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Simon SJ, Furches A, Chhetri H, Evans L, Abeyratne CR, Jones P, Wimp G, Macaya-Sanz D, Jacobson D, Tschaplinski TJ, Tuskan GA, DiFazio SP. Genetic underpinnings of arthropod community distributions in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 242:1307-1323. [PMID: 38488269 DOI: 10.1111/nph.19660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.
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Affiliation(s)
- Sandra J Simon
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Anna Furches
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hari Chhetri
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
- Computational Systems Biology Group, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Luke Evans
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, 80309, USA
| | | | - Piet Jones
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Gina Wimp
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Daniel Jacobson
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Timothy J Tschaplinski
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
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2
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Yamamichi M. How does genetic architecture affect eco-evolutionary dynamics? A theoretical perspective. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200504. [PMID: 35634922 PMCID: PMC9149794 DOI: 10.1098/rstb.2020.0504] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies have revealed the importance of feedbacks between contemporary rapid evolution (i.e. evolution that occurs through changes in allele frequencies) and ecological dynamics. Despite its inherent interdisciplinary nature, however, studies on eco-evolutionary feedbacks have been mostly ecological and tended to focus on adaptation at the phenotypic level without considering the genetic architecture of evolutionary processes. In empirical studies, researchers have often compared ecological dynamics when the focal species under selection has a single genotype with dynamics when it has multiple genotypes. In theoretical studies, common approaches are models of quantitative traits where mean trait values change adaptively along the fitness gradient and Mendelian traits with two alleles at a single locus. On the other hand, it is well known that genetic architecture can affect short-term evolutionary dynamics in population genetics. Indeed, recent theoretical studies have demonstrated that genetic architecture (e.g. the number of loci, linkage disequilibrium and ploidy) matters in eco-evolutionary dynamics (e.g. evolutionary rescue where rapid evolution prevents extinction and population cycles driven by (co)evolution). I propose that theoretical approaches will promote the synthesis of functional genomics and eco-evolutionary dynamics through models that combine population genetics and ecology as well as nonlinear time-series analyses using emerging big data.
This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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3
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Little CJ, Rizzuto M, Luhring TM, Monk JD, Nowicki RJ, Paseka RE, Stegen JC, Symons CC, Taub FB, Yen JDL. Movement with meaning: integrating information into meta‐ecology. OIKOS 2022. [DOI: 10.1111/oik.08892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chelsea J. Little
- Biodiversity Research Centre, Univ. of British Columbia Vancouver BC Canada
- School of Environmental Science, Simon Fraser Univ. Burnaby BC Canada
| | - Matteo Rizzuto
- Dept of Biology, Memorial Univ. of Newfoundland St. John's NL Canada
| | | | - Julia D. Monk
- School of the Environment, Yale Univ. New Haven CT USA
| | - Robert J. Nowicki
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory Summerland Key FL USA
| | - Rachel E. Paseka
- Dept of Ecology, Evolution and Behavior, Univ. of Minnesota Saint Paul MN USA
| | | | - Celia C. Symons
- Dept of Ecology and Evolutionary Biology, Univ. of California Irvine CA USA
| | - Frieda B. Taub
- School of Aquatic and Fishery Sciences, Univ. of Washington Seattle WA USA
| | - Jian D. L. Yen
- School of BioSciences, Univ. of Melbourne, Melbourne, Australia, and Arthur Rylah Inst. for Environmental Reserach Heidelberg Victoria Australia
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4
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Rubio‐Ríos J, Pérez J, Salinas MJ, Fenoy E, Boyero L, Casas JJ. Climate‐induced plasticity in leaf traits of riparian plants. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Juan Rubio‐Ríos
- Department of Biology and Geology University of Almeria (UAL) Almería Spain
- Andalusian Centre for the Evaluation and Monitoring of Global Change CAESCG Almería Spain
| | - Javier Pérez
- Department of Plant Biology and Ecology University of the Basque Country (UPV/EHU) Leioa Spain
| | - María J. Salinas
- Department of Biology and Geology University of Almeria (UAL) Almería Spain
- Andalusian Centre for the Evaluation and Monitoring of Global Change CAESCG Almería Spain
| | - Encarnación Fenoy
- Department of Biology and Geology University of Almeria (UAL) Almería Spain
- Andalusian Centre for the Evaluation and Monitoring of Global Change CAESCG Almería Spain
| | - Luz Boyero
- Department of Plant Biology and Ecology University of the Basque Country (UPV/EHU) Leioa Spain
| | - José Jesús Casas
- Department of Biology and Geology University of Almeria (UAL) Almería Spain
- Andalusian Centre for the Evaluation and Monitoring of Global Change CAESCG Almería Spain
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5
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Stange M, Barrett RDH, Hendry AP. The importance of genomic variation for biodiversity, ecosystems and people. Nat Rev Genet 2020; 22:89-105. [PMID: 33067582 DOI: 10.1038/s41576-020-00288-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 11/09/2022]
Abstract
The 2019 United Nations Global assessment report on biodiversity and ecosystem services estimated that approximately 1 million species are at risk of extinction. This primarily human-driven loss of biodiversity has unprecedented negative consequences for ecosystems and people. Classic and emerging approaches in genetics and genomics have the potential to dramatically improve these outcomes. In particular, the study of interactions among genetic loci within and between species will play a critical role in understanding the adaptive potential of species and communities, and hence their direct and indirect effects on biodiversity, ecosystems and people. We explore these population and community genomic contexts in the hope of finding solutions for maintaining and improving ecosystem services and nature's contributions to people.
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Affiliation(s)
- Madlen Stange
- Redpath Museum, McGill University, Montreal, QC, Canada
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6
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Simon SJ, Tschaplinski TJ, M. LeBoldus J, Keefover‐Ring K, Azeem M, Chen J, Macaya‐Sanz D, MacDonald WL, Muchero W, DiFazio SP. Host plant genetic control of associated fungal and insect species in a Populus hybrid cross. Ecol Evol 2020; 10:5119-5134. [PMID: 32551087 PMCID: PMC7297788 DOI: 10.1002/ece3.6266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 11/10/2022] Open
Abstract
Plants employ a diverse set of defense mechanisms to mediate interactions with insects and fungi. These relationships can leave lasting impacts on host plant genome structure such as rapid expansion of gene families through tandem duplication. These genomic signatures provide important clues about the complexities of plant/biotic stress interactions and evolution. We used a pseudo-backcross hybrid family to identify quantitative trait loci (QTL) controlling associations between Populus trees and several common Populus diseases and insects. Using whole-genome sequences from each parent, we identified candidate genes that may mediate these interactions. Candidates were partially validated using mass spectrometry to identify corresponding QTL for defensive compounds. We detected significant QTL for two interacting fungal pathogens and three insects. The QTL intervals contained candidate genes potentially involved in physical and chemical mechanisms of host-plant resistance and susceptibility. In particular, we identified adjoining QTLs for a phenolic glycoside and Phyllocolpa sawfly abundance. There was also significant enrichment of recent tandem duplications in the genomic intervals of the native parent, but not the exotic parent. Tandem gene duplication may be an important mechanism for rapid response to biotic stressors, enabling trees with long juvenile periods to reach maturity despite many coevolving biotic stressors.
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Affiliation(s)
- Sandra J. Simon
- Department of BiologyWest Virginia UniversityMorgantownWest Virginia
| | - Timothy J. Tschaplinski
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Jared M. LeBoldus
- Forest Engineering, Resources & ManagementOregon State UniversityCorvallisOregon
- Botany and Plant PathologyOregon State UniversityCorvallisOregon
| | - Ken Keefover‐Ring
- Department of BotanyUniversity of Wisconsin-MadisonMadisonWisconsin
- Department of GeographyUniversity of WisconsinMadisonWisconsin
| | - Muhammad Azeem
- Department of BotanyUniversity of Wisconsin-MadisonMadisonWisconsin
- Department of GeographyUniversity of WisconsinMadisonWisconsin
- Department of ChemistryCOMSATS University IslamabadAbbottabadPakistan
| | - Jin‐Gui Chen
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - David Macaya‐Sanz
- Department of BiologyWest Virginia UniversityMorgantownWest Virginia
| | - William L. MacDonald
- Division of Plant and Soil SciencesWest Virginia UniversityMorgantownWest Virginia
| | - Wellington Muchero
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
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7
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Lemmen KD, Butler OM, Koffel T, Rudman SM, Symons CC. Stoichiometric Traits Vary Widely Within Species: A Meta-Analysis of Common Garden Experiments. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00339] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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8
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Busby PE, Crutsinger G, Barbour M, Newcombe G. Contingency rules for pathogen competition and antagonism in a genetically based, plant defense hierarchy. Ecol Evol 2019; 9:6860-6868. [PMID: 31380021 PMCID: PMC6662256 DOI: 10.1002/ece3.5253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/29/2019] [Accepted: 04/06/2019] [Indexed: 01/19/2023] Open
Abstract
Plant defense against pathogens includes a range of mechanisms, including, but not limited to, genetic resistance, pathogen-antagonizing endophytes, and pathogen competitors. The relative importance of each mechanism can be expressed in a hierarchical view of defense. Several recent studies have shown that pathogen antagonism is inconsistently expressed within the plant defense hierarchy. Our hypothesis is that the hierarchy is governed by contingency rules that determine when and where antagonists reduce plant disease severity.Here, we investigated whether pathogen competition influences pathogen antagonism using Populus as a model system. In three independent field experiments, we asked whether competition for leaf mesophyll cells between a Melampsora rust pathogen and a microscopic, eriophyid mite affects rust pathogen antagonism by fungal leaf endophytes. The rust pathogen has an annual, phenological disadvantage in competition with the mite because the rust pathogen must infect its secondary host in spring before infecting Populus. We varied mite-rust competition by utilizing Populus genotypes characterized by differential genetic resistance to the two organisms. We inoculated plants with endophytes and allowed mites and rust to infect plants naturally.Two contingency rules emerged from the three field experiments: (a) Pathogen antagonism by endophytes can be preempted by host genes for resistance that suppress pathogen development, and (b) pathogen antagonism by endophytes can secondarily be preempted by competitive exclusion of the rust by the mite. Synthesis: Our results point to a Populus defense hierarchy with resistance genes on top, followed by pathogen competition, and finally pathogen antagonism by endophytes. We expect these rules will help to explain the variation in pathogen antagonism that is currently attributed to context dependency.
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Affiliation(s)
- Posy E. Busby
- Botany and Plant Pathology DepartmentOregon State UniversityCorvallisOregon
| | - Gregory Crutsinger
- Department of ZoologyUniversity of British ColumbiaVancouverBritish Columbia
| | - Matthew Barbour
- Department of ZoologyUniversity of British ColumbiaVancouverBritish Columbia
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9
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Rudman SM, Goos JM, Burant JB, Brix KV, Gibbons TC, Brauner CJ, Jeyasingh PD. Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback. Ecol Lett 2019; 22:645-653. [DOI: 10.1111/ele.13225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/22/2018] [Accepted: 01/05/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Seth M. Rudman
- Department of Biology University of Pennsylvania Philadelphia PA USA
| | - Jared M. Goos
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
| | - Joseph B. Burant
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Kevin V. Brix
- Department of Marine Biology and Ecology University of Miami RSMAS Miami FL USA
| | - Taylor C. Gibbons
- Department of Zoology University of British Columbia Vancouver BC Canada
| | - Colin J. Brauner
- Department of Zoology University of British Columbia Vancouver BC Canada
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10
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Affiliation(s)
- Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill University Montreal Quebec Canada
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11
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Raffard A, Santoul F, Cucherousset J, Blanchet S. The community and ecosystem consequences of intraspecific diversity: a meta-analysis. Biol Rev Camb Philos Soc 2018; 94:648-661. [PMID: 30294844 DOI: 10.1111/brv.12472] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
Understanding the relationships between biodiversity and ecosystem functioning has major implications. Biodiversity-ecosystem functioning relationships are generally investigated at the interspecific level, although intraspecific diversity (i.e. within-species diversity) is increasingly perceived as an important ecological facet of biodiversity. Here, we provide a quantitative and integrative synthesis testing, across diverse plant and animal species, whether intraspecific diversity is a major driver of community dynamics and ecosystem functioning. We specifically tested (i) whether the number of genotypes/phenotypes (i.e. intraspecific richness) or the specific identity of genotypes/phenotypes (i.e. intraspecific variation) in populations modulate the structure of communities and the functioning of ecosystems, (ii) whether the ecological effects of intraspecific richness and variation are strong in magnitude, and (iii) whether these effects vary among taxonomic groups and ecological responses. We found a non-linear relationship between intraspecific richness and community and ecosystem dynamics that follows a saturating curve shape, as observed for biodiversity-function relationships measured at the interspecific level. Importantly, intraspecific richness modulated ecological dynamics with a magnitude that was equal to that previously reported for interspecific richness. Our results further confirm, based on a database containing more than 50 species, that intraspecific variation also has substantial effects on ecological dynamics. We demonstrated that the effects of intraspecific variation are twice as high as expected by chance, and that they might have been underestimated previously. Finally, we found that the ecological effects of intraspecific variation are not homogeneous and are actually stronger when intraspecific variation is manipulated in primary producers than in consumer species, and when they are measured at the ecosystem rather than at the community level. Overall, we demonstrated that the two facets of intraspecific diversity (richness and variation) can both strongly affect community and ecosystem dynamics, which reveals the pivotal role of within-species biodiversity for understanding ecological dynamics.
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Affiliation(s)
- Allan Raffard
- CNRS, Station d'Écologie Théorique et Expérimentale du CNRS à Moulis UMR-5321, Université Toulouse III Paul Sabatier, 2 route du CNRS, F-09200, Moulis, France.,EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062 Toulouse, France
| | - Frédéric Santoul
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, 31062 Toulouse, France
| | - Julien Cucherousset
- CNRS, IRD, UPS, Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse, 118 route de Narbonne, Toulouse 31062, France
| | - Simon Blanchet
- CNRS, Station d'Écologie Théorique et Expérimentale du CNRS à Moulis UMR-5321, Université Toulouse III Paul Sabatier, 2 route du CNRS, F-09200, Moulis, France.,CNRS, IRD, UPS, Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse, 118 route de Narbonne, Toulouse 31062, France
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12
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Priming of leaf litter decomposition by algae seems of minor importance in natural streams during autumn. PLoS One 2018; 13:e0200180. [PMID: 30192753 PMCID: PMC6128472 DOI: 10.1371/journal.pone.0200180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Allochthonous detritus of terrestrial origin is one of the main energy sources in forested headwater streams, but its poor nutritional quality makes it difficult to use by heterotrophs. It has been suggested that algae growing on this detritus can enhance its nutritional quality and promote decomposition. So far, most evidence of this "priming effect” is derived from laboratory or mesocosm experiments, and its importance under natural conditions is unclear. We measured accrual of algae, phosphorus uptake capacity, and decomposition of poplar leaves in autumn in open- and closed-canopy reaches in 3 forest and 3 agricultural streams. Chlorophyll a abundance did not change significantly with stream type or with canopy cover, although in some agricultural streams it was higher in open than in closed canopy reaches. Canopy cover did not affect either phosphate uptake capacity or microbial decomposition. On the other hand, although there was no effect of canopy cover on invertebrate fragmentation rate, a significant interaction between canopy cover and stream suggests priming occurs at least in some streams. Overall, the results point to a weak or no priming effect of algae on litter decomposition in natural streams during autumn.
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13
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Abstract
The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.
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14
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Compson ZG, Hungate BA, Whitham TG, Koch GW, Dijkstra P, Siders AC, Wojtowicz T, Jacobs R, Rakestraw DN, Allred KE, Sayer CK, Marks JC. Linking tree genetics and stream consumers: isotopic tracers elucidate controls on carbon and nitrogen assimilation. Ecology 2018; 99:1759-1770. [DOI: 10.1002/ecy.2224] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Zacchaeus G. Compson
- Center for Ecosystem Science and Society; 800 S. Beaver Street, P.O. Box 5620 Flagstaff Arizona 86011-5620 USA
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society; 800 S. Beaver Street, P.O. Box 5620 Flagstaff Arizona 86011-5620 USA
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Thomas G. Whitham
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - George W. Koch
- Center for Ecosystem Science and Society; 800 S. Beaver Street, P.O. Box 5620 Flagstaff Arizona 86011-5620 USA
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society; 800 S. Beaver Street, P.O. Box 5620 Flagstaff Arizona 86011-5620 USA
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Adam C. Siders
- Center for Ecosystem Science and Society; 800 S. Beaver Street, P.O. Box 5620 Flagstaff Arizona 86011-5620 USA
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Todd Wojtowicz
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Ryan Jacobs
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - David N. Rakestraw
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Kiel E. Allred
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Chelsea K. Sayer
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
| | - Jane C. Marks
- Center for Ecosystem Science and Society; 800 S. Beaver Street, P.O. Box 5620 Flagstaff Arizona 86011-5620 USA
- Merriam-Powell Center for Environmental Research; 800 S. Beaver Street, P.O. Box 6077 Flagstaff Arizona 86011-6077 USA
- Department of Biological Sciences; Northern Arizona University; 617 S. Beaver Street, P.O. Box 5640 Flagstaff Arizona 86011-5640 USA
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15
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Matthews B, Best RJ, Feulner PGD, Narwani A, Limberger R. Evolution as an ecosystem process: insights from genomics. Genome 2017; 61:298-309. [PMID: 29241022 DOI: 10.1139/gen-2017-0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.
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Affiliation(s)
- Blake Matthews
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Rebecca J Best
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,b School of Earth Sciences and Environmental Sustainability, Northern Arizona University, 525 S. Beaver Street, Flagstaff, AZ 86011, USA
| | - Philine G D Feulner
- c Eawag, Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,d University of Bern, Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, Bern, Switzerland
| | - Anita Narwani
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Romana Limberger
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,e Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
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16
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Rudman SM, Barbour MA, Csilléry K, Gienapp P, Guillaume F, Hairston Jr NG, Hendry AP, Lasky JR, Rafajlović M, Räsänen K, Schmidt PS, Seehausen O, Therkildsen NO, Turcotte MM, Levine JM. What genomic data can reveal about eco-evolutionary dynamics. Nat Ecol Evol 2017; 2:9-15. [DOI: 10.1038/s41559-017-0385-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/16/2017] [Indexed: 01/17/2023]
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17
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Slinn HL, Barbour MA, Crawford KM, Rodriguez-Cabal MA, Crutsinger GM. Genetic variation in resistance to leaf fungus indirectly affects spider density. Ecology 2017; 98:875-881. [DOI: 10.1002/ecy.1708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Heather L. Slinn
- Department of Biology; University of Nevada; 1664 N Virginia street Reno Nevada 89557 USA
| | - Matthew A. Barbour
- Department of Zoology; University of British Columbia; Vancouver British Columbia V6T 1Z4 Canada
| | - Kerri M. Crawford
- Department of Biology and Biochemistry; University of Houston; Houston Texas 77204 USA
| | - Mariano A. Rodriguez-Cabal
- Grupo de Ecologia de Invasiones; INIBIOMA - CONICET; Universidad Nacional del Comahue; CP. 8400 San Carlos de Bariloche Argentina
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18
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Farkas TE, Mononen T, Comeault AA, Nosil P. Observational evidence that maladaptive gene flow reduces patch occupancy in a wild insect metapopulation. Evolution 2016; 70:2879-2888. [PMID: 27683197 DOI: 10.1111/evo.13076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 08/25/2016] [Accepted: 09/11/2016] [Indexed: 01/27/2023]
Abstract
Theory predicts that dispersal throughout metapopulations has a variety of consequences for the abundance and distribution of species. Immigration is predicted to increase abundance and habitat patch occupancy, but gene flow can have both positive and negative demographic consequences. Here, we address the eco-evolutionary effects of dispersal in a wild metapopulation of the stick insect Timema cristinae, which exhibits variable degrees of local adaptation throughout a heterogeneous habitat patch network of two host-plant species. To disentangle the ecological and evolutionary contributions of dispersal to habitat patch occupancy and abundance, we contrasted the effects of connectivity to populations inhabiting conspecific host plants and those inhabiting the alternate host plant. Both types of connectivity should increase patch occupancy and abundance through increased immigration and sharing of beneficial alleles through gene flow. However, connectivity to populations inhabiting the alternate host-plant species may uniquely cause maladaptive gene flow that counters the positive demographic effects of immigration. Supporting these predictions, we find the relationship between patch occupancy and alternate-host connectivity to be significantly smaller in slope than the relationship between patch occupancy and conspecific-host connectivity. Our findings illustrate the ecological and evolutionary roles of dispersal in driving the distribution and abundance of species.
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Affiliation(s)
- Timothy E Farkas
- Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269
| | - Tommi Mononen
- Metapopulation Research Centre, Biosciences, University of Helsinki, Helsinki, 00014, Finland.,Neuroscience and Biomedical Engineering, Aalto University, Aalto, FI-00076, Finland
| | - Aaron A Comeault
- Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Department of Biology, University of North Carolina, Durham, North Carolina, 27599
| | - Patrik Nosil
- Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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19
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Rudman SM, Rodriguez-Cabal MA, Stier A, Sato T, Heavyside J, El-Sabaawi RW, Crutsinger GM. Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem. Proc Biol Sci 2016. [PMID: 26203004 DOI: 10.1098/rspb.2015.1234] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns.
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Affiliation(s)
- Seth M Rudman
- Department of Zoology, University of British Columbia, 4200-6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4
| | - Mariano A Rodriguez-Cabal
- Department of Zoology, University of British Columbia, 4200-6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4 Grupo de Ecologia de Invasiones, INIBIOMA-CONICET, Universidad Nacional del Comahue-Av. De los Pioneros, Bariloche Rio Negro, CP 8400, Argentina
| | - Adrian Stier
- Department of Zoology, University of British Columbia, 4200-6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4 National Center for Ecological Analysis and Synthesis, 735 State Street, Santa Barbara, CA 93101, USA
| | - Takuya Sato
- Department of Biology, Graduate school of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Julian Heavyside
- Department of Zoology, University of British Columbia, 4200-6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4
| | - Rana W El-Sabaawi
- Department of Biology, University of Victoria, Cunningham 202, 3800 Finnerty Road, Victoria, BC, Canada V8P 5C2
| | - Gregory M Crutsinger
- Department of Zoology, University of British Columbia, 4200-6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4
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20
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Crutsinger GM. A community genetics perspective: opportunities for the coming decade. THE NEW PHYTOLOGIST 2016; 210:65-70. [PMID: 26171846 DOI: 10.1111/nph.13537] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
Community genetics was originally proposed as a novel approach to identifying links between genes and ecosystems, and merging ecological and evolutional perspectives. The dozen years since the birth of community genetics have seen many empirical studies and common garden experiments, as well as the rise of eco-evolutionary dynamics research and a general shift in ecology to incorporate intraspecific variation. So what have we learned from community genetics? Can individual genes affect entire ecosystems? Are there interesting questions left to be answered, or has community genetics run its course? This perspective makes a series of key points about the general patterns that have emerged and calls attention to gaps in our understanding to be addressed in the coming years.
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Affiliation(s)
- Gregory M Crutsinger
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, V6T1Z4, Canada
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21
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Kinnison MT, Hairston NG, Hendry AP. Cryptic eco-evolutionary dynamics. Ann N Y Acad Sci 2016; 1360:120-44. [PMID: 26619300 DOI: 10.1111/nyas.12974] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 12/17/2022]
Abstract
Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.
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Affiliation(s)
| | - Nelson G Hairston
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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