest tree root transcriptome and is unusual in its six canonical mannose binding domains (QxDxNxVxY), each with a unique amino acid sequence. Remarkably, ML6 displays antitumor activity that is >105 times more potent than standard chemotherapeutics, while being almost completely inactive towards non-transformed, healthy cells. This activity, in combination with results from glycan binding studies, suggests ML6 differentiates healthy and malignant cells by exploiting divergent glycosylation pathways that yield naïve and incomplete cell surface glycans in tumors. Thus, ML6 and other high-valence lectins may serve as novel biochemical tools to elucidate the glycomic signature of different human tumors and aid in the rational design of carbohydrate-directed therapies. Further, understanding how nature evolves proteins, like ML6, to combat the changing defenses of competing microorganisms may allow for fundamental advances in the way we approach combinatorial therapies to fight therapeutic resistance in cancer.
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Affiliation(s)
- Atip Lawanprasert
- Department of Biomedical Engineering, Penn State University, University Park, PA, United States of America
| | - Caitlin A. Guinan
- Department of Biology, Penn State University, University Park, PA, United States of America
| | - Erica A. Langford
- Department of Biology, Penn State University, University Park, PA, United States of America
| | - Carly E. Hawkins
- Department of Biology, Penn State University, University Park, PA, United States of America
| | - Janna N. Sloand
- Department of Biomedical Engineering, Penn State University, University Park, PA, United States of America
| | - Howard W. Fescemyer
- Department of Biology, Penn State University, University Park, PA, United States of America
| | - Matthew R. Aronson
- Department of Biomedical Engineering, Penn State University, University Park, PA, United States of America
| | - Jacob A. Halle
- Department of Biomedical Engineering, Penn State University, University Park, PA, United States of America
| | - James H. Marden
- Department of Biology, Penn State University, University Park, PA, United States of America
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA, United States of America
| | - Scott H. Medina
- Department of Biomedical Engineering, Penn State University, University Park, PA, United States of America
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20
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Calderón‐Sanou I, Ríos LD, Cascante‐Marín A, Barrantes G, Fuchs EJ. The effect of conspecific density, herbivory, and bamboo on seedling dynamics of a dominant oak in a Neotropical highland forest. Biotropica 2019. [DOI: 10.1111/btp.12714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Luis Diego Ríos
- Escuela de Biología Universidad de Costa Rica San José Costa Rica
| | | | | | - Eric J. Fuchs
- Escuela de Biología Universidad de Costa Rica San José Costa Rica
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21
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Pizano C, Kitajima K, Graham JH, Mangan SA. Negative plant-soil feedbacks are stronger in agricultural habitats than in forest fragments in the tropical Andes. Ecology 2019; 100:e02850. [PMID: 31351010 DOI: 10.1002/ecy.2850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 11/07/2022]
Abstract
There is now strong evidence suggesting that interactions between plants and their species-specific antagonistic microbes can maintain native plant community diversity. In contrast, the decay in diversity in plant communities invaded by nonnative plant species might be caused by weakening negative feedback strengths, perhaps because of the increased relative importance of plant mutualists such as arbuscular mycorrhizal fungi (AMF). Although the vast majority of studies examining plant-soil feedbacks have been conducted in a single habitat type, there are fewer studies that have tested how the strength and direction of these feedbacks change across habitats with differing dominating plants. In a fragmented montane agricultural system in Colombia, we experimentally teased apart the relative importance of AMF and non-AMF microbes (a microbial filtrate) to the strength and direction of feedbacks in both native and nonnative plant species. We hypothesized that native tree species of forest fragments would exhibit stronger negative feedbacks with a microbial filtrate that likely contained pathogens than with AMF alone, whereas nonnative plant species, especially a highly invasive dominant grass, would exhibit overall weaker negative feedbacks or even positive feedbacks regardless of the microbial type. We reciprocally inoculated each of 10 plant species separately with either the AMF community or the microbial filtrate originating from their own conspecifics, or with the AMF or microbial filtrate originating from each of the other nine heterospecific plant species. Overall, we found that the strength of negative feedback mediated by the filtrate was much stronger than feedbacks mediated by AMF. Surprisingly, we found that the two nonnative species, Urochloa brizantha and Coffea arabica, experienced stronger negative feedbacks with microbial filtrate than did the native forest tree species, suggesting that species-specific antagonistic microbes accumulate when a single host species dominates, as is the case in agricultural habitats. However, negative feedback between forest trees and agricultural species suggests that soil community dynamics may contribute to the re-establishment of native species into abandoned agricultural lands. Furthermore, our finding of no negative feedbacks among trees in forest fragments may be due to a loss in diversity of those microbes that drive diversity-maintaining processes in intact tropical forests.
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Affiliation(s)
- Camila Pizano
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA.,Biología de la Conservación, Cenicafé, Km4 vía antigua, Chinchiná-Manizales, Colombia
| | - Kaoru Kitajima
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA.,Smithsonian Tropical Research Institute, Balboa, Panama
| | - James H Graham
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, Florida, 33850, USA
| | - Scott A Mangan
- Smithsonian Tropical Research Institute, Balboa, Panama.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
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22
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Todesco M, Cronk Q. The genetic dimension of pest pressure in the tropical rainforest. Mol Ecol 2019; 26:2407-2409. [PMID: 28449375 DOI: 10.1111/mec.14078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 10/19/2022]
Abstract
Wet tropical forests are among the most diverse ecosystems on Earth and can host several hundreds of tree species per hectare. To maintain such diversity, the community must contain large numbers of relatively rare species rather than be dominated by a few very common trees, as is often the case in temperate forests. Explaining the mechanisms preventing dominance by common species has been a major task of tropical forest ecology. One of the most promising mechanisms is negative density dependence (NDD) of tree abundance driven by pests, including fungal diseases ('pest pressure'). NDD entails that the chance of survival of a sapling increases with the distance from a mature tree of the same species, thus preventing species from becoming locally dominant. Curiously, the strength of NDD is negatively correlated with abundance, meaning that tree species that are more common generally show weaker NDD (Comita et al. ). Interactions between plants and soil pathogens have been shown to play an important role in NDD (Klironomos ), and rare species are apparently more strongly affected (Mangan et al. ). However, the genetic mechanisms underlying this phenomenon have remained obscure. In this issue of Molecular Ecology, Marden et al. () suggest that reduced diversity of the genes involved in pathogen recognition (Resistance genes or R genes) could explain why NDD is stronger in locally rare species.
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Affiliation(s)
- Marco Todesco
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin Cronk
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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23
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Liu Y, He F. Incorporating the disease triangle framework for testing the effect of soil‐borne pathogens on tree species diversity. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13345] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yu Liu
- ECNU‐Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences East China Normal University Shanghai China
- Shanghai Institute of Pollution Control and Ecological Security Shanghai China
| | - Fangliang He
- ECNU‐Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences East China Normal University Shanghai China
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada
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24
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Evidence of within-species specialization by soil microbes and the implications for plant community diversity. Proc Natl Acad Sci U S A 2019; 116:7371-7376. [PMID: 30842279 DOI: 10.1073/pnas.1810767116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbes are thought to maintain diversity in plant communities by specializing on particular species, but it is not known whether microbes that specialize within species (i.e., on genotypes) affect diversity or dynamics in plant communities. Here we show that soil microbes can specialize at the within-population level in a wild plant species, and that such specialization could promote species diversity and seed dispersal in plant communities. In a shadehouse experiment in Panama, we found that seedlings of the native tree species, Virola surinamensis (Myristicaceae), had reduced performance in the soil microbial community of their maternal tree compared with in the soil microbial community of a nonmaternal tree from the same population. Performance differences were unrelated to soil nutrients or to colonization by mycorrhizal fungi, suggesting that highly specialized pathogens were the mechanism reducing seedling performance in maternal soils. We then constructed a simulation model to explore the ecological and evolutionary consequences of genotype-specific pathogens in multispecies plant communities. Model results indicated that genotype-specific pathogens promote plant species coexistence-albeit less strongly than species-specific pathogens-and are most effective at maintaining species richness when genetic diversity is relatively low. Simulations also revealed that genotype-specific pathogens select for increased seed dispersal relative to species-specific pathogens, potentially helping to create seed dispersal landscapes that allow pathogens to more effectively promote diversity. Combined, our results reveal that soil microbes can specialize within wild plant populations, affecting seedling performance near conspecific adults and influencing plant community dynamics on ecological and evolutionary time scales.
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25
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Pokou DN, Fister AS, Winters N, Tahi M, Klotioloma C, Sebastian A, Marden JH, Maximova SN, Guiltinan MJ. Resistant and susceptible cacao genotypes exhibit defense gene polymorphism and unique early responses to Phytophthora megakarya inoculation. PLANT MOLECULAR BIOLOGY 2019; 99:499-516. [PMID: 30739243 DOI: 10.1007/s11103-019-00832-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/24/2019] [Indexed: 05/26/2023]
Abstract
Key genes potentially involved in cacao disease resistance were identified by transcriptomic analysis of important cacao cultivars. Defense gene polymorphisms were identified which could contribute to pathogen recognition capacity. Cacao suffers significant annual losses to the water mold Phytophthora spp. (Oomycetes). In West Africa, P. megakarya poses a major threat to farmer livelihood and the stability of cocoa production. As part of a long-term goal to define key disease resistance genes in cacao, here we use a transcriptomic analysis of the disease-resistant cacao clone SCA6 and the susceptible clone NA32 to characterize basal differences in gene expression, early responses to infection, and polymorphisms in defense genes. Gene expression measurements by RNA-seq along a time course revealed the strongest transcriptomic response 24 h after inoculation in the resistant genotype. We observed strong regulation of several pathogenesis-related genes, pattern recognition receptors, and resistance genes, which could be critical for the ability of SCA6 to combat infection. These classes of genes also showed differences in basal expression between the two genotypes prior to infection, suggesting that prophylactic expression of defense-associated genes could contribute to SCA6's broad-spectrum disease resistance. Finally, we analyzed polymorphism in a set of defense-associated receptors, identifying coding variants between SCA6 and NA32 which could contribute to unique capacities for pathogen recognition. This work is an important step toward characterizing genetic differences underlying a successful defense response in cacao.
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Affiliation(s)
- Désiré N Pokou
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Andrew S Fister
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
| | - Noah Winters
- Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mathias Tahi
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Coulibaly Klotioloma
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Aswathy Sebastian
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - James H Marden
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA.
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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26
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Khan AL, Mabood F, Akber F, Ali A, Shahzad R, Al-Harrasi A, Al-Rawahi A, Shinwari ZK, Lee IJ. Endogenous phytohormones of frankincense producing Boswellia sacra tree populations. PLoS One 2018; 13:e0207910. [PMID: 30566477 PMCID: PMC6300221 DOI: 10.1371/journal.pone.0207910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/08/2018] [Indexed: 12/17/2022] Open
Abstract
Boswellia sacra, an endemic tree to Oman, is exposed to man-made incisions for commercial level frankincense production, whereas unsustainable harvesting may lead to population decline. In this case, assessment of endogenous phytohormones (gibberellic acid (GA), indole-acetic acid (IAA), salicylic acid (SA) and kinetin) can help to understand population health and growth dynamics. Hence, it was aimed to devise a robust method using Near-Infrared spectroscopy (NIRS) coupled with multivariate methods for phytohormone analysis of thirteen different populations of B. sacra. NIRS data was recorded in absorption mode (10000-4000 cm-1) to build partial least squares regression model (calibration set 70%). Model was externally cross validated (30%) as a test set to check their prediction ability before the application to quantify the unknown amount of phytohormones in thirteen different populations of B. sacra. The results showed that phytohormonal contents varied significantly, showing a trend of SA>GA/IAA>kinetin across different populations. SA and GA contents were significantly higher in Pop13 (Hasik), followed by Pop2 (Dowkah)-an extreme end of B. sacra tree cover in Dhofar region. A similar trend in the concentration of phytohormones was found when the samples from 13 populations were subjected to advance liquid chromatography mass spectrophotometer and gas chromatograph with selected ion monitor analysis. The current analysis provides alternative tool to assess plant health, which could be important to in situ propagation of tree population as well as monitoring tree population growth dynamics.
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Affiliation(s)
- Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Fazal Mabood
- Department of Biological Sciences & Chemistry, University of Nizwa, Nizwa, Oman
| | - Fazal Akber
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Amjad Ali
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Rawahi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | | | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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27
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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28
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Krishnadas M, Bagchi R, Sridhara S, Comita LS. Weaker plant-enemy interactions decrease tree seedling diversity with edge-effects in a fragmented tropical forest. Nat Commun 2018; 9:4523. [PMID: 30375390 PMCID: PMC6207651 DOI: 10.1038/s41467-018-06997-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/05/2018] [Indexed: 11/17/2022] Open
Abstract
In fragmented forests, tree diversity declines near edges but the ecological processes underlying this loss of diversity remain poorly understood. Theory predicts that top-down regulation of seedling recruitment by insect herbivores and fungal pathogens contributes to maintaining tree diversity in forests, but it is unknown whether proximity to forest edges compromises these diversity-enhancing biotic interactions. Here we experimentally demonstrate that weakened activity of fungal pathogens and insect herbivores reduced seedling diversity, despite similar diversity of seed rain, during recruitment near forest edges in a human-modified tropical landscape. Only at sites farthest from forest edges (90-100 m) did the application of pesticides lower seedling diversity relative to control plots. Notably, lower seedling diversity corresponded with weaker density-dependent mortality attributable to insects and fungi during the seed-to-seedling transition. We provide mechanistic evidence that edge-effects can manifest as cryptic losses of crucial biotic interactions that maintain diversity.
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Affiliation(s)
- Meghna Krishnadas
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA.
| | - Robert Bagchi
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75N. Eagleville Road, Storrs, CT, 06269, USA
| | - Sachin Sridhara
- National Center for Biological Sciences, GKVK Campus, Bellary Road, Bangalore, Karnataka, 560096, India
| | - Liza S Comita
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA
- Smithsonian Tropical Research Institute, Box, 0843-03092, Balboa, Ancón, Panama
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29
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Stump SM, Comita LS. Interspecific variation in conspecific negative density dependence can make species less likely to coexist. Ecol Lett 2018; 21:1541-1551. [PMID: 30129216 DOI: 10.1111/ele.13135] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/05/2018] [Accepted: 07/15/2018] [Indexed: 01/19/2023]
Abstract
Conspecific negative density dependence (CNDD) is thought to promote plant species diversity. Theoretical studies showing the importance of CNDD often assumed that all species are equally susceptible to CNDD; however, recent empirical studies have shown species can differ greatly in their susceptibility to CNDD. Using a theoretical model, we show that interspecific variation in CNDD can dramatically alter its impact on diversity. First, if the most common species are the least regulated by CNDD, then the stabilising benefit of CNDD is reduced. Second, when seed dispersal is limited, seedlings that are susceptible to CNDD are at a competitive disadvantage. When parameterised with estimates of CNDD from a tropical tree community in Panama, our model suggests that the competitive inequalities caused by interspecific variation in CNDD may undermine many species' ability to persist. Thus, our model suggests that variable CNDD may make communities less stable, rather than more stable.
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Affiliation(s)
- Simon Maccracken Stump
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA
| | - Liza S Comita
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA.,Smithsonian Tropical Research Institute Balboa, Ancón, Panama
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30
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Browne L, Karubian J. Rare genotype advantage promotes survival and genetic diversity of a tropical palm. THE NEW PHYTOLOGIST 2018; 218:1658-1667. [PMID: 29603256 DOI: 10.1111/nph.15107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
Negative density dependence, where survival decreases as density increases, is a well-established driver of species diversity at the community level, but the degree to which a similar process might act on the density or frequency of genotypes within a single plant species to maintain genetic diversity has not been well studied in natural systems. In this study, we determined the maternal genotype of naturally dispersed seeds of the palm Oenocarpus bataua within a tropical forest in northwest Ecuador, tracked the recruitment of each seed, and assessed the role of individual-level genotypic rarity on survival. We demonstrate that negative frequency-dependent selection within this species conferred a survival advantage to rare maternal genotypes and promoted population-level genetic diversity. The strength of the observed rare genotype survival advantage was comparable to the effect of conspecific density regardless of genotype. These findings corroborate an earlier, experimental study and implicate negative frequency-dependent selection of genotypes as an important, but currently underappreciated, determinant of plant recruitment and within-species genetic diversity. Incorporating intraspecific genetic variation into studies and theory of forest dynamics may improve our ability to understand and manage forests, and the processes that maintain their diversity.
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Affiliation(s)
- Luke Browne
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs, New Orleans, LA, 70118, USA
- Foundation for the Conservation of the Tropical Andes, Quito, Ecuador
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs, New Orleans, LA, 70118, USA
- Foundation for the Conservation of the Tropical Andes, Quito, Ecuador
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31
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Schroeder JW, Martin JT, Angulo DF, Barbosa JM, Perea R, Arias-Del Razo I, Sebastián-González E, Dirzo R. Community composition and diversity of Neotropical root-associated fungi in common and rare trees. Biotropica 2018. [DOI: 10.1111/btp.12553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- John W. Schroeder
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
| | - Jessica T. Martin
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
| | - Diego F. Angulo
- Red de Biología Evolutiva; Instituto de Ecología AC; Carretera antigua a Coatepec 351 91070 Xalapa Veracruz Mexico
- Departamento de Ecología Tropical; Campus de Ciencias Biológicas y Agropecuarias; Universidad Autónoma de Yucatán; Apartado Postal 4-116, Itzimná 97000 Mérida Yucatán México
| | - Jomar M. Barbosa
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
- Department of Applied Biology; Universidad Miguel Hernández; Avda Universidad s/n Elche Alicante Spain
| | - Ramón Perea
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
- Departmento de Sistemas y Recursos Naturales; Universidad Politécnica de Madrid; Ciudad Universitaria s/n Madrid Spain
| | - Itzel Arias-Del Razo
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
- Centro Tlaxcala de Biología de la Conducta; Universidad Autónoma de Tlaxcala; Carretera Tlaxcala -Puebla Km 1.5 s/n, CP 90062 Tlaxcala Tlaxcala México
| | - Esther Sebastián-González
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
- Department of Applied Biology; Universidad Miguel Hernández; Avda Universidad s/n Elche Alicante Spain
| | - Rodolfo Dirzo
- Department of Biology; Stanford University; 385 Serra Mall Stanford CA 94305 USA
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32
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Zhu Y, Queenborough SA, Condit R, Hubbell SP, Ma KP, Comita LS. Density‐dependent survival varies with species life‐history strategy in a tropical forest. Ecol Lett 2018; 21:506-515. [DOI: 10.1111/ele.12915] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/03/2017] [Accepted: 01/03/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Y. Zhu
- School of Forestry and Environmental Studies Yale University New Haven CT06511 USA
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences 20 Nanxincun, Xiangshan Beijing100093 China
| | - S. A. Queenborough
- School of Forestry and Environmental Studies Yale University New Haven CT06511 USA
| | - R. Condit
- Morton Arboretum 4100 Illinois Rte. 53 Lisle IL60532 USA
- Field Museum of Natural History 1400 S. Lake Shore Dr. Chicago IL60605USA
| | - S. P. Hubbell
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA90095 USA
- Smithsonian Tropical Research Institute Box 0843‐03092 Balboa Ancón Panama
| | - K. P. Ma
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences 20 Nanxincun, Xiangshan Beijing100093 China
| | - L. S. Comita
- School of Forestry and Environmental Studies Yale University New Haven CT06511 USA
- Smithsonian Tropical Research Institute Box 0843‐03092 Balboa Ancón Panama
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33
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LaManna JA, Mangan SA, Alonso A, Bourg NA, Brockelman WY, Bunyavejchewin S, Chang LW, Chiang JM, Chuyong GB, Clay K, Condit R, Cordell S, Davies SJ, Furniss TJ, Giardina CP, Gunatilleke IAUN, Gunatilleke CVS, He F, Howe RW, Hubbell SP, Hsieh CF, Inman-Narahari FM, Janík D, Johnson DJ, Kenfack D, Korte L, Král K, Larson AJ, Lutz JA, McMahon SM, McShea WJ, Memiaghe HR, Nathalang A, Novotny V, Ong PS, Orwig DA, Ostertag R, Parker GG, Phillips RP, Sack L, Sun IF, Tello JS, Thomas DW, Turner BL, Vela Díaz DM, Vrška T, Weiblen GD, Wolf A, Yap S, Myers JA. Plant diversity increases with the strength of negative density dependence at the global scale. Science 2018; 356:1389-1392. [PMID: 28663501 DOI: 10.1126/science.aam5678] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/14/2017] [Accepted: 05/16/2017] [Indexed: 01/24/2023]
Abstract
Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only stronger CNDD at tropical versus temperate latitudes but also a latitudinal shift in the relationship between CNDD and species abundance. CNDD was stronger for rare species at tropical versus temperate latitudes, potentially causing the persistence of greater numbers of rare species in the tropics. Our study reveals fundamental differences in the nature of local-scale biotic interactions that contribute to the maintenance of species diversity across temperate and tropical communities.
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Affiliation(s)
- Joseph A LaManna
- Tyson Research Center, Washington University in St. Louis, St. Louis, MO, USA. .,Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Scott A Mangan
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Alfonso Alonso
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Norman A Bourg
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, USA.,National Research Program - Eastern Branch, U.S. Geological Survey, Reston, VA, USA
| | - Warren Y Brockelman
- Ecology Laboratory, BIOTEC, National Science and Technology Development Agency, Science Park, Pathum Thani, Thailand.,Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Sarayudh Bunyavejchewin
- Research Office, Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - Li-Wan Chang
- Taiwan Forestry Research Institute, Taipei 10066, Taiwan
| | - Jyh-Min Chiang
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - George B Chuyong
- Department of Botany and Plant Physiology, University of Buea, Buea, Cameroon
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Richard Condit
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Susan Cordell
- Institute of Pacific Islands Forestry, U.S. Department of Agriculture Forest Service, Hilo, HI, USA
| | - Stuart J Davies
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Republic of Panama.,Department of Botany, National Museum of Natural History, Washington, DC, USA
| | - Tucker J Furniss
- Wildland Resources Department, Utah State University, Logan, UT, USA
| | - Christian P Giardina
- Institute of Pacific Islands Forestry, U.S. Department of Agriculture Forest Service, Hilo, HI, USA
| | | | | | - Fangliang He
- Joint Lab for Biodiversity Conservation, Sun Yat-sen University (SYSU)-University of Alberta, State Key Laboratory of Biocontrol, School of Life Sciences, SYSU, Guangzhou 510275, China.,Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Robert W Howe
- Department of Natural and Applied Sciences, University of Wisconsin-Green Bay, Green Bay, WI, USA
| | - Stephen P Hubbell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chang-Fu Hsieh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Faith M Inman-Narahari
- Institute of Pacific Islands Forestry, U.S. Department of Agriculture Forest Service, Hilo, HI, USA
| | - David Janík
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | | | - David Kenfack
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Republic of Panama.,Department of Botany, National Museum of Natural History, Washington, DC, USA
| | - Lisa Korte
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Kamil Král
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | - Andrew J Larson
- Department of Forest Management, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - James A Lutz
- Wildland Resources Department, Utah State University, Logan, UT, USA
| | - Sean M McMahon
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Environmental Research Center, Edgewater, MD, USA.,Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - William J McShea
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, USA
| | - Hervé R Memiaghe
- Institut de Recherche en Ecologie Tropicale, Centre National de la Recherche Scientifique et Technologique, Libreville, Gabon
| | - Anuttara Nathalang
- Ecology Laboratory, BIOTEC, National Science and Technology Development Agency, Science Park, Pathum Thani, Thailand
| | - Vojtech Novotny
- New Guinea Binatang Research Centre, P.O. Box 604, Madang, Papua New Guinea.,Biology Centre, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 31, Ceske Budejovice 370 05, Czech Republic
| | - Perry S Ong
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines
| | - David A Orwig
- Harvard Forest, Harvard University, Petersham, MA, USA
| | | | - Geoffrey G Parker
- Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | | | - Lawren Sack
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - I-Fang Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualian, Taiwan
| | - J Sebastián Tello
- Center for Conservation and Sustainable Development, Missouri Botanical Gardens, St. Louis, MO, USA
| | - Duncan W Thomas
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Dilys M Vela Díaz
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Tomáš Vrška
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | - George D Weiblen
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Amy Wolf
- Department of Natural and Applied Sciences, University of Wisconsin-Green Bay, Green Bay, WI, USA.,Department of Biology, University of Wisconsin-Green Bay, Green Bay, WI, USA
| | - Sandra Yap
- Institute of Arts and Sciences, Far Eastern University Manila, Manila, Philippines
| | - Jonathan A Myers
- Tyson Research Center, Washington University in St. Louis, St. Louis, MO, USA.,Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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Murphy SJ, Wiegand T, Comita LS. Distance-dependent seedling mortality and long-term spacing dynamics in a neotropical forest community. Ecol Lett 2017; 20:1469-1478. [PMID: 28980377 DOI: 10.1111/ele.12856] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/17/2017] [Accepted: 09/01/2017] [Indexed: 01/25/2023]
Abstract
Negative distance dependence (NDisD), or reduced recruitment near adult conspecifics, is thought to explain the astounding diversity of tropical forests. While many studies show greater mortality at near vs. far distances from adults, these studies do not seek to track changes in the peak seedling curve over time, thus limiting our ability to link NDisD to coexistence. Using census data collected over 12 years from central Panama in conjunction with spatial mark-connection functions, we show evidence for NDisD for many species, and find that the peak seedling curve shifts away from conspecific adults over time. We find wide variation in the strength of NDisD, which was correlated with seed size and canopy position, but other life-history traits showed no relationship with variation in NDisD mortality. Our results document shifts in peak seedling densities over time, thus providing evidence for the hypothesized spacing mechanism necessary for diversity maintenance in tropical forests.
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Affiliation(s)
- Stephen J Murphy
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210-1293, USA.,School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA
| | - Thorsten Wiegand
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Liza S Comita
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA.,Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Panama
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