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Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. J Biogeogr 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
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Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
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2
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McLaughlin CM, Li M, Perryman M, Heymans A, Schneider H, Lasky JR, Sawers RJH. Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize. Evol Appl 2024; 17:e13673. [PMID: 38468714 PMCID: PMC10925829 DOI: 10.1111/eva.13673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
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Affiliation(s)
- Chloee M. McLaughlin
- Intercollege Graduate Degree Program in Plant BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Meng Li
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Melanie Perryman
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Adrien Heymans
- Umeå Plant Science Centre, Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
- Earth and Life InstituteUC LouvainLouvain‐la‐NeuveBelgium
| | - Hannah Schneider
- Department of Physiology and Cell BiologyLeibniz Institute for Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jesse R. Lasky
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Ruairidh J. H. Sawers
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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3
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Lawrence-Paul EH, Lasky JR. Ontogenetic changes in ecophysiology are an understudied yet important component of plant adaptation. Am J Bot 2024; 111:e16294. [PMID: 38384001 DOI: 10.1002/ajb2.16294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/23/2024]
Affiliation(s)
- Erica H Lawrence-Paul
- Pennsylvania State University, Department of Biology, University Park, Pennsylvania, 16802, USA
| | - Jesse R Lasky
- Pennsylvania State University, Department of Biology, University Park, Pennsylvania, 16802, USA
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4
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Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky JR, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo VL, Lucas SM, Lazic D, Gailing O, Carlson J, Staton M. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (Bethesda) 2023; 13:jkad209. [PMID: 37708394 PMCID: PMC10627279 DOI: 10.1093/g3journal/jkad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.
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Affiliation(s)
- Beant Kapoor
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Tatyana Zhebentyayeva
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40506, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Kuelheim
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, MI 49931, USA
| | - Mark Coggeshall
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chris Heim
- Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Leites
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, USDA-FS, SRS-4160, Department of Ecology & Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Victoria L DeLeo
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Lucas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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5
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Lawrence-Paul EH, Poethig RS, Lasky JR. Vegetative phase change causes age-dependent changes in phenotypic plasticity. New Phytol 2023; 240:613-625. [PMID: 37571856 PMCID: PMC10551844 DOI: 10.1111/nph.19174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Phenotypic plasticity allows organisms to optimize traits for their environment. As organisms age, they experience diverse environments that benefit from varying degrees of phenotypic plasticity. Developmental transitions can control these age-dependent changes in plasticity, and as such, the timing of these transitions can determine when plasticity changes in an organism. Here, we investigate how the transition from juvenile-to adult-vegetative development known as vegetative phase change (VPC) contributes to age-dependent changes in phenotypic plasticity and how the timing of this transition responds to environment using both natural accessions and mutant lines in the model plant Arabidopsis thaliana. We found that the adult phase of vegetative development has greater plasticity in leaf morphology than the juvenile phase and confirmed that this difference in plasticity is caused by VPC using mutant lines. Furthermore, we found that the timing of VPC, and therefore the time when increased plasticity is acquired, varies significantly across genotypes and environments. The consistent age-dependent changes in plasticity caused by VPC suggest that VPC may be adaptive. This genetic and environmental variation in the timing of VPC indicates the potential for population-level adaptive evolution of VPC.
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Affiliation(s)
- Erica H. Lawrence-Paul
- Pennsylvania State University, Department of Biology, University Park, PA 16802
- University of Pennsylvania, Department of Biology, Philadelphia, PA 19104
| | - R. Scott Poethig
- University of Pennsylvania, Department of Biology, Philadelphia, PA 19104
| | - Jesse R. Lasky
- Pennsylvania State University, Department of Biology, University Park, PA 16802
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6
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Pak D, Swamy V, Alvarez-Loayza P, Cornejo-Valverde F, Queenborough SA, Metz MR, Terborgh J, Valencia R, Wright SJ, Garwood NC, Lasky JR. Multiscale phenological niches of seed fall in diverse Amazonian plant communities. Ecology 2023; 104:e4022. [PMID: 36890666 DOI: 10.1002/ecy.4022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 03/10/2023]
Abstract
Phenology has long been hypothesized as an avenue for niche partitioning or interspecific facilitation, both promoting species coexistence. Tropical plant communities exhibit striking diversity in reproductive phenology, but many are also noted for large synchronous reproductive events. Here we study whether the phenology of seed fall in such communities is non-random, what are the temporal scales of phenological patterns, and ecological factors that drive reproductive phenology. We applied multivariate wavelet analyses to test for phenological synchrony versus compensatory dynamics (i.e. anti-synchronous patterns where one species' decline is compensated by the rise of another) among species and across temporal scales. We used data from long-term seed rain monitoring of hyperdiverse plant communities in the western Amazon. We found significant synchronous whole-community phenology at multiple time scales, consistent with shared environmental responses or positive interactions among species. We also observed both compensatory and synchronous phenology within groups of species (confamilials) likely to share traits and seed dispersal mechanisms. Wind-dispersed species exhibited significant synchrony at ~6 mo scales, suggesting these species might share phenological niches to match seasonality of wind. Our results suggest that community phenology is shaped by shared environmental responses but that the diversity of tropical plant phenology may partly result from temporal niche partitioning. The scale-specificity and time-localized nature of community phenology patterns highlights the importance of multiple and shifting drivers of phenology.
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Affiliation(s)
- Damie Pak
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Varun Swamy
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | | | - Margaret R Metz
- Department of Biology, Lewis & Clark College, Portland, OR, USA
| | - John Terborgh
- Center for Tropical Conservation, Nicholas School of the Environment, Duke University, Durham, NC, USA
| | | | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Republic of Panama
| | - Nancy C Garwood
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
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7
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Lasky JR, Josephs EB, Morris GP. Genotype-environment associations to reveal the molecular basis of environmental adaptation. Plant Cell 2023; 35:125-138. [PMID: 36005926 PMCID: PMC9806588 DOI: 10.1093/plcell/koac267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/23/2022] [Indexed: 06/14/2023]
Abstract
A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.
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Affiliation(s)
- Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily B Josephs
- Department of Plant Biology; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Sciences; Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80526, USA
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8
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Sutherland J, Bell T, Trexler RV, Carlson JE, Lasky JR. Host genomic influence on bacterial composition in the switchgrass rhizosphere. Mol Ecol 2022; 31:3934-3950. [PMID: 35621390 PMCID: PMC10150372 DOI: 10.1111/mec.16549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
Abstract
Host genetic variation can shape the diversity and composition of associated microbiomes, which may reciprocally influence host traits and performance. While the genetic basis of phenotypic diversity of plant populations in nature has been studied, comparatively little research has investigated the genetics of host effects on their associated microbiomes. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial, grass species with substantial locally adaptive diversity across its native North American range. Here, we compared 383 switchgrass accessions in a common garden to determine the host genotypic influence on rhizosphere bacterial composition. We hypothesized that the composition and diversity of rhizosphere bacterial assemblages would differentiate due to genotypic differences between hosts (potentially due to root phenotypes and associated life history variation). We observed higher alpha diversity of bacteria associated with upland ecotypes and tetraploids, compared to lowland ecotypes and octoploids, respectively. Alpha diversity correlated negatively with flowering time and plant height, indicating that bacterial composition varies along switchgrass life history axes. Narrow-sense heritability (h2 ) of the relative abundance of twenty-one core bacterial families was observed. Overall compositional differences among tetraploids, due to genetic variation, supports wide-spread genotypic influence on the rhizosphere microbiome. Tetraploids were only considered due to complexities associated with the octoploid genomes. Lastly, a genome-wide association study identified 1,861 single-nucleotide polymorphisms associated with 110 families and genes containing them related to potential regulatory functions. Our findings suggest that switchgrass genomic and life-history variation influences bacterial composition in the rhizosphere, potentially due to host adaptation to local environments.
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Affiliation(s)
- Jeremy Sutherland
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.,Intercollege Graduate Degree Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA, USA.,Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Terrence Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.,Intercollege Graduate Degree Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, USA
| | - Ryan V Trexler
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, USA.,Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, USA
| | - John E Carlson
- Intercollege Graduate Degree Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, PA, USA.,Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, USA
| | - Jesse R Lasky
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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9
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Weeks BC, Naeem S, Lasky JR, Tobias JA. Diversity and extinction risk are inversely related at a global scale. Ecol Lett 2022; 25:697-707. [PMID: 35199919 PMCID: PMC9303290 DOI: 10.1111/ele.13860] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/07/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022]
Abstract
Increases in biodiversity often lead to greater, and less variable, levels of ecosystem functioning. However, whether species are less likely to go extinct in more diverse ecosystems is unclear. We use comprehensive estimates of avian taxonomic, phylogenetic and functional diversity to characterise the global relationship between multiple dimensions of diversity and extinction risk in birds, focusing on contemporary threat status and latent extinction risk. We find that more diverse assemblages have lower mean IUCN threat status despite being composed of species with attributes that make them more vulnerable to extinction, such as large body size or small range size. Indeed, the reduction in current threat status associated with greater diversity far outweighs the increased risk associated with the accumulation of extinction‐prone species in more diverse assemblages. Our results suggest that high diversity reduces extinction risk, and that species conservation targets may therefore best be achieved by maintaining high levels of overall biodiversity in natural ecosystems.
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Affiliation(s)
- Brian C Weeks
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| | - Shahid Naeem
- Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, UK
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10
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Lasky JR, Hooten MB, Adler PB. What processes must we understand to forecast regional-scale population dynamics? Proc Biol Sci 2020; 287:20202219. [PMID: 33290672 PMCID: PMC7739927 DOI: 10.1098/rspb.2020.2219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
An urgent challenge facing biologists is predicting the regional-scale population dynamics of species facing environmental change. Biologists suggest that we must move beyond predictions based on phenomenological models and instead base predictions on underlying processes. For example, population biologists, evolutionary biologists, community ecologists and ecophysiologists all argue that the respective processes they study are essential. Must our models include processes from all of these fields? We argue that answering this critical question is ultimately an empirical exercise requiring a substantial amount of data that have not been integrated for any system to date. To motivate and facilitate the necessary data collection and integration, we first review the potential importance of each mechanism for skilful prediction. We then develop a conceptual framework based on reaction norms, and propose a hierarchical Bayesian statistical framework to integrate processes affecting reaction norms at different scales. The ambitious research programme we advocate is rapidly becoming feasible due to novel collaborations, datasets and analytical tools.
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Affiliation(s)
- Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Mevin B. Hooten
- U.S. Geological Survey, Colorado Cooperative Fish and Wildlife Research Unit, Colorado State University, Fort Collins, CO, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
- Department of Statistics, Colorado State University, Fort Collins, CO, USA
| | - Peter B. Adler
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, UT, USA
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11
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Turner KG, Lorts CM, Haile AT, Lasky JR. Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis. Proc Biol Sci 2020; 287:20202041. [PMID: 33081615 PMCID: PMC7661305 DOI: 10.1098/rspb.2020.2041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
Biodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of Arabidopsis thaliana affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we a priori predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high-resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.
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Affiliation(s)
- Kathryn G. Turner
- Department of Biology, Pennsylvania State University, USA
- Department of Biological Sciences, Idaho State University, USA
| | | | - Asnake T. Haile
- Department of Biology, Pennsylvania State University, USA
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Ethiopia
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, USA
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12
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Lopez L, Turner KG, Bellis ES, Lasky JR. Genomics of natural history collections for understanding evolution in the wild. Mol Ecol Resour 2020; 20:1153-1160. [DOI: 10.1111/1755-0998.13245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Lua Lopez
- Department of Biology California State University San Bernardino San Bernardino CaliforniaUSA
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
| | - Kathryn G. Turner
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
- Department of Biological Sciences Idaho State University Pocatello IdahoUSA
| | - Emily S. Bellis
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
- Arkansas Biosciences Institute & Department of Computer Science Arkansas State University Jonesboro ArkansasUSA
| | - Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
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13
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Lorts CM, Lasky JR. Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits. New Phytol 2020; 227:1060-1072. [PMID: 32267968 DOI: 10.1111/nph.16593] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Populations often exhibit genetic diversity in traits involved in responses to abiotic stressors, but what maintains this diversity is unclear. Arabidopsis thaliana exhibits high within-population variation in drought response. One hypothesis is that competition, varying at small scales, promotes diversity in resource use strategies. However, little is known about natural variation in competition effects on Arabidopsis physiology. We imposed drought and competition treatments on diverse genotypes. We measured resource economics traits, physiology, and fitness to characterize plasticity and selection in response to treatments. Plastic responses to competition differed depending on moisture availability. We observed genotype-drought-competition interactions for relative fitness: competition had little effect on relative fitness under well-watered conditions, whereas competition caused rank changes in fitness under drought. Early flowering was always selected. Higher δ13 C was selected only in the harshest treatment (drought and competition). Competitive context significantly changed the direction of selection on aboveground biomass and inflorescence height in well-watered environments. Our results highlight how local biotic conditions modify abiotic selection, in some cases promoting diversity in abiotic stress response. The ability of populations to adapt to environmental change may thus depend on small-scale biotic heterogeneity.
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Affiliation(s)
- Claire M Lorts
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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14
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Gutaker RM, Groen SC, Bellis ES, Choi JY, Pires IS, Bocinsky RK, Slayton ER, Wilkins O, Castillo CC, Negrão S, Oliveira MM, Fuller DQ, Guedes JAD, Lasky JR, Purugganan MD. Genomic history and ecology of the geographic spread of rice. Nat Plants 2020; 6:492-502. [PMID: 32415291 DOI: 10.1038/s41477-020-0659-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/02/2020] [Indexed: 05/22/2023]
Abstract
Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.
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Affiliation(s)
- Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Emily S Bellis
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Jae Y Choi
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Inês S Pires
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | | | - Emma R Slayton
- Carnegie Mellon University Libraries, Pittsburgh, PA, USA
| | - Olivia Wilkins
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Cristina C Castillo
- Institute of Archaeology, University College London, London, United Kingdom
- School of Cultural Heritage, North-West University, Xi'an, China
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, United Kingdom
- School of Cultural Heritage, North-West University, Xi'an, China
| | - Jade A d'Alpoim Guedes
- Department of Anthropology and Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- Institute for the Study of the Ancient World, New York University, New York, NY, USA.
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15
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Bellis ES, Kelly EA, Lorts CM, Gao H, DeLeo VL, Rouhan G, Budden A, Bhaskara GB, Hu Z, Muscarella R, Timko MP, Nebie B, Runo SM, Chilcoat ND, Juenger TE, Morris GP, dePamphilis CW, Lasky JR. Genomics of sorghum local adaptation to a parasitic plant. Proc Natl Acad Sci U S A 2020; 117:4243-4251. [PMID: 32047036 PMCID: PMC7049153 DOI: 10.1073/pnas.1908707117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.
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Affiliation(s)
- Emily S Bellis
- Department of Biology, The Pennsylvania State University, University Park, PA 16802;
- Arkansas Biosciences Institute, Arkansas State University, State University, AR 72467
- Department of Computer Science, Arkansas State University, State University, AR 72467
| | - Elizabeth A Kelly
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
| | - Claire M Lorts
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Huirong Gao
- Applied Science and Technology, Corteva Agriscience, Johnston, IA 50131
| | - Victoria L DeLeo
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
| | - Germinal Rouhan
- Institut Systématique Evolution Biodiversité, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, École Pratique des Hautes Études, CP39, 75005 Paris, France
| | - Andrew Budden
- Identification & Naming, Royal Botanic Gardens, Kew, TW9 3AB Richmond, United Kingdom
| | - Govinal B Bhaskara
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Robert Muscarella
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE-75236 Uppsala, Sweden
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - Baloua Nebie
- West and Central Africa Regional Program, International Crops Research Institute for the Semi-Arid Tropics, BP 320 Bamako, Mali
| | - Steven M Runo
- Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - N Doane Chilcoat
- Applied Science and Technology, Corteva Agriscience, Johnston, IA 50131
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Jesse R Lasky
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
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16
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 DOI: 10.1101/642306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 05/26/2023] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest Management Colorado State University Fort Collins CO USA
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Lua Lopez
- Department of Biology Binghamton University (State University of New York) Binghamton NY USA
| | - Adrian E Platts
- Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor NY USA
- Department of Biology Center for Genomics and Systems Biology New York University New York NY USA
| | - Jesse R Lasky
- Department of Biology Pennsylvania State University University Park PA USA
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17
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 PMCID: PMC7042746 DOI: 10.1002/ece3.6002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest ManagementColorado State UniversityFort CollinsCOUSA
- Department of Biological SciencesUniversity of CyprusNicosiaCyprus
| | - Lua Lopez
- Department of BiologyBinghamton University (State University of New York)BinghamtonNYUSA
| | - Adrian E. Platts
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
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18
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DeLeo VL, Menge DNL, Hanks EM, Juenger TE, Lasky JR. Effects of two centuries of global environmental variation on phenology and physiology of Arabidopsis thaliana. Glob Chang Biol 2020; 26:523-538. [PMID: 31665819 DOI: 10.1111/gcb.14880] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/28/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Intraspecific trait variation is caused by genetic and plastic responses to environment. This intraspecific diversity is captured in immense natural history collections, giving us a window into trait variation across continents and through centuries of environmental shifts. Here we tested if hypotheses based on life history and the leaf economics spectrum explain intraspecific trait changes across global spatiotemporal environmental gradients. We measured phenotypes on a 216-year time series of Arabidopsis thaliana accessions from across its native range and applied spatially varying coefficient models to quantify region-specific trends in trait coordination and trait responses to climate gradients. All traits exhibited significant change across space or through time. For example, δ15 N decreased over time across much of the range and leaf C:N increased, consistent with predictions based on anthropogenic changes in land use and atmosphere. Plants were collected later in the growing season in more recent years in many regions, possibly because populations shifted toward more spring germination and summer flowering as opposed to fall germination and spring flowering. When climate variables were considered, collection dates were earlier in warmer years, while summer rainfall had opposing associations with collection date depending on regions. There was only a modest correlation among traits, indicating a lack of a single life history/physiology axis. Nevertheless, leaf C:N was low for summer- versus spring-collected plants, consistent with a life history-physiology axis from slow-growing winter annuals to fast-growing spring/summer annuals. Regional heterogeneity in phenotype trends indicates complex responses to spatiotemporal environmental gradients potentially due to geographic genetic variation and climate interactions with other aspects of environment. Our study demonstrates how natural history collections can be used to broadly characterize trait responses to environment, revealing heterogeneity in response to anthropogenic change.
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Affiliation(s)
- Victoria L DeLeo
- Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA
| | - Duncan N L Menge
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Ephraim M Hanks
- Department of Statistics, Pennsylvania State University, University Park, PA, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jesse R Lasky
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Earth Institute, Columbia University, New York, NY, USA
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19
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Lasky JR, Forester BR, Reimherr M. Corrigendum to “Coherent synthesis of genomic associations with phenotypes and home environments”. Mol Ecol Resour 2019. [DOI: 10.1111/1755-0998.13058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park Pennsylvania
| | | | - Matthew Reimherr
- Department of Statistics Pennsylvania State University University Park Pennsylvania
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20
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Abstract
Co-occurring species often differ in intraspecific genetic diversity, which in turn can affect adaptation in response to environmental change. Specifically, the simultaneous evolutionary responses of co-occurring species to temporal environmental change may influence community dynamics. Local adaptation along environmental gradients combined with gene flow can enhance genetic diversity of traits within populations. Quantitative genetic theory shows that having greater gene flow results in (a) lower equilibrium population size due to maladaptive immigrant genotypes (migration load), but (b) faster adaptation to changing environments. Here, I build off this theory to study community dynamics of locally adapted species in response to temporal environmental changes akin to warming temperatures. Although an abrupt environmental change leaves all species initially maladapted, high gene flow species subsequently adapt faster due to greater genetic diversity. As a result, species can transiently reverse their relative abundances, but sometimes only after long lag periods. If constant temporal environmental change is applied, the community exhibits a shift toward stable dominance by species with intermediate gene flow. Notably, fast-adapting high gene flow species can increase in absolute abundance under environmental change (although often only for a transient period) because the change suppresses superior competitors with lower gene flow. This eco-evolutionary competitive release stabilizes ecosystem function. The eco-evolutionary community turnover studied here parallels the purely ecological successional dynamics following disturbances. My results demonstrate how interspecific variation in life history can have far-reaching impacts on eco-evolutionary community response to environmental change.
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Affiliation(s)
- Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania
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21
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Kalladan R, Lasky JR, Sharma S, Kumar MN, Juenger TE, Des Marais DL, Verslues PE. Natural Variation in 9-Cis-Epoxycartenoid Dioxygenase 3 and ABA Accumulation. Plant Physiol 2019; 179:1620-1631. [PMID: 30710052 PMCID: PMC6446753 DOI: 10.1104/pp.18.01185] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/23/2019] [Indexed: 05/18/2023]
Abstract
The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms controlling ABA levels are unclear. At low water potential, ABA accumulation in the Arabidopsis (Arabidopsis thaliana) accession Shahdara (Sha) was less than that in Landsberg erecta (Ler) or Columbia. Analysis of a Ler × Sha recombinant inbred line population revealed a single major-effect quantitative trait locus for ABA accumulation, which included 9-cis-epoxycarotenoid dioxygenase3 (NCED3) as a candidate gene. NCED3 encodes a rate-limiting enzyme for stress-induced ABA synthesis. Complementation experiments indicated that Sha has a reduced-function NCED3 allele. Compared with Ler, Sha did not have reduced NCED3 gene expression or protein level but did have four amino acid substitutions within NCED3. Sha differed from Ler in the apparent molecular mass of NCED3, indicative of altered NCED3 proteolytic processing in the chloroplast. Site-directed mutagenesis demonstrated that substitution at amino acid 271 was critical for the altered NCED3 molecular mass pattern, while the other Sha NCED3 polymorphisms were also involved in the reduced ABA accumulation. Sha did not have a reduced level of thylakoid-bound NCED3 but did differ from Ler in the apparent molecular mass of stromal NCED3. As Sha was not impaired in known factors critical for NCED3 function in ABA synthesis (expression, chloroplast import, and thylakoid binding), the differences between Ler and Sha NCED3 may affect NCED3 activity or other factors influencing NCED3 function. These results identify functionally important sites on NCED3 and indicate a complex pattern of NCED3 posttranslational regulation in the chloroplast.
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Affiliation(s)
- Rajesh Kalladan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sandeep Sharma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - M Nagaraj Kumar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
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22
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Fortunel C, Lasky JR, Uriarte M, Valencia R, Wright SJ, Garwood NC, Kraft NJB. Topography and neighborhood crowding can interact to shape species growth and distribution in a diverse Amazonian forest. Ecology 2018; 99:2272-2283. [PMID: 29975420 DOI: 10.1002/ecy.2441] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/15/2018] [Accepted: 06/11/2018] [Indexed: 11/09/2022]
Abstract
Abiotic constraints and biotic interactions act simultaneously to shape communities. However, these community assembly mechanisms are often studied independently, which can limit understanding of how they interact to affect species dynamics and distributions. We develop a hierarchical Bayesian neighborhood modeling approach to quantify the simultaneous effects of topography and crowding by neighbors on the growth of 124,704 individual stems ≥1 cm DBH for 1,047 tropical tree species in a 25-ha mapped rainforest plot in Amazonian Ecuador. We build multi-level regression models to evaluate how four key functional traits (specific leaf area, maximum tree size, wood specific gravity and seed mass) mediate tree growth response to topography and neighborhood crowding. Tree growth is faster in valleys than on ridges and is reduced by neighborhood crowding. Topography and crowding interact to influence tree growth in ~10% of the species. Specific leaf area, maximum tree size and seed mass are associated with growth responses to topography, but not with responses to neighborhood crowding or with the interaction between topography and crowding. In sum, our study reveals that topography and neighborhood crowding each influence tree growth in tropical forests, but act largely independently in shaping species distributions. While traits were associated with species response to topography, their role in species response to neighborhood crowding was less clear, which suggests that trait effects on neighborhood dynamics may depend on the direction (negative/positive) and degree of symmetry of biotic interactions. Our study emphasizes the importance of simultaneously assessing the individual and interactive role of multiple mechanisms in shaping species dynamics in high diversity tropical systems.
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Affiliation(s)
- Claire Fortunel
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, 90095-1606, USA.,AMAP (botAnique et Modélisation de l'Architecture des Plantes et des végétations), IRD, CIRAD, CNRS, INRA, Université de Montpellier, 34398, Montpellier Cedex 5, France
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - María Uriarte
- Department of Ecology, Evolution & Environmental Biology, Columbia University, New York, New York, 10027, USA
| | - Renato Valencia
- Laboratorio de Ecología de Plantas, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Apartado 17-01-2184, Quito, Ecuador
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Panama
| | - Nancy C Garwood
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901-6509, USA
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, 90095-1606, USA
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23
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Forester BR, Lasky JR, Wagner HH, Urban DL. Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations. Mol Ecol 2018; 27:2215-2233. [DOI: 10.1111/mec.14584] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Brenna R. Forester
- Nicholas School of the Environment; Duke University; Durham North Carolina
| | - Jesse R. Lasky
- Department of Biology; Pennsylvania State University; University Park Pennsylvania
| | - Helene H. Wagner
- Department of Biology; University of Toronto Mississauga; Mississauga ON Canada
| | - Dean L. Urban
- Nicholas School of the Environment; Duke University; Durham North Carolina
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24
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/16/2017] [Indexed: 01/17/2023]
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25
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Gienapp P, Fior S, Guillaume F, Lasky JR, Sork VL, Csilléry K. Genomic Quantitative Genetics to Study Evolution in the Wild. Trends Ecol Evol 2017; 32:897-908. [PMID: 29050794 DOI: 10.1016/j.tree.2017.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022]
Abstract
Quantitative genetic theory provides a means of estimating the evolutionary potential of natural populations. However, this approach was previously only feasible in systems where the genetic relatedness between individuals could be inferred from pedigrees or experimental crosses. The genomic revolution opened up the possibility of obtaining the realized proportion of genome shared among individuals in natural populations of virtually any species, which could promise (more) accurate estimates of quantitative genetic parameters in virtually any species. Such a 'genomic' quantitative genetics approach relies on fewer assumptions, offers a greater methodological flexibility, and is thus expected to greatly enhance our understanding of evolution in natural populations, for example, in the context of adaptation to environmental change, eco-evolutionary dynamics, and biodiversity conservation.
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Affiliation(s)
- Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
| | - Simone Fior
- Plant Ecological Genetics, ETH Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Katalin Csilléry
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland; Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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26
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Lasky JR, Forester BR, Reimherr M. Coherent synthesis of genomic associations with phenotypes and home environments. Mol Ecol Resour 2017; 18:91-106. [DOI: 10.1111/1755-0998.12714] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Jesse R. Lasky
- Department of Biology; Pennsylvania State University; University Park PA USA
| | | | - Matthew Reimherr
- Department of Statistics; Pennsylvania State University; University Park PA USA
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27
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Des Marais DL, Guerrero RF, Lasky JR, Scarpino SV. Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. Proc Biol Sci 2017; 284:20170914. [PMID: 28615505 PMCID: PMC5474086 DOI: 10.1098/rspb.2017.0914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/17/2017] [Indexed: 01/26/2023] Open
Abstract
Molecular interactions affect the evolution of complex traits. For instance, adaptation may be constrained by pleiotropic or epistatic effects, both of which can be reflected in the structure of molecular interaction networks. To date, empirical studies investigating the role of molecular interactions in phenotypic evolution have been idiosyncratic, offering no clear patterns. Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors-drought and cold-in Arabidopsis thaliana Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly more peripheral and cold response genes being significantly more central than genes which do not show GxE. We suggest that the observed topologies reflect different constraints on the genetic pathways involved in environmental response. The approach presented here may inform predictive models linking genetic variation in molecular signalling networks with phenotypic variation, specifically traits involved in environmental response.
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Affiliation(s)
- David L Des Marais
- Arnold Arboretum and Department of Organismic and Evolutionary Biology, Harvard University, 1300 Centre Street, Boston, MA 20131, USA
| | - Rafael F Guerrero
- Department of Biology, Indiana University, Jordan Hall 142, Bloomington, IN 47405, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, 408 Life Sciences Building, University Park, PA 16802, USA
| | - Samuel V Scarpino
- Department of Mathematics and Statistics and Vermont Complex Systems Center, University of Vermont, 210 Colchester Avenue, Burlington, VT 05405, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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Bay RA, Rose N, Barrett R, Bernatchez L, Ghalambor CK, Lasky JR, Brem RB, Palumbi SR, Ralph P. Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures. Am Nat 2017; 189:463-473. [DOI: 10.1086/691233] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Des Marais DL, Lasky JR, Verslues PE, Chang TZ, Juenger TE. Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. New Phytol 2017; 214:132-144. [PMID: 27864966 DOI: 10.1111/nph.14316] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/03/2016] [Indexed: 05/21/2023]
Abstract
An enduring question in plant physiology and evolution is how single genotypes of plants optimize performance in diverse, often highly variable, environments. We grew 35 natural accessions of the grass Brachypodium distachyon in four environments in the glasshouse, contrasting soil water deficit, elevated temperature and their interaction. We modeled treatment, genotype and interactive effects on leaf-level and whole-plant traits, including fecundity. We also assessed the relationship between glasshouse-measured traits and parameters related to climate at the place of origin. We found abundant genetic variation in both constitutive and induced traits related to plant-water relations. Most traits showed strong interaction between temperature and water availability, and we observed genotype-by-environment interaction for several traits. Notably, leaf free proline abundance showed a strong effect of genotype × temperature × water. We found strong associations between phenology, biomass and water use efficiency (WUE) with parameters describing climate of origin. Plants respond to multiple stressors in ways not directly predictable from single stressors, underscoring the complex and trait-specific mechanisms of environmental response. Climate-trait correlations support a role for WUE and phenology in local adaptation to climate in B. distachyon.
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Affiliation(s)
- David L Des Marais
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Trent Z Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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Hudson LN, Newbold T, Contu S, Hill SLL, Lysenko I, De Palma A, Phillips HRP, Alhusseini TI, Bedford FE, Bennett DJ, Booth H, Burton VJ, Chng CWT, Choimes A, Correia DLP, Day J, Echeverría‐Londoño S, Emerson SR, Gao D, Garon M, Harrison MLK, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, Pask‐Hale GD, Pynegar EL, Robinson AN, Sanchez‐Ortiz K, Senior RA, Simmons BI, White HJ, Zhang H, Aben J, Abrahamczyk S, Adum GB, Aguilar‐Barquero V, Aizen MA, Albertos B, Alcala EL, del Mar Alguacil M, Alignier A, Ancrenaz M, Andersen AN, Arbeláez‐Cortés E, Armbrecht I, Arroyo‐Rodríguez V, Aumann T, Axmacher JC, Azhar B, Azpiroz AB, Baeten L, Bakayoko A, Báldi A, Banks JE, Baral SK, Barlow J, Barratt BIP, Barrico L, Bartolommei P, Barton DM, Basset Y, Batáry P, Bates AJ, Baur B, Bayne EM, Beja P, Benedick S, Berg Å, Bernard H, Berry NJ, Bhatt D, Bicknell JE, Bihn JH, Blake RJ, Bobo KS, Bóçon R, Boekhout T, Böhning‐Gaese K, Bonham KJ, Borges PAV, Borges SH, Boutin C, Bouyer J, Bragagnolo C, Brandt JS, Brearley FQ, Brito I, Bros V, Brunet J, Buczkowski G, Buddle CM, Bugter R, Buscardo E, Buse J, Cabra‐García J, Cáceres NC, Cagle NL, Calviño‐Cancela M, Cameron SA, Cancello EM, Caparrós R, Cardoso P, Carpenter D, Carrijo TF, Carvalho AL, Cassano CR, Castro H, Castro‐Luna AA, Rolando CB, Cerezo A, Chapman KA, Chauvat M, Christensen M, Clarke FM, Cleary DF, Colombo G, Connop SP, Craig MD, Cruz‐López L, Cunningham SA, D'Aniello B, D'Cruze N, da Silva PG, Dallimer M, Danquah E, Darvill B, Dauber J, Davis ALV, Dawson J, de Sassi C, de Thoisy B, Deheuvels O, Dejean A, Devineau J, Diekötter T, Dolia JV, Domínguez E, Dominguez‐Haydar Y, Dorn S, Draper I, Dreber N, Dumont B, Dures SG, Dynesius M, Edenius L, Eggleton P, Eigenbrod F, Elek Z, Entling MH, Esler KJ, de Lima RF, Faruk A, Farwig N, Fayle TM, Felicioli A, Felton AM, Fensham RJ, Fernandez IC, Ferreira CC, Ficetola GF, Fiera C, Filgueiras BKC, Fırıncıoğlu HK, Flaspohler D, Floren A, Fonte SJ, Fournier A, Fowler RE, Franzén M, Fraser LH, Fredriksson GM, Freire GB, Frizzo TLM, Fukuda D, Furlani D, Gaigher R, Ganzhorn JU, García KP, Garcia‐R JC, Garden JG, Garilleti R, Ge B, Gendreau‐Berthiaume B, Gerard PJ, Gheler‐Costa C, Gilbert B, Giordani P, Giordano S, Golodets C, Gomes LGL, Gould RK, Goulson D, Gove AD, Granjon L, Grass I, Gray CL, Grogan J, Gu W, Guardiola M, Gunawardene NR, Gutierrez AG, Gutiérrez‐Lamus DL, Haarmeyer DH, Hanley ME, Hanson T, Hashim NR, Hassan SN, Hatfield RG, Hawes JE, Hayward MW, Hébert C, Helden AJ, Henden J, Henschel P, Hernández L, Herrera JP, Herrmann F, Herzog F, Higuera‐Diaz D, Hilje B, Höfer H, Hoffmann A, Horgan FG, Hornung E, Horváth R, Hylander K, Isaacs‐Cubides P, Ishida H, Ishitani M, Jacobs CT, Jaramillo VJ, Jauker B, Hernández FJ, Johnson MF, Jolli V, Jonsell M, Juliani SN, Jung TS, Kapoor V, Kappes H, Kati V, Katovai E, Kellner K, Kessler M, Kirby KR, Kittle AM, Knight ME, Knop E, Kohler F, Koivula M, Kolb A, Kone M, Kőrösi Á, Krauss J, Kumar A, Kumar R, Kurz DJ, Kutt AS, Lachat T, Lantschner V, Lara F, Lasky JR, Latta SC, Laurance WF, Lavelle P, Le Féon V, LeBuhn G, Légaré J, Lehouck V, Lencinas MV, Lentini PE, Letcher SG, Li Q, Litchwark SA, Littlewood NA, Liu Y, Lo‐Man‐Hung N, López‐Quintero CA, Louhaichi M, Lövei GL, Lucas‐Borja ME, Luja VH, Luskin MS, MacSwiney G MC, Maeto K, Magura T, Mallari NA, Malone LA, Malonza PK, Malumbres‐Olarte J, Mandujano S, Måren IE, Marin‐Spiotta E, Marsh CJ, Marshall EJP, Martínez E, Martínez Pastur G, Moreno Mateos D, Mayfield MM, Mazimpaka V, McCarthy JL, McCarthy KP, McFrederick QS, McNamara S, Medina NG, Medina R, Mena JL, Mico E, Mikusinski G, Milder JC, Miller JR, Miranda‐Esquivel DR, Moir ML, Morales CL, Muchane MN, Muchane M, Mudri‐Stojnic S, Munira AN, Muoñz‐Alonso A, Munyekenye BF, Naidoo R, Naithani A, Nakagawa M, Nakamura A, Nakashima Y, Naoe S, Nates‐Parra G, Navarrete Gutierrez DA, Navarro‐Iriarte L, Ndang'ang'a PK, Neuschulz EL, Ngai JT, Nicolas V, Nilsson SG, Noreika N, Norfolk O, Noriega JA, Norton DA, Nöske NM, Nowakowski AJ, Numa C, O'Dea N, O'Farrell PJ, Oduro W, Oertli S, Ofori‐Boateng C, Oke CO, Oostra V, Osgathorpe LM, Otavo SE, Page NV, Paritsis J, Parra‐H A, Parry L, Pe'er G, Pearman PB, Pelegrin N, Pélissier R, Peres CA, Peri PL, Persson AS, Petanidou T, Peters MK, Pethiyagoda RS, Phalan B, Philips TK, Pillsbury FC, Pincheira‐Ulbrich J, Pineda E, Pino J, Pizarro‐Araya J, Plumptre AJ, Poggio SL, Politi N, Pons P, Poveda K, Power EF, Presley SJ, Proença V, Quaranta M, Quintero C, Rader R, Ramesh BR, Ramirez‐Pinilla MP, Ranganathan J, Rasmussen C, Redpath‐Downing NA, Reid JL, Reis YT, Rey Benayas JM, Rey‐Velasco JC, Reynolds C, Ribeiro DB, Richards MH, Richardson BA, Richardson MJ, Ríos RM, Robinson R, Robles CA, Römbke J, Romero‐Duque LP, Rös M, Rosselli L, Rossiter SJ, Roth DS, Roulston TH, Rousseau L, Rubio AV, Ruel J, Sadler JP, Sáfián S, Saldaña‐Vázquez RA, Sam K, Samnegård U, Santana J, Santos X, Savage J, Schellhorn NA, Schilthuizen M, Schmiedel U, Schmitt CB, Schon NL, Schüepp C, Schumann K, Schweiger O, Scott DM, Scott KA, Sedlock JL, Seefeldt SS, Shahabuddin G, Shannon G, Sheil D, Sheldon FH, Shochat E, Siebert SJ, Silva FAB, Simonetti JA, Slade EM, Smith J, Smith‐Pardo AH, Sodhi NS, Somarriba EJ, Sosa RA, Soto Quiroga G, St‐Laurent M, Starzomski BM, Stefanescu C, Steffan‐Dewenter I, Stouffer PC, Stout JC, Strauch AM, Struebig MJ, Su Z, Suarez‐Rubio M, Sugiura S, Summerville KS, Sung Y, Sutrisno H, Svenning J, Teder T, Threlfall CG, Tiitsaar A, Todd JH, Tonietto RK, Torre I, Tóthmérész B, Tscharntke T, Turner EC, Tylianakis JM, Uehara‐Prado M, Urbina‐Cardona N, Vallan D, Vanbergen AJ, Vasconcelos HL, Vassilev K, Verboven HAF, Verdasca MJ, Verdú JR, Vergara CH, Vergara PM, Verhulst J, Virgilio M, Vu LV, Waite EM, Walker TR, Wang H, Wang Y, Watling JI, Weller B, Wells K, Westphal C, Wiafe ED, Williams CD, Willig MR, Woinarski JCZ, Wolf JHD, Wolters V, Woodcock BA, Wu J, Wunderle JM, Yamaura Y, Yoshikura S, Yu DW, Zaitsev AS, Zeidler J, Zou F, Collen B, Ewers RM, Mace GM, Purves DW, Scharlemann JPW, Purvis A. The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project. Ecol Evol 2017; 7:145-188. [PMID: 28070282 PMCID: PMC5215197 DOI: 10.1002/ece3.2579] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/10/2016] [Accepted: 09/22/2016] [Indexed: 11/29/2022] Open
Abstract
The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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Affiliation(s)
| | - Tim Newbold
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and EnvironmentResearchUniversity College LondonLondonUK
| | - Sara Contu
- Department of Life SciencesNatural History MuseumLondonUK
| | - Samantha L. L. Hill
- Department of Life SciencesNatural History MuseumLondonUK
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
| | - Igor Lysenko
- Department of Life SciencesImperial College LondonAscotUK
| | - Adriana De Palma
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | - Helen R. P. Phillips
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | | | | | | | - Hollie Booth
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
- Frankfurt Zoological SocietyAfrica Regional OfficeArushaTanzania
| | - Victoria J. Burton
- Department of Life SciencesNatural History MuseumLondonUK
- Science and Solutions for a Changing Planet DTP and the Department of Life SciencesImperial College LondonSouth KensingtonLondonUK
| | | | - Argyrios Choimes
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | | | - Julie Day
- Department of Life SciencesImperial College LondonAscotUK
| | - Susy Echeverría‐Londoño
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| | | | - Di Gao
- Department of Life SciencesNatural History MuseumLondonUK
| | - Morgan Garon
- Department of Life SciencesImperial College LondonAscotUK
| | | | | | - Martin Jung
- School of Life SciencesUniversity of SussexBrightonUK
| | - Victoria Kemp
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Lucinda Kirkpatrick
- School of Biological and Ecological SciencesUniversity of StirlingStirlingUK
| | - Callum D. Martin
- School of Biological SciencesRoyal Holloway University of LondonEgham, SurreyUK
| | - Yuan Pan
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldUK
| | | | - Edwin L. Pynegar
- School of EnvironmentNatural Resources and GeographyBangor UniversityBangorGwyneddUK
| | | | | | - Rebecca A. Senior
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldUK
| | | | - Hannah J. White
- School of Biological SciencesQueen's University BelfastBelfastUK
| | | | - Job Aben
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
- Evolutionary Ecology GroupUniversity of AntwerpAntwerpBelgium
| | | | - Gilbert B. Adum
- Wildlife and Range Management DepartmentFaculty of Renewable Natural Resources (FRNR)College of Agriculture and Natural Resources (CANR)Kwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
- SAVE THE FROGS! GhanaAdum‐KumasiGhana
| | | | - Marcelo A. Aizen
- Laboratorio Ecotono‐CRUBUniversidad Nacional del Comahue and INIBIOMARío NegroArgentina
| | - Belén Albertos
- Departamento de BotánicaFacultad de FarmaciaUniversidad de ValenciaBurjassot, ValenciaSpain
| | - E. L. Alcala
- Marine LaboratorySilliman University‐Angelo King Center for Research and Environmental ManagementSilliman UniversityDumaguete CityPhilippines
| | - Maria del Mar Alguacil
- Department of Soil and Water ConservationCSIC‐Centro de Edafología y Biología Aplicada del SeguraMurciaSpain
| | - Audrey Alignier
- INRAUR 0980 SAD‐PaysageRennes CedexFrance
- INRAUMR 1201 DYNAFORCastanet Tolosan CedexFrance
| | - Marc Ancrenaz
- HUTAN – Kinabatangan Orang‐utan Conservation ProgrammeKota KinabaluMalaysia
- Borneo FuturesKota KinabaluMalaysia
| | | | - Enrique Arbeláez‐Cortés
- Museo de ZoologíaFacultad de CienciasUniversidad Nacional Autónoma de MéxicoMéxico D.F.Mexico
- Colección de TejidosInstituto de Investigación de Recursos Biológicos Alexander von HumboldtValle del CaucaColombia
| | | | - Víctor Arroyo‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMexico
| | - Tom Aumann
- College of Science, Engineering & HealthRMIT UniversityMelbourneVic.Australia
| | - Jan C. Axmacher
- UCL Department of GeographyUniversity College LondonLondonUK
| | - Badrul Azhar
- Biodiversity UnitInstitute of BioscienceUniversiti Putra MalaysiaSerdangMalaysia
- Faculty of ForestryUniversiti Putra MalaysiaSerdangMalaysia
| | - Adrián B. Azpiroz
- Departamento de Biodiversidad y GenéticaInstituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
| | - Lander Baeten
- Forest & Nature LabDepartment of Forest and Water ManagementGhent UniversityGontrodeBelgium
- Terrestrial Ecology UnitDepartment of BiologyGhent UniversityGhentBelgium
| | - Adama Bakayoko
- UFR Science de la NatureUniversité Naangui AbrogouaAbidjanIvory Coast
- Centre Suisse de Recherches Scientifiques en Côte d'IvoireAbidjanIvory Coast
| | - András Báldi
- MTA Centre for Ecological ResearchVácrátótHungary
| | | | | | - Jos Barlow
- Lancaster Environment CentreLancaster UniversityLancasterUK
- MCT/Museu Paraense Emílio GoeldiBelémBrazil
| | | | - Lurdes Barrico
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
| | | | - Diane M. Barton
- AgResearch LimitedInvermay Agricultural CentrePuddle Alley, MosgielNew Zealand
| | - Yves Basset
- Smithsonian Tropical Research InstituteBalboaAnconPanama CityRepublic of Panama
| | - Péter Batáry
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | - Adam J. Bates
- BiosciencesSchool of Science & TechnologyNottingham Trent UniversityClifton, NottinghamUK
- University of BirminghamEdgbaston, BirminghamUK
| | - Bruno Baur
- Section of Conservation BiologyDepartment of Environmental SciencesUniversity of BaselBaselSwitzerland
| | - Erin M. Bayne
- Department of Biological SciencesUniversity of AlbertaEdmontonABCanada
| | - Pedro Beja
- CIBIO/InBioCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Suzan Benedick
- Faculty of Sustainable AgricultureUniversiti Malaysia SabahSandakanMalaysia
| | - Åke Berg
- The Swedish University of Agricultural SciencesThe Swedish Biodiversity CentreUppsalaSweden
| | - Henry Bernard
- Institute for Tropical Biology and ConservationUniversiti Malaysia Sabah, Jalan UMSKota KinabaluMalaysia
| | | | - Dinesh Bhatt
- Department of Zoology & Environmental ScienceGurukula Kangri UniversityHaridwarIndia
| | - Jake E. Bicknell
- Durrell Institute of Conservation and Ecology (DICE)School of Anthropology and ConservationUniversity of KentCanterburyUK
- Iwokrama International Centre for Rainforest Conservation and DevelopmentGeorgetownGuyana
| | - Jochen H. Bihn
- Department of Ecology‐Animal EcologyFaculty of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Robin J. Blake
- Compliance Services InternationalPentlands Science ParkPenicuik, EdinburghUK
- Centre for Agri‐Environmental ResearchSchool of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
| | - Kadiri S. Bobo
- School for the Training of Wildlife Specialists GarouaGarouaCameroon
- Department of ForestryFaculty of Agronomy and Agricultural SciencesUniversity of DschangDschangCameroon
| | - Roberto Bóçon
- Mater Natura – Instituto de Estudos AmbientaisCuritibaBrazil
| | - Teun Boekhout
- CBS Fungal Biodiversity Centre (CBS‐KNAW)UtrechtThe Netherlands
| | - Katrin Böhning‐Gaese
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F)Frankfurt am MainGermany
- Institute for Ecology, Evolution & DiversityGoethe University FrankfurtBiologicum, Frankfurt am MainGermany
| | - Kevin J. Bonham
- School of Land and FoodUniversity of TasmaniaSandy BayTas.Australia
| | - Paulo A. V. Borges
- Departamento de Ciências AgráriascE3c – Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresAngra do Heroísmo, AçoresPortugal
| | | | - Céline Boutin
- Environment and Climate Change Canada, Science & Technology BranchCarleton UniversityOttawaONCanada
| | - Jérémy Bouyer
- Unité Mixte de Recherche Contrôle des Maladies Animales Exotiques et EmergentesCentre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)MontpellierFrance
- Unité Mixte de Recherche 1309 Contrôle des Maladies Animales Exotiques et EmergentesInstitut national de la recherche agronomique (INRA)MontpellierFrance
| | - Cibele Bragagnolo
- Departamento de ZoologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Jodi S. Brandt
- Human Environment Systems CenterBoise State UniversityBoiseIDUSA
| | - Francis Q. Brearley
- School of Science and the EnvironmentManchester Metropolitan UniversityManchesterUK
| | | | - Vicenç Bros
- Natural Parks Technical OfficeDiputació de BarcelonaBarcelonaSpain
- Natural History Museum of BarcelonaBarcelona, CataloniaSpain
| | - Jörg Brunet
- Swedish University of Agricultural SciencesSouthern Swedish Forest Research CentreAlnarpSweden
| | | | | | - Rob Bugter
- Alterra, part of Wageningen University and ResearchRB WageningenThe Netherlands
| | - Erika Buscardo
- Departamento de Ciências da VidaCentro de Ecologia FuncionalUniversidade de CoimbraCoimbraPortugal
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCampinasBrazil
- Department of BotanySchool of Natural SciencesTrinity College DublinDublin 2Ireland
| | - Jörn Buse
- Institute for Environmental SciencesUniversity Koblenz‐LandauLandauGermany
| | - Jimmy Cabra‐García
- Departamento de ZoologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
- Departamento de BiologíaGrupo de investigación en BiologíaEcología y Manejo de HormigasSección de EntomologíaUniversidad del ValleCaliColombia
| | - Nilton C. Cáceres
- Department of BiologyFederal University of Santa Maria, CCNESanta MariaBrazil
| | | | - María Calviño‐Cancela
- Department of Ecology and Animal BiologyFaculty of SciencesUniversity of VigoVigoSpain
| | - Sydney A. Cameron
- Department of EntomologyUniversity of IllinoisUrbanaILUSA
- Program in Ecology, Evolution and Conservation BiologyUniversity of IllinoisUrbanaILUSA
| | | | - Rut Caparrós
- Departamento de BotánicaFacultad de FarmaciaUniversidad de ValenciaBurjassot, ValenciaSpain
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | - Pedro Cardoso
- Departamento de Ciências AgráriascE3c – Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresAngra do Heroísmo, AçoresPortugal
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Dan Carpenter
- Parks and CountrysideBracknell Forest CouncilBracknellUK
- Soil Biodiversity GroupLife Sciences DepartmentNatural History MuseumLondonUK
| | | | | | - Camila R. Cassano
- Laboratório de Ecologia Aplicada à ConservaçãoUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Helena Castro
- Centre for Functional EcologyDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal
| | | | - Cerda B. Rolando
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)Tropical Agricultural Research and Higher Education CenterTurrialbaCosta Rica
| | - Alexis Cerezo
- Department of Quantitative Methods and Information SystemsFaculty of AgronomyUniversity of Buenos AiresBuenos AiresArgentina
| | | | - Matthieu Chauvat
- Normandie UnivEA 1293 ECODIV‐RouenSFR SCALEUFR Sciences et TechniquesMont Saint Aignan CedexFrance
| | | | - Francis M. Clarke
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
| | | | - Giorgio Colombo
- Dipartimento di BiologiaUniversità degli Studi di MilanoMilanoItaly
| | - Stuart P. Connop
- Sustainability Research InstituteUniversity of East LondonLondonUK
| | - Michael D. Craig
- Centre of Excellence for Environmental DecisionsSchool of Plant BiologyUniversity of Western AustraliaNedlandsWAAustralia
- School of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
| | - Leopoldo Cruz‐López
- Grupo Ecología de Artrópodos y Manejo de PlagasEl Colegio de la Frontera SurTapachulaMexico
| | | | - Biagio D'Aniello
- Dipartimento di BiologiaUniversità di Napoli Federico IINapoliItaly
| | - Neil D'Cruze
- Wildlife Conservation Research UnitDepartment of ZoologyUniversity of OxfordRecanati‐Kaplan CentreTubneyUK
| | - Pedro Giovâni da Silva
- Programa de Pós‐Graduação em EcologiaUniversidade Federal de Santa CatarinaFlorianópolisBrazil
| | - Martin Dallimer
- Sustainability Research InstituteSchool of Earth and EnvironmentUniversity of LeedsLeedsUK
| | - Emmanuel Danquah
- Wildlife and Range Management DepartmentFaculty of Renewable Natural Resources (FRNR)College of Agriculture and Natural Resources (CANR)Kwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
| | | | - Jens Dauber
- Thünen Institute of BiodiversityBraunschweigGermany
| | - Adrian L. V. Davis
- Scarab Research GroupDepartment of Zoology & EntomologyUniversity of PretoriaHatfieldSouth Africa
| | - Jeff Dawson
- Durrell Wildlife Conservation TrustTrinityJersey
| | | | | | - Olivier Deheuvels
- CIRADUMR SystemMontpellierFrance
- ICRAFRegional Office for Latin AmericaLimaPeru
| | - Alain Dejean
- UPSINPLaboratoire Écologie Fonctionnelle et EnvironnementUniversité de ToulouseToulouseFrance
- CNRS – UMR 5245EcolabToulouseFrance
- CNRS – UMR 8172Écologie des Forêts de GuyaneKourou cedexFrance
| | | | - Tim Diekötter
- Department of Landscape EcologyInstitute of Natural Resource ConservationKiel UniversityKielGermany
- Department of Biology, Nature ConservationUniversity MarburgMarburgGermany
- Institute of Integrative BiologyETH ZürichZürichSwitzerland
| | - Jignasu V. Dolia
- Post Graduate Program in Wildlife Biology and ConservationNational Centre for Biological SciencesBangaloreIndia
- Wildlife Conservation Society (India Program)Centre for Wildlife StudiesBangaloreIndia
| | - Erwin Domínguez
- Instituto de Investigaciones Agropecuarias – INIA – CRI – KampenaikePunta ArenasChile
| | | | - Silvia Dorn
- Applied EntomologyETH ZürichZürichSwitzerland
| | - Isabel Draper
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | - Niels Dreber
- Unit for Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
- Department of Ecosystem ModellingBüsgen‐InstituteGeorg‐August‐University of GöttingenGöttingenGermany
| | | | - Simon G. Dures
- Department of Life SciencesImperial College LondonAscotUK
- Institute of ZoologyZoological Society of London, Regents ParkLondonUK
| | - Mats Dynesius
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | - Lars Edenius
- Department of Wildlife, Fish and Environmental StudiesSwedish University of Agricultural SciencesUmeaSweden
| | - Paul Eggleton
- Department of Life SciencesNatural History MuseumLondonUK
| | - Felix Eigenbrod
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Zoltán Elek
- MTA‐ELTE‐MTM Ecology Research GroupHungarian Academy of Sciencesc/o Biological InstituteEötvös Lóránd UniversityBudapestHungary
- Hungarian Natural History MuseumBudapestHungary
| | - Martin H. Entling
- Institute for Environmental SciencesUniversity of Koblenz‐LandauLandauGermany
| | - Karen J. Esler
- Department of Conservation Ecology and EntomologyStellenbosch UniversityMatielandSouth Africa
- Centre for Invasion BiologyStellenbosch UniversityMatielandSouth Africa
| | - Ricardo F. de Lima
- CE3C – Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
- Associação Monte PicoMonte CaféMé ZóchiSão Tomé and Príncipe
| | - Aisyah Faruk
- Kew GardensWakehurstArdingly, Haywards Heath, SussexUK
- Wild AsiaUpper PenthouseWisma RKTKuala LumpurMalaysia
| | - Nina Farwig
- Conservation EcologyFaculty of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Tom M. Fayle
- Department of Life SciencesImperial College LondonAscotUK
- Institute of EntomologyBiology Centre of Academy of Sciences Czech RepublicČeské BudějoviceCzech Republic
- Institute for Tropical Biology and ConservationUniversiti Malaysia SabahKota KinabaluMalaysia
| | | | | | - Roderick J. Fensham
- Department of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
- Queensland Herbarium (DSITIA)ToowongQldAustralia
| | | | | | | | - Cristina Fiera
- Institute of Biology Bucharest of Romanian AcademyBucharestRomania
| | | | | | - David Flaspohler
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMIUSA
| | - Andreas Floren
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Steven J. Fonte
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
- Department of Soil and Crop SciencesColorado State UniversityFort CollinsCOUSA
| | | | | | - Markus Franzén
- Department of Community EcologyUFZHelmholtz Centre for Environmental ResearchHalleGermany
| | - Lauchlan H. Fraser
- Department of Natural Resource SciencesThompson Rivers UniversityKamloopsBCCanada
| | - Gabriella M. Fredriksson
- Institute for Biodiversity and Ecosystem Dynamics (IBED)University of AmsterdamGE AmsterdamThe Netherlands
- PanEco/Yayasan Ekosistem LestariSumatran Orangutan Conservation ProgrammeMedanIndonesia
| | - Geraldo B. Freire
- Programa de Pós Graduação em EcologiaUniversidade de BrasíliaBrasília, Distrito FederalBrazil
| | - Tiago L. M. Frizzo
- Programa de Pós Graduação em EcologiaUniversidade de BrasíliaBrasília, Distrito FederalBrazil
| | | | - Dario Furlani
- Dipartimento di BiologiaUniversità degli Studi di MilanoMilanoItaly
| | - René Gaigher
- Department of Conservation Ecology and EntomologyStellenbosch UniversityMatielandSouth Africa
| | | | - Karla P. García
- Departamento de ZoologíaFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Departamento de Planificación TerritorialFacultad de Ciencias AmbientalesCentro EULA‐ChileUniversidad de ConcepciónConcepciónChile
| | | | - Jenni G. Garden
- Seed Consulting ServicesAdelaideSAAustralia
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
- Barbara Hardy InstituteUniversity of South AustraliaMawson LakesSAAustralia
| | - Ricardo Garilleti
- Departamento de BotánicaFacultad de FarmaciaUniversidad de ValenciaBurjassot, ValenciaSpain
| | - Bao‐Ming Ge
- Jiangsu Key Laboratory for Bioresources of Saline SoilsYancheng Teachers UniversityYanchengChina
| | - Benoit Gendreau‐Berthiaume
- Département des sciences biologiquesCentre d’études de la forêt Université du Québec à Montréal Succursale Centre‐villeMontréalQCCanada
| | | | - Carla Gheler‐Costa
- Ecologia Aplicada/Applied EcologyUniversidade Sagrado Coração (USC)BauruBrazil
| | - Benjamin Gilbert
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | | | | | | | | | - Rachelle K. Gould
- Rubenstein School of Natural ResourcesUniversity of VermontBurlingtonVTUSA
| | - Dave Goulson
- School of Life SciencesUniversity of SussexBrightonUK
| | - Aaron D. Gove
- Astron Environmental ServicesEast PerthWAAustralia
- Department of Environment and AgricultureCurtin UniversityPerthWAAustralia
| | - Laurent Granjon
- Centre de Biologie pour la Gestion des Populations (CBGP)INRAIRDCIRADSUPAGROMontferrier‐sur‐Lez cedexFrance
| | - Ingo Grass
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
- Conservation EcologyFaculty of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Claudia L. Gray
- School of Life SciencesUniversity of SussexBrightonUK
- Department of ZoologyUniversity of OxfordOxfordUK
| | - James Grogan
- Department of Biological SciencesMount Holyoke CollegeSouth HadleyMAUSA
| | - Weibin Gu
- China International Engineering Consulting CorporationHaidian DistrictBeijingChina
| | | | | | - Alvaro G. Gutierrez
- Departamento de Ciencias Ambientales y Recursos Naturales RenovablesFacultad de Ciencias AgronómicasUniversidad de ChileLa PintanaChile
| | | | - Daniela H. Haarmeyer
- Biodiversity, Evolution and Ecology of Plants (BEE)Biocentre Klein Flottbek and Botanical GardenUniversity of HamburgHamburgGermany
| | - Mick E. Hanley
- School of Biological ScienceUniversity of PlymouthPlymouthUK
| | | | - Nor R. Hashim
- International University of Malaya‐Wales, Jalan Tun IsmailKuala LumpurMalaysia
| | - Shombe N. Hassan
- Department of Wildlife ManagementSokoine University of AgricultureMorogoroTanzania
| | | | - Joseph E. Hawes
- Animal & Environment Research GroupDepartment of Life SciencesAnglia Ruskin UniversityCambridgeUK
| | - Matt W. Hayward
- Walter Sisulu UniversityMthatha, TranskeiSouth Africa
- Centre for African Conservation EcologyNelson Mandela Metropolitan UniversityPort ElizabethSouth Africa
- College of Natural SciencesBangor UniversityBangor, GwyneddUK
| | - Christian Hébert
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CentreQuébecQCCanada
| | - Alvin J. Helden
- Animal & Environment Research GroupDepartment of Life SciencesAnglia Ruskin UniversityCambridgeUK
| | - John‐André Henden
- Department of Arctic and Marine BiologyUniversity of TromsøTromsøNorway
| | | | - Lionel Hernández
- Universidad Nacional Experimental de GuayanaPuerto OrdazVenezuela
| | - James P. Herrera
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Farina Herrmann
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | | | | | - Branko Hilje
- Earth and Atmospheric Sciences DepartmentUniversity of AlbertaEdmontonABCanada
| | - Hubert Höfer
- State Museum of Natural History Karlsruhe (SMNK)BiosciencesKarlsruheGermany
| | - Anke Hoffmann
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Finbarr G. Horgan
- University of Technology SydneySydneyNSWAustralia
- University of New BrunswickFrederictonNBCanada
| | - Elisabeth Hornung
- Department of EcologyFaculty of Veterinary ScienceSZIE UniversityBudapestHungary
| | - Roland Horváth
- Department of EcologyUniversity of DebrecenDebrecenHungary
| | - Kristoffer Hylander
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Paola Isaacs‐Cubides
- Instituto de Investigaciones y Recursos Biológicos Alexander von HumboldtBogotá, Colombia
| | - Hiroaki Ishida
- Institute of Natural and Environmental SciencesUniversity of HyogoHyogoJapan
| | | | - Carmen T. Jacobs
- Scarab Research GroupDepartment of Zoology & EntomologyUniversity of PretoriaHatfieldSouth Africa
| | - Víctor J. Jaramillo
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMéxico C.P.Mexico
| | - Birgit Jauker
- Department of Animal EcologyJustus‐Liebig‐UniversityGiessenGermany
| | | | | | - Virat Jolli
- Biodiversity and Environmental SustainabilityRohiniIndia
- Department of Environmental StudiesShivaji College (University of Delhi)New DelhiIndia
| | - Mats Jonsell
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - S. Nur Juliani
- School of Biological SciencesUniversiti Sains MalaysiaMindenMalaysia
| | | | | | - Heike Kappes
- Cologne BiocenterZoological InstituteUniversity of CologneKölnGermany
| | - Vassiliki Kati
- Department of Environmental & Natural Resources ManagementUniversity of PatrasAgrinioGreece
| | - Eric Katovai
- Centre for Tropical Environmental and Sustainability Science (TESS) & College of Marine and Environmental SciencesJames Cook UniversityCairnsQldAustralia
- School of Science and TechnologyPacific Adventist UniversityPort MoresbyPapua New Guinea
| | - Klaus Kellner
- Unit for Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
| | - Michael Kessler
- Department of Systematic and Evolutionary BotanyUniversity of ZürichZürichSwitzerland
| | - Kathryn R. Kirby
- Department of Ecology and Evolutionary Biology and Department of Geography and PlanningUniversity of TorontoTorontoONCanada
| | | | | | - Eva Knop
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Florian Kohler
- Section EnvironnementDéveloppement durable et TerritoireDivision Environnement et TerritoireBundesamt für StatistikNeuchâtelSwitzerland
| | - Matti Koivula
- School of Forest SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Annette Kolb
- Institute of Ecology, FB2University of BremenBremenGermany
| | - Mouhamadou Kone
- Université Peleforo Gon CoulibalyKorhogoIvory Coast
- Station d'Ecologie de LamtoN'DouciIvory Coast
| | - Ádám Kőrösi
- MTA‐ELTE‐MTM Ecology Research GroupHungarian Academy of Sciencesc/o Biological InstituteEötvös Lóránd UniversityBudapestHungary
- Theoretical Evolutionary Ecology GroupDepartment of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Ajith Kumar
- Wildlife Conservation Society‐IndiaNational Centre for Biological SciencesBangaloreIndia
| | | | - David J. Kurz
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | - Alex S. Kutt
- School of BioSciencesUniversity of MelbourneMelbourneVic.Australia
| | - Thibault Lachat
- School of Agricultural, Forest and Food Sciences HAFLBern University of Applied SciencesZollikofenSwitzerland
- Swiss Federal Institute for ForestSnow and Landscape Research WSLBirmensdorfSwitzerland
| | - Victoria Lantschner
- Instituto Nacional de Tecnología AgropecuariaEEA BarilocheBarilocheArgentina
| | - Francisco Lara
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - William F. Laurance
- Centre for Tropical Environmental and Sustainability SciencesCollege of Marine and Environmental ScienceJames Cook UniversityCairnsQldAustralia
| | - Patrick Lavelle
- Université Pierre‐et‐Marie‐CurieParisFrance
- Institute of Ecology and Environmental SciencesParisFrance
| | | | - Gretchen LeBuhn
- Department of BiologySan Francisco State UniversitySan FranciscoCAUSA
| | - Jean‐Philippe Légaré
- Laboratoire de diagnostic en phytoprotectionMinistère de l'agriculture, des pêcheries et de l'alimentation du QuébecVille de QuébecQCCanada
| | - Valérie Lehouck
- Research Unit Terrestrial EcologyGhent UniversityGhentBelgium
| | - María V. Lencinas
- Laboratorio de Recursos AgroforestalesCentro Austral de Investigaciones Científicas (CADIC)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)UshuaiaArgentina
| | - Pia E. Lentini
- School of BiosciencesUniversity of MelbourneParkvilleVic.Australia
| | | | - Qi Li
- Institute of Applied EcologyChinese Academy of SciencesShenyangChina
| | - Simon A. Litchwark
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - Yunhui Liu
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | | | | | - Mounir Louhaichi
- International Center for Agricultural Research in the Dry Areas (ICARDA)Amman OfficeAmmanJordan
- Animal and Rangeland Sciences DepartmentOregon State UniversityCorvallisORUSA
| | - Gabor L. Lövei
- Department of AgroecologyFlakkebjerg Research CentreAarhus UniversitySlagelseDenmark
| | - Manuel Esteban Lucas‐Borja
- Department of Agroforestry Technology and Science and GeneticsSchool of Advanced Agricultural EngineeringCastilla La Mancha UniversityAlbaceteSpain
| | - Victor H. Luja
- Unidad Académica de TurismoCoordinación de Investigación y PosgradoUniversidad Autónoma de NayaritTepicMexico
| | - Matthew S. Luskin
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | | | - Kaoru Maeto
- Graduate School of Agricultural ScienceKobe UniversityKobeJapan
| | - Tibor Magura
- Department of EcologyUniversity of DebrecenDebrecenHungary
| | - Neil Aldrin Mallari
- Center for Conservation InnovationSan Jose Tagaytay CityPhilippines
- Biology DepartmentDe La Salle UniversityManilaPhilippines
| | - Louise A. Malone
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | | | - Jagoba Malumbres‐Olarte
- Center for Macroecology, Evolution and ClimateNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
| | - Salvador Mandujano
- Red de Biología y Conservación de VertebradosInstituto de Ecología A.C.XalapaMexico
| | | | | | | | | | - Eliana Martínez
- Universidad Nacional de Colombia, Ciudad UniversitariaBogotáColombia
| | - Guillermo Martínez Pastur
- Laboratorio de Recursos AgroforestalesCentro Austral de Investigaciones Científicas (CADIC)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)UshuaiaArgentina
| | | | | | - Vicente Mazimpaka
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
| | | | - Kyle P. McCarthy
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
| | | | - Sean McNamara
- Centre for Mined Land RehabilitationThe University of QueenslandBrisbaneQldAustralia
| | - Nagore G. Medina
- Departamento de Biología (Botánica)Facultad de CienciasUniversidad Autonoma de MadridMadridSpain
- Departamento de Biogeografía y Cambio GlobalMuseo Nacional de Ciencias Naturales (CSIC)MadridSpain
| | - Rafael Medina
- Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Jose L. Mena
- Museo de Historia Natural “Vera Alleman Haeghebaert”Universidad Ricardo PalmaLima 33Peru
| | - Estefania Mico
- Centro Iberoamericano de la Biodiversidad (CIBIO)Universidad de AlicanteAlicanteSpain
| | - Grzegorz Mikusinski
- Department of EcologySwedish University of Agricultural Sciences, Grimsö Wildlife Research StationRiddarhyttanSweden
| | - Jeffrey C. Milder
- Rainforest AllianceNew YorkNYUSA
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | - James R. Miller
- Department of Natural Resources & Environmental SciencesUniversity of IllinoisUrbanaILUSA
| | | | - Melinda L. Moir
- School of BiosciencesUniversity of MelbourneParkvilleVic.Australia
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
| | - Carolina L. Morales
- Lab. EcotonoINIBIOMA (Universidad Nacional del Comahue‐CONICET)BarilocheArgentina
| | | | - Muchai Muchane
- Department of Wildlife ManagementUniversity of EldoretEldoretKenya
| | - Sonja Mudri‐Stojnic
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - A. Nur Munira
- School of Biological SciencesUniversiti Sains MalaysiaPenangMalaysia
| | - Antonio Muoñz‐Alonso
- El Colegio de la Frontera SurEcología Evolutiva y ConservaciónSan Cristóbal de las CasasMexico
| | | | | | - A. Naithani
- Independent Research ScholarNew DelhiIndia
- Avian Diversity and Bioacoustic LabDepartment of ZoologyGurukula Kangri UniversityHaridwarIndia
| | - Michiko Nakagawa
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
| | - Akihiro Nakamura
- Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunChina
- Environmental Futures Research Institute, and Griffith School of EnvironmentGriffith UniversityNathanBrisbaneQldAustralia
| | | | - Shoji Naoe
- Forestry and Forest Products Research InstituteTsukubaJapan
| | - Guiomar Nates‐Parra
- Laboratorio de Investigaciones en Abejas (Departamento de Biología)Universidad Nacional de ColombiaBogotáColombia
| | | | | | - Paul K. Ndang'ang'a
- BirdLife International – Africa Partnership SecretariatNairobiKenya
- Ornithology SectionNational Museums of KenyaNairobiKenya
| | - Eike L. Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F)Frankfurt am MainGermany
| | | | - Violaine Nicolas
- Institut de Systématique, Évolution, BiodiversitéISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHEMuséum national d'Histoire naturelleSorbonne UniversitésParisFrance
| | | | - Norbertas Noreika
- Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
- Department of Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Olivia Norfolk
- School of BiologyThe University of NottinghamUniversity ParkNottinghamUK
| | - Jorge Ari Noriega
- Laboratorio de Zoología y Ecología Acuática – LAZOEAUniversidad de Los AndesBogotáColombia
| | - David A. Norton
- School of ForestryUniversity of CanterburyChristchurchNew Zealand
| | | | - A. Justin Nowakowski
- Department of Wildlife, Fish and Conservation BiologyUniversity of California, DavisDavisCAUSA
| | - Catherine Numa
- IUCN‐Centre for Mediterranean CooperationCampanillas, MálagaSpain
| | - Niall O'Dea
- Oxford University Centre for the EnvironmentUniversity of OxfordOxfordUK
| | - Patrick J. O'Farrell
- Natural Resources and the EnvironmentCSIRStellenboschSouth Africa
- Plant Conservation UnitBiological SciencesUniversity of Cape TownRondeboschSouth Africa
| | - William Oduro
- Wildlife and Range Management DepartmentFaculty of Renewable Natural Resources (FRNR)College of Agriculture and Natural Resources (CANR)Kwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
- International Programme Office (IPO)Vice Chancellor's OfficeKwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
| | - Sabine Oertli
- Naturschutz – Planung und BeratungWiesendangenSwitzerland
| | - Caleb Ofori‐Boateng
- Department of Wildlife and Range ManagementKwame Nkrumah University of Science and TechnologyKumasiGhana
- Forestry Research Institute of GhanaKumasiGhana
| | | | - Vicencio Oostra
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | | | - Samuel Eduardo Otavo
- Laboratorio de Ecología del PaisajeFacultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
| | | | - Juan Paritsis
- Laboratorio EcotonoCONICET–INIBIOMAUniversidad Nacional del ComahueBarilocheArgentina
| | - Alejandro Parra‐H
- Laboratorio de Investigaciones en AbejasLABUNUniversidad Nacional de ColombiaBogotá D.C.Colombia
| | - Luke Parry
- Lancaster Environment CentreLancaster UniversityLancasterUK
- Universidade Federal do Pará (UFPA)Núcleo de Altos Estudos Amazonicos (NAEA)BelémBrazil
| | - Guy Pe'er
- Department of Community EcologyUFZHelmholtz Centre for Environmental ResearchHalleGermany
- German Centre for Integrative Biodiversity Research (iDiv)Halle‐Jena‐LeipzigLeipzigGermany
| | - Peter B. Pearman
- Department of Plant Biology and EcologyFaculty of Science and TechnologyUniversity of the Basque CountryLeioaSpain
- IKERBASQUE. Basque Foundation for ScienceBilbaoSpain
| | - Nicolás Pelegrin
- Instituto de Diversidad y Ecología Animal (IDEA, CONICET‐UNC) and Centro de Zoología AplicadaFCEFyNUniversidad Nacional de CórdobaCórdobaArgentina
| | - Raphaël Pélissier
- IRDUMR AMAPTA A51/PS2Montpellier cedex 05France
- French Institute of PondicherryUMIFRE 21 CNRS‐MAEEPuducherryIndia
| | - Carlos A. Peres
- School of Environmental SciencesUniversity of East AngliaNorwichUK
| | - Pablo L. Peri
- National Institute of Agricultural Technology (INTA)Río GallegosArgentina
- National University of Southern Patagonia (UNPA)Río GallegosArgentina
- National Commission of Scientist Research and Technology (CONICET)Buenos Aires, Argentina
| | | | - Theodora Petanidou
- Laboratory of Biogeography & EcologyDepartment of GeographyUniversity of the AegeanMytileneGreece
| | - Marcell K. Peters
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | | | - Ben Phalan
- Conservation Science GroupDepartment of ZoologyUniversity of CambridgeCambridgeUK
| | - T. Keith Philips
- Systematics and Evolution LaboratoryDepartment of BiologyWestern Kentucky UniversityBowling GreenKYUSA
| | - Finn C. Pillsbury
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmesIAUSA
| | - Jimmy Pincheira‐Ulbrich
- Departamento de ZoologíaFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Facultad de Recursos NaturalesEscuela de Ciencias AmbientalesLaboratorio de Planificación TerritorialUniversidad Católica de TemucoTemucoChile
| | - Eduardo Pineda
- Biología y Conservación de VertebradosInstituto de Ecología A.C.El Haya, XalapaMexico
| | - Joan Pino
- CREAFCerdanyola del Vallès, CataloniaSpain
- Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Jaime Pizarro‐Araya
- Laboratorio de Entomología EcológicaDepartamento de BiologíaFacultad de CienciasUniversidad de La SerenaLa SerenaChile
| | - A. J. Plumptre
- Albertine Rift ProgramWildlife Conservation SocietyKampalaUganda
| | - Santiago L. Poggio
- IFEVA/Cátedra de Producción VegetalDepartamento de Producción VegetalFacultad de AgronomíaUniversidad de Buenos Aires/CONICET.Buenos AiresArgentina
| | - Natalia Politi
- Directora del Programa Conservación de Biodiversidad en Bosques SubtropicalesCátedra de Desarrollo Sustentable y BiodiversidadFacultad de Ciencias AgrariasUniversidad Nacional de JujuyCIT‐Jujuy CONICET, Fundaciòn CEBioSan Salvador de Jujuy, Argentina
| | - Pere Pons
- Departament de Ciències AmbientalsUniversitat de GironaGironaSpain
| | | | - Eileen F. Power
- BotanySchool of Natural SciencesTrinity College DublinDublin 2Ireland
| | - Steven J. Presley
- Center for Environmental Sciences and Engineering & Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Vânia Proença
- MARETEC, Instituto Superior TécnicoUniversidade de LisboaLisbonPortugal
| | - Marino Quaranta
- CREA‐ABP, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'agrobiologia e la pedologiaFirenzeItaly
| | - Carolina Quintero
- Laboratorio EcotonoCONICET–INIBIOMAUniversidad Nacional del ComahueBarilocheArgentina
| | - Romina Rader
- Ecosystem Management, School of Environment and Rural ScienceUniversity of New EnglandArmidaleNSWAustralia
| | - B. R. Ramesh
- French Institute of PondicherryUMIFRE 21 CNRS‐MAEEPuducherryIndia
| | | | - Jai Ranganathan
- National Center for Ecological Analysis and SynthesisUniversity of California, Santa BarbaraSanta BarbaraCAUSA
| | | | | | - J. Leighton Reid
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSaint LouisMOUSA
| | - Yana T. Reis
- Departamento de BiologiaUniversidade Federal de SergipeSão Cristóvão/SeBrazil
| | | | - Juan Carlos Rey‐Velasco
- Entomology Colletion, Systematics and Biogeography LaboratorySchool of BiologyIndustrial University of SantanderBucaramangaColombia
| | - Chevonne Reynolds
- Percy FitzPatrick Institute of African OrnithologyDST/NRF Centre of ExcellenceUniversity of Cape TownRondeboschCape TownSouth Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandWitsSouth Africa
| | - Danilo Bandini Ribeiro
- Centro de Ciências Biológicas e da SaúdeUniversidade Federal de Mato Grosso do SulCampo GrandeBrazil
| | | | - Barbara A. Richardson
- EdinburghUK
- Luquillo LTER, Institute for Tropical Ecosystem Studies, College of Natural SciencesUniversity of Puerto Rico at Rio PiedrasSan JuanPRUSA
| | - Michael J. Richardson
- EdinburghUK
- Luquillo LTER, Institute for Tropical Ecosystem Studies, College of Natural SciencesUniversity of Puerto Rico at Rio PiedrasSan JuanPRUSA
| | - Rodrigo Macip Ríos
- Escuela Nacional de Estudios SuperioresUniversidad Nacional Autónoma de MéxicoMoreliaMexico
| | - Richard Robinson
- Science and Conservation DivisionDepartment of Parks and WildlifeManjimupWAAustralia
| | - Carolina A. Robles
- PROPLAME‐PRHIDEB‐CONICETDepartamento de Biodiversidad y Biología ExperimentalFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad Universitaria(CP1428EHA) Ciudad Autónoma de Buenos AiresArgentina
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
- LOEWE Biodiversity and Climate Research Centre BiK‐FFrankfurt/MainGermany
| | - Luz Piedad Romero‐Duque
- Facultad de Ciencias AmbientalesUniversidad de Ciencias Aplicadas y Ambientales U.D.C.ABogotáColombia
| | - Matthias Rös
- Catedras CONACYTCIIDIR, Unidad Oaxaca, IPNSanta Cruz Xoxocotlán, Mexico
| | - Loreta Rosselli
- Universidad de Ciencias Aplicadas y Ambientales U.D.C.A.BogotáColombia
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Dana S. Roth
- School of Natural Resources and EnvironmentUniversity of MichiganAnn ArborMIUSA
| | - T'ai H. Roulston
- Department of Environmental SciencesUniversity of VirginiaCharlottesvilleVAUSA
- Blandy Experimental FarmBoyceVAUSA
| | - Laurent Rousseau
- Département des sciences biologiques (SB)Universitédu Québec à Montréal (UQÀM)MontréalQCCanada
| | | | | | - Jonathan P. Sadler
- School of Geography, Earth and Environmental SciencesUniversity of BirminghamBirminghamUK
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest ProtectionUniversity of West HungarySopronHungary
| | - Romeo A. Saldaña‐Vázquez
- Red de Ecología FuncionalInstituto de Ecología A.C. Carretera antigua a CoatepecEl Haya, XalapaMexico
| | - Katerina Sam
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
- Biology Centre CASInstitute of EntomologyCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Ulrika Samnegård
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Department of Biology/BiodiversityLund UniversityLundSweden
| | - Joana Santana
- CIBIO/InBioCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Xavier Santos
- CIBIO/InBioCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | | | | | - Menno Schilthuizen
- Naturalis Biodiversity CenterCR LeidenThe Netherlands
- Institute for Tropical Biology and ConservationUniversiti Malaysia Sabah, Jalan UMSKota KinabaluMalaysia
| | - Ute Schmiedel
- Biocentre Klein Flottbek & Botanical GardenUniversity of HamburgHamburgGermany
| | - Christine B. Schmitt
- Center for Development Research (ZEF)University of BonnBonnGermany
- Chair for Landscape ManagementUniversity of FreiburgFreiburgGermany
| | - Nicole L. Schon
- AgResearch LimitedLincoln Research CentreChristchurchNew Zealand
| | - Christof Schüepp
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Katharina Schumann
- Institute for Ecology, Evolution and DiversityGoethe University FrankfurtFrankfurt am MainGermany
| | - Oliver Schweiger
- Department of Community EcologyUFZHelmholtz Centre for Environmental ResearchHalleGermany
| | - Dawn M. Scott
- Biology and Biomedical Sciences DivisionUniversity of BrightonBrightonUK
| | | | | | - Steven S. Seefeldt
- School of Natural Resources and ExtensionUniversity of Alaska FairbanksFairbanksAKUSA
| | | | - Graeme Shannon
- College of Natural SciencesBangor UniversityBangor, GwyneddUK
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Douglas Sheil
- Department of Ecology and Natural Resource Management (INA)Norwegian University of Life Sciences (NMBU)ÅsNorway
| | - Frederick H. Sheldon
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLAUSA
- Baton RougeLAUSA
| | - Eyal Shochat
- Department of Life SciencesBen‐Gurion University of the NegevBe'er ShevaIsrael
- The Yerucham Center of Ornithology and EcologyYeruchamIsrael
| | - Stefan J. Siebert
- Unit for Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
| | | | | | | | - Jo Smith
- Organic Research CentreElm FarmNewburyUK
| | - Allan H. Smith‐Pardo
- United States Department of AgricultureSouth San FranciscoCAUSA
- Universidad Nacional de ColombiaSede MedellinMedellinColombia
| | - Navjot S. Sodhi
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Eduardo J. Somarriba
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)Tropical Agricultural Research and Higher Education CenterTurrialbaCosta Rica
| | - Ramón A. Sosa
- Ecología de Comunidades Ãridas y Semiaridas (EComAS)Departamento de RecursosFacultad de Ciencias Exactas y NaturalesUNLPam.Santa rosaLa PampaUruguay
| | - Grimaldo Soto Quiroga
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)Tropical Agricultural Research and Higher Education CenterTurrialbaCosta Rica
- Gobierno Autónomo Departamental Santa CruzSanta Cruz de la SierraBolivia
| | - Martin‐Hugues St‐Laurent
- Université du Québec à RimouskiCentre for Northern Research, Centre for Forest StudiesRimouskiQCCanada
| | | | - Constanti Stefanescu
- CREAFCerdanyola del Vallès, CataloniaSpain
- Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- Museu de Ciències Naturals de GranollersGranollersBarcelonaSpain
| | - Ingolf Steffan‐Dewenter
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Philip C. Stouffer
- School of Renewable Natural ResourcesLouisiana State University Agricultural CenterBaton RougeLAUSA
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da AmazôniaManausBrazil
| | - Jane C. Stout
- BotanySchool of Natural SciencesTrinity College DublinDublin 2Ireland
| | - Ayron M. Strauch
- Department of Natural Resources and Environmental ManagementUniversity of HawaiiManoaHonoluluHIUSA
| | - Matthew J. Struebig
- Durrell Institute of Conservation and Ecology (DICE)School of Anthropology and ConservationUniversity of KentCanterburyUK
| | - Zhimin Su
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesChaoyang DistrictBeijingChina
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
| | - Marcela Suarez‐Rubio
- Institute of ZoologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Shinji Sugiura
- Graduate School of Agricultural ScienceKobe UniversityKobeJapan
| | | | - Yik‐Hei Sung
- Department of BiologyHong Kong Baptist UniversityKowloon Tong, Hong Kong SARChina
| | - Hari Sutrisno
- Zoological DivisionResearch Center For BiologyThe Indonesian Institute of SciencesCibinongBogorIndonesia
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & BiodiversityDepartment of BioscienceAarhus UniversityAarhus CDenmark
| | - Tiit Teder
- Department of Zoology, Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Caragh G. Threlfall
- School of Ecosystem and Forest Science, Faculty of ScienceThe University of MelbourneRichmondVic.Australia
| | - Anu Tiitsaar
- Department of Zoology, Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Jacqui H. Todd
- The New Zealand Institute for Plant & Food Research LimitedAucklandNew Zealand
| | | | - Ignasi Torre
- Museu de Ciències Naturals de GranollersGranollersBarcelonaSpain
| | - Béla Tóthmérész
- MTA‐DE Biodiversity and Ecosystem Services Research GroupDebrecenHungary
| | - Teja Tscharntke
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | - Edgar C. Turner
- Insect Ecology GroupDepartment of ZoologyUniversity of CambridgeCambridgeUK
| | - Jason M. Tylianakis
- Department of Life SciencesImperial College LondonAscotUK
- Centre for Integrative Ecology, School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - Nicolas Urbina‐Cardona
- Department of Ecology and TerritorySchool of Environmental and Rural StudiesPontificia Universidad JaverianaBogotaColombia
| | - Denis Vallan
- Naturhistorisches Museum BaselLeiter BiowissenschaftenBaselSwitzerland
| | | | | | - Kiril Vassilev
- Institute of Biodiversity and Ecosystem ResearchBulgarian Academy of ScienceSofiaBulgaria
| | - Hans A. F. Verboven
- Division Forest, Nature, and LandscapeDepartment of Earth & Environmental SciencesKU LeuvenLeuvenBelgium
| | - Maria João Verdasca
- Museu Nacional de História Natural e da CiênciaBorboletário – Depart. ZoologiaLisboaPortugal
| | - José R. Verdú
- Centro Iberoamericano de la Biodiversidad (CIBIO)Universidad de AlicanteAlicanteSpain
| | - Carlos H. Vergara
- Departamento de Ciencias Químico‐BiológicasUniversidad de las Américas PueblaCholulaMexico
| | - Pablo M. Vergara
- Departamento de Gestión AgrariaUniversidad de Santiago de ChileSantiagoChile
| | | | | | - Lien Van Vu
- Vietnam National Museum of NatureVietnam Academy of Science and TechnologyCau GiayHanoiVietnam
| | | | - Tony R. Walker
- School of BiologyThe University of NottinghamUniversity ParkNottinghamUK
- School for Resource and Environmental StudiesFaculty of ManagementDalhousie UniversityHalifaxNSCanada
| | - Hua‐Feng Wang
- Key Laboratory of Protection and Development Utilization of Tropical Crop Germplasm Resource, Ministry of Education, College of Horticulture and Landscape AgricultureHainan UniversityHaikouChina
| | - Yanping Wang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | - James I. Watling
- Department of BiologyJohn Carroll UniversityUniversity HeightsOHUSA
| | - Britta Weller
- Biocentre GrindelUniversity of HamburgHamburgGermany
| | - Konstans Wells
- The Environment Institute and School of Earth and Environmental SciencesThe University of AdelaideAdelaideSAAustralia
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | - Catrin Westphal
- AgroecologyDepartment of Crop SciencesGeorg‐August UniversityGöttingenGermany
| | - Edward D. Wiafe
- Department of Environmental and Natural ResourcesPresbyterian University CollegeAkropong AkuapemGhana
| | | | - Michael R. Willig
- Center for Environmental Sciences & EngineeringUniversity of ConnecticutStorrsCTUSA
- Department of Ecology & Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | | | - Jan H. D. Wolf
- Institute for Biodiversity and Ecosystem Dynamics (IBED)University of AmsterdamGE AmsterdamThe Netherlands
| | - Volkmar Wolters
- Department of Animal EcologyJustus‐Liebig‐UniversityGiessenGermany
| | - Ben A. Woodcock
- NERC Centre for Ecology & HydrologyCrowmarsh GiffordWallingfordUK
| | - Jihua Wu
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Joseph M. Wunderle
- International Institute of Tropical ForestryUSDA Forest Service, Sabana Field Research StationLuquilloPRUSA
| | - Yuichi Yamaura
- Forestry and Forest Products Research InstituteTsukubaJapan
| | | | - Douglas W. Yu
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichUK
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Andrey S. Zaitsev
- Department of Animal EcologyJustus‐Liebig‐UniversityGiessenGermany
- A. N. Severtsov Institute of Ecology and EvolutionMoscowRussia
| | - Juliane Zeidler
- Integrated Environmental Consultants Namibia (IECN)WindhoekNamibia
| | - Fasheng Zou
- Guangdong Entomological Institute/South China Institute of Endangered AnimalsGuangzhouChina
| | - Ben Collen
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and EnvironmentResearchUniversity College LondonLondonUK
| | - Rob M. Ewers
- Department of Life SciencesImperial College LondonAscotUK
| | - Georgina M. Mace
- Department of Genetics, Evolution and EnvironmentCentre for Biodiversity and EnvironmentResearchUniversity College LondonLondonUK
| | - Drew W. Purves
- Computational Ecology and Environmental ScienceMicrosoft ResearchCambridgeUK
| | - Jörn P. W. Scharlemann
- United Nations Environment Programme World Conservation Monitoring CentreCambridgeUK
- School of Life SciencesUniversity of SussexBrightonUK
| | - Andy Purvis
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
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Nelson EJ, Helmus MR, Cavender-Bares J, Polasky S, Lasky JR, Zanne AE, Pearse WD, Kraft NJB, Miteva DA, Fagan WF. Commercial Plant Production and Consumption Still Follow the Latitudinal Gradient in Species Diversity despite Economic Globalization. PLoS One 2016; 11:e0163002. [PMID: 27706180 PMCID: PMC5051709 DOI: 10.1371/journal.pone.0163002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 08/31/2016] [Indexed: 11/29/2022] Open
Abstract
Increasing trade between countries and gains in income have given consumers around the world access to a richer and more diverse set of commercial plant products (i.e., foods and fibers produced by farmers). According to the economic theory of comparative advantage, countries open to trade will be able to consume more–in terms of volume and diversity–if they concentrate production on commodities that they can most cost-effectively produce, while importing goods that are expensive to produce, relative to other countries. Here, we perform a global analysis of traded commercial plant products and find little evidence that increasing globalization has incentivized agricultural specialization. Instead, a country’s plant production and consumption patterns are still largely determined by local evolutionary legacies of plant diversification. Because tropical countries harbor a greater diversity of lineages across the tree of life than temperate countries, tropical countries produce and consume a greater diversity of plant products than do temperate countries. In contrast, the richer and more economically advanced temperate countries have the capacity to produce and consume more plant species than the generally poorer tropical countries, yet this collection of plant species is drawn from fewer branches on the tree of life. Why have countries not increasingly specialized in plant production despite the theoretical financial incentive to do so? Potential explanations include the persistence of domestic agricultural subsidies that distort production decisions, cultural preferences for diverse local food production, and that diverse food production protects rural households in developing countries from food price shocks. Less specialized production patterns will make crop systems more resilient to zonal climatic and social perturbations, but this may come at the expense of global crop production efficiency, an important step in making the transition to a hotter and more crowded world.
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Affiliation(s)
- Erik J. Nelson
- Department of Economics, Bowdoin College, Brunswick, Maine, United States of America
- * E-mail:
| | - Matthew R. Helmus
- Center for Biodiversity, Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Ecological Sciences—Animal Ecology, Vrije Universiteit, Amsterdam, Netherlands
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Institute on Environment, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Stephen Polasky
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Institute on Environment, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Applied Economics, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jesse R. Lasky
- Earth Institute, Columbia University, New York, New York, United States of America
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, United States of America
| | - Amy E. Zanne
- Department of Biological Sciences, George Washington University, Washington, D.C., United States of America
| | - William D. Pearse
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan J. B. Kraft
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Daniela A. Miteva
- Department of Agricultural, Environmental, and Development Economics, The Ohio State University, Columbus, Ohio, United States of America
| | - William F. Fagan
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
- National Socio-environmental Synthesis Center (SESYNC), University of Maryland, Annapolis, Maryland, United States of America
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32
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Fransz P, Linc G, Lee C, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. Plant J 2016; 88:159-178. [PMID: 27436134 PMCID: PMC5113708 DOI: 10.1111/tpj.13262] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 05/02/2023]
Abstract
Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.
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Affiliation(s)
- Paul Fransz
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
| | - Gabriella Linc
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Centre for Agricultural ResearchHungarian Academy of SciencesAgricultural InstituteMartonvásárHungary
| | - Cheng‐Ruei Lee
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - Hoda Ali
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address: Department of Genetics and CytologyNational Research CenterCairoEgypt
| | - Janny Peters
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Peter van Dam
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
- Present address: Department of Molecular Plant PathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Xianwen Ji
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
| | - Mateusz Kuzak
- MAD, Dutch Genomics Service & Support ProviderSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Netherlands eScience CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Tom Gerats
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Ingo Schubert
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | - Vincent Colot
- Unité de Recherche en Génomique Végétale (URGV)INRA/CNRS/UEVE 2 Rue Gaston CrémieuxEvry Cedex91057France
- Present address: Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - Rob Martienssen
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkNY11724USA
| | - Maarten Koornneef
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
- Max Planck Institute for Plant Breeding ResearchKöln50829Germany
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Hans de Jong
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
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33
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Monroe JG, McGovern C, Lasky JR, Grogan K, Beck J, McKay JK. Adaptation to warmer climates by parallel functional evolution of
CBF
genes in
Arabidopsis thaliana. Mol Ecol 2016; 25:3632-44. [DOI: 10.1111/mec.13711] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/20/2016] [Indexed: 01/05/2023]
Affiliation(s)
- J. Grey Monroe
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO 80523 USA
| | - Cullen McGovern
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
| | - Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park PA 16802 USA
| | - Kelsi Grogan
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
| | - James Beck
- Department of Biological Sciences Wichita State University Wichita KS 67260 USA
- Botanical Research Institute of Texas Fort Worth TX 76107 USA
| | - John K. McKay
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO 80523 USA
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34
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Keller TE, Lasky JR, Yi SV. The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana. Mol Ecol 2016; 25:1823-37. [PMID: 26850505 DOI: 10.1111/mec.13573] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/30/2015] [Accepted: 12/17/2015] [Indexed: 02/03/2023]
Abstract
Epigenetic changes can occur due to extracellular environmental conditions. Consequently, epigenetic mechanisms can play an intermediate role to translate environmental signals to intracellular changes. Such a role might be particularly important in plants, which often show strong local adaptation and have the potential for heritable epigenetic states. However, little is currently known about the role of epigenetic variation in the ecological mechanisms of adaptation. Here, we used multivariate redundancy analyses to examine genomewide associations between DNA methylation polymorphisms and climate variation in two independent panels of Arabidopsis accessions, including 122 Eurasian accessions as well as in a regional panel of 148 accessions in Sweden. At the single-nucleotide methylation level, climate and space (geographic spatial structure) explain small yet significant amount of variation in both panels. On the other hand, when viewed in a context of genomic clusters of methylated and unmethylated cytosines, climate and space variables explain much greater amounts of variation in DNA methylation than those explained by variation at the single-nucleotide level. We found that the single-nucleotide methylation polymorphisms with the strongest associations with climate were enriched in transposable elements and in potentially RNA-directed methylation contexts. When viewed in the context of genomic clusters, variation of DNA methylation at different sequence contexts exhibit distinctive segregation along different axes of variation in the redundancy analyses. Genomewide methylation showed much stronger associations with climate within the regional panel (Sweden) compared to the global (Eurasia). Together, these findings indicate that genetic and epigenetic variation across the genome may play a role in response to climate conditions and local adaptation.
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Affiliation(s)
- Thomas E Keller
- School of Biology, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jesse R Lasky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA.,Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Soojin V Yi
- School of Biology, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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35
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Uriarte M, Lasky JR, Boukili VK, Chazdon RL. A trait‐mediated, neighbourhood approach to quantify climate impacts on successional dynamics of tropical rainforests. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12576] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- María Uriarte
- Department of Ecology, Evolution & Environmental Biology Columbia University New York NY 10027 USA
| | - Jesse R. Lasky
- Department of Ecology, Evolution & Environmental Biology Columbia University New York NY 10027 USA
| | - Vanessa K. Boukili
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269 USA
| | - Robin L. Chazdon
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269 USA
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36
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Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR. Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes. Mol Ecol 2015; 25:104-20. [PMID: 26576498 DOI: 10.1111/mec.13476] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 12/18/2022]
Abstract
The spatial structure of the environment (e.g. the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multiscale habitat structure common in nature. Here, we use simulations to pursue two goals: (i) we explore how landscape heterogeneity, dispersal ability and selection affect the strength of local adaptation, and (ii) we evaluate the performance of several genotype-environment association (GEA) methods for detecting loci involved in local adaptation. We found that the strength of local adaptation increased in spatially aggregated selection regimes, but remained strong in patchy landscapes when selection was moderate to strong. Weak selection resulted in weak local adaptation that was relatively unaffected by landscape heterogeneity. In general, the power of detection methods closely reflected levels of local adaptation. False-positive rates (FPRs), however, showed distinct differences across GEA methods based on levels of population structure. The univariate GEA approach had high FPRs (up to 55%) under limited dispersal scenarios, due to strong isolation by distance. By contrast, multivariate, ordination-based methods had uniformly low FPRs (0-2%), suggesting these approaches can effectively control for population structure. Specifically, constrained ordinations had the best balance of high detection and low FPRs and will be a useful addition to the GEA toolkit. Our results provide both theoretical and practical insights into the conditions that shape local adaptation and how these conditions impact our ability to detect selection.
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Affiliation(s)
- Brenna R Forester
- Nicholas School of the Environment, University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Stéphane Joost
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory of Geographic Information Systems (LASIG), CH-1015, Lausanne, Switzerland
| | - Erin L Landguth
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Jesse R Lasky
- Earth Institute, and Department of Ecology, Evolution & Environmental Biology, Columbia University, New York, NY, 10027, USA.,Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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37
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Lasky JR, Bachelot B, Muscarella R, Schwartz N, Forero-Montaña J, Nytch CJ, Swenson NG, Thompson J, Zimmerman JK, Uriarte M. Ontogenetic shifts in trait-mediated mechanisms of plant community assembly. Ecology 2015; 96:2157-69. [PMID: 26405741 DOI: 10.1890/14-1809.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Identifying the processes that maintain highly diverse plant communities remains a central goal in ecology. Species variation in growth and survival rates across ontogeny, represented by tree size classes and life history stage-specific niche partitioning, are potentially important mechanisms for promoting forest diversity. However, the role of ontogeny in mediating competitive dynamics and promoting functional diversity is not well understood, particular in high-diversity systems such as tropical forests. The interaction between interspecific functional trait variation and ontogenetic shifts in competitive dynamics may yield insights into the ecophysiological mechanisms promoting community diversity. We investigated how functional trait (seed size, maximum height, SLA, leaf N, and wood density) associations with growth, survival, and response to competing neighbors differ among seedlings and two size classes of trees in a subtropical rain forest in Puerto Rico. We used a hierarchical Bayes model of diameter growth and survival to infer trait relationships with ontogenetic change in competitive dynamics. Traits were more strongly associated with average growth and survival than with neighborhood interactions, and were highly consistent across ontogeny for most traits. The associations between trait values and tree responses to crowding by neighbors showed significant shifts as trees grew. Large trees exhibited greater growth as the difference in species trait values among neighbors increased, suggesting trait-associated niche partitioning was important for the largest size class. Our results identify potential axes of niche partitioning and performance-equalizing functional trade-offs across ontogeny, promoting species coexistence in this diverse forest community.
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Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP. Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 2015; 1:e1400218. [PMID: 26601206 PMCID: PMC4646766 DOI: 10.1126/sciadv.1400218] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/26/2015] [Indexed: 05/15/2023]
Abstract
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.
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Affiliation(s)
- Jesse R. Lasky
- Earth Institute, and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10025, USA
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Punna Ramu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - C. Tom Hash
- ICRISAT Sahelian Center, BP 12404, Niamey, Niger
| | - Jason Bonnette
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA
| | - Katie Hyma
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Charlotte Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture–Agricultural Research Service, Ithaca, NY 14853, USA
| | - Zachary Brenton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Stephen Kresovich
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Geoffrey P. Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Corresponding author. E-mail:
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Lasky JR, Uriarte M, Boukili VK, Erickson DL, John Kress W, Chazdon RL. Corrigendum to “The relationship between tree biodiversity and biomass dynamics changes with tropical forest succession”. Ecol Lett 2014. [DOI: 10.1111/ele.12370] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jesse R. Lasky
- Earth Institute; Columbia University; New York NY USA
- Department of Ecology; Evolution and Environmental Biology; Columbia University; New York NY USA
| | - María Uriarte
- Department of Ecology; Evolution and Environmental Biology; Columbia University; New York NY USA
| | - Vanessa K. Boukili
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
| | - David L. Erickson
- Department of Botany; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - W. John Kress
- Department of Botany; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Robin L. Chazdon
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
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Lasky JR, Des Marais DL, Lowry DB, Povolotskaya I, McKay JK, Richards JH, Keitt TH, Juenger TE. Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana. Mol Biol Evol 2014; 31:2283-96. [PMID: 24850899 PMCID: PMC4137704 DOI: 10.1093/molbev/msu170] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients.
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Affiliation(s)
- Jesse R Lasky
- Department of Integrative Biology, University of Texas at AustinEarth Institute and Department of Ecology, Evolution and Environmental Biology, Columbia University
| | | | - David B Lowry
- Department of Integrative Biology, University of Texas at Austin
| | - Inna Povolotskaya
- Bioinformatics and Genomics Program, Centre for Genomic Regulation, Barcelona, Spain
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University
| | | | - Timothy H Keitt
- Department of Integrative Biology, University of Texas at Austin
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin
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Whitfeld TJS, Lasky JR, Damas K, Sosanika G, Molem K, Montgomery RA. Species Richness, Forest Structure, and Functional Diversity During Succession in the New Guinea Lowlands. Biotropica 2014. [DOI: 10.1111/btp.12136] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy J. S. Whitfeld
- Department of Ecology and Evolutionary Biology; Brown University; 34 Olive Street, Box G-B225 Providence RI 02912 U.S.A
| | - Jesse R. Lasky
- The Earth Institute; Columbia University; New York NY 10027 U.S.A
- Department of Ecology, Evolution and Environmental Biology; Columbia University; New York NY 10027 U.S.A
| | - Kipiro Damas
- PNG Forest Research Institute; PO Box 314 Lae Morobe Province Papua New Guinea
| | - Gibson Sosanika
- The New Guinea Binatang Research Center; PO Box 604 Madang Papua New Guinea
- Griffith University; 170 Kessels Road Nathan QLD 4111 Australia
| | - Kenneth Molem
- The New Guinea Binatang Research Center; PO Box 604 Madang Papua New Guinea
| | - Rebecca A. Montgomery
- Department of Forest Resources; University of Minnesota; 1530 Cleveland Ave. N St. Paul MN 55108 U.S.A
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Lasky JR, Uriarte M, Boukili VK, Erickson DL, John Kress W, Chazdon RL. The relationship between tree biodiversity and biomass dynamics changes with tropical forest succession. Ecol Lett 2014; 17:1158-67. [DOI: 10.1111/ele.12322] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/01/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Jesse R. Lasky
- Earth Institute; Columbia University; New York NY USA
- Department of Ecology, Evolution and Environmental Biology; Columbia University; New York NY USA
| | - María Uriarte
- Department of Ecology, Evolution and Environmental Biology; Columbia University; New York NY USA
| | - Vanessa K. Boukili
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
| | - David L. Erickson
- Department of Botany; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - W. John Kress
- Department of Botany; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Robin L. Chazdon
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
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Lasky JR, Yang J, Zhang G, Cao M, Tang Y, Keitt TH. The role of functional traits and individual variation in the co-occurrence ofFicusspecies. Ecology 2014; 95:978-90. [DOI: 10.1890/13-0437.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Verslues PE, Lasky JR, Juenger TE, Liu TW, Kumar MN. Genome-wide association mapping combined with reverse genetics identifies new effectors of low water potential-induced proline accumulation in Arabidopsis. Plant Physiol 2014; 164:144-59. [PMID: 24218491 PMCID: PMC3875797 DOI: 10.1104/pp.113.224014] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/10/2013] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) exhibits natural genetic variation in drought response, including varying levels of proline (Pro) accumulation under low water potential. As Pro accumulation is potentially important for stress tolerance and cellular redox control, we conducted a genome-wide association (GWAS) study of low water potential-induced Pro accumulation using a panel of natural accessions and publicly available single-nucleotide polymorphism (SNP) data sets. Candidate genomic regions were prioritized for subsequent study using metrics considering both the strength and spatial clustering of the association signal. These analyses found many candidate regions likely containing gene(s) influencing Pro accumulation. Reverse genetic analysis of several candidates identified new Pro effector genes, including thioredoxins and several genes encoding Universal Stress Protein A domain proteins. These new Pro effector genes further link Pro accumulation to cellular redox and energy status. Additional new Pro effector genes found include the mitochondrial protease LON1, ribosomal protein RPL24A, protein phosphatase 2A subunit A3, a MADS box protein, and a nucleoside triphosphate hydrolase. Several of these new Pro effector genes were from regions with multiple SNPs, each having moderate association with Pro accumulation. This pattern supports the use of summary approaches that incorporate clusters of SNP associations in addition to consideration of individual SNP probability values. Further GWAS-guided reverse genetics promises to find additional effectors of Pro accumulation. The combination of GWAS and reverse genetics to efficiently identify new effector genes may be especially applicable for traits difficult to analyze by other genetic screening methods.
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Lovell JT, Juenger TE, Michaels SD, Lasky JR, Platt A, Richards JH, Yu X, Easlon HM, Sen S, McKay JK. Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation. Proc Biol Sci 2013; 280:20131043. [PMID: 23698015 PMCID: PMC3774242 DOI: 10.1098/rspb.2013.1043] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 05/02/2013] [Indexed: 01/12/2023] Open
Abstract
An evolutionary response to selection requires genetic variation; however, even if it exists, then the genetic details of the variation can constrain adaptation. In the simplest case, unlinked loci and uncorrelated phenotypes respond directly to multivariate selection and permit unrestricted paths to adaptive peaks. By contrast, 'antagonistic' pleiotropic loci may constrain adaptation by affecting variation of many traits and limiting the direction of trait correlations to vectors that are not favoured by selection. However, certain pleiotropic configurations may improve the conditions for adaptive evolution. Here, we present evidence that the Arabidopsis thaliana gene FRI (FRIGIDA) exhibits 'adaptive' pleiotropy, producing trait correlations along an axis that results in two adaptive strategies. Derived, low expression FRI alleles confer a 'drought escape' strategy owing to fast growth, low water use efficiency and early flowering. By contrast, a dehydration avoidance strategy is conferred by the ancestral phenotype of late flowering, slow growth and efficient water use during photosynthesis. The dehydration avoidant phenotype was recovered when genotypes with null FRI alleles were transformed with functional alleles. Our findings indicate that the well-documented effects of FRI on phenology result from differences in physiology, not only a simple developmental switch.
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Affiliation(s)
- John T. Lovell
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Thomas E. Juenger
- Section of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Jesse R. Lasky
- Section of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Alexander Platt
- Department of Ecology and Evolutionary Biology and Interdepartmental Program on Bioinformatics, University of California, Los Angeles, CA, USA
| | - James H. Richards
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Xuhong Yu
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Hsien M. Easlon
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Saunak Sen
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - John K. McKay
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
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Lasky JR, Des Marais DL, McKay JK, Richards JH, Juenger TE, Keitt TH. Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate. Mol Ecol 2012; 21:5512-29. [PMID: 22857709 DOI: 10.1111/j.1365-294x.2012.05709.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well-studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214 051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large-scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among nonsynonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation.
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Affiliation(s)
- Jesse R Lasky
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78712-0253, USA.
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Affiliation(s)
- Jesse R. Lasky
- Section of Integrative Biology; University of Texas at Austin; 1 University Station A6700; 78712-0253; Austin; Texas
| | - Timothy H. Keitt
- Section of Integrative Biology; University of Texas at Austin; 1 University Station A6700; 78712-0253; Austin; Texas
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Lowry DB, Sheng CC, Lasky JR, Willis JH. Five anthocyanin polymorphisms are associated with an R2R3-MYB cluster in Mimulus guttatus (Phrymaceae). Am J Bot 2012; 99:82-91. [PMID: 22186184 DOI: 10.3732/ajb.1100285] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF STUDY Botanists have long been interested in the reasons for genetic variation among individuals, populations, and species of plants. The anthocyanin pathway is ideal for studying the evolution of such phenotypic variation. METHODS We used a combination of quantitative trait loci mapping and association studies to understand the genetic basis of variation in five anthocyanin phenotypes including calyx, corolla, and leaf coloration patterns that vary within and among populations of Mimulus guttatus. We then examined what genes might be responsible for this phenotypic variation and whether one of the traits, calyx spotting, is randomly distributed across the geographic range of the species. KEY RESULTS All five phenotypes in M. guttatus were primarily controlled by the same major locus (PLA1), which contains a tandem array of three R2R3-MYB genes known to be involved in the evolution of flower color in a related species of Mimulus. Calyx spotting was nonrandomly distributed across the range of M. guttatus and correlated with multiple climate variables. CONCLUSIONS The results of this study suggest that variation in R2R3-MYB genes is the primary cause of potentially important anthocyanin phenotypic variation within and among populations of M. guttatus, a finding consistent with recent theoretical and empirical research on flower color evolution.
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Affiliation(s)
- David B Lowry
- University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Lasky JR, Jetz W, Keitt TH. Conservation biogeography of the US-Mexico border: a transcontinental risk assessment of barriers to animal dispersal. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00765.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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