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Hulse SV, Bruns EL. The Emergence of Non-Linear Evolutionary Trade-offs and the Maintenance of Genetic Polymorphisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.595890. [PMID: 38853830 PMCID: PMC11160725 DOI: 10.1101/2024.05.29.595890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Evolutionary models of quantitative traits often assume trade-offs between beneficial and detrimental traits, requiring modelers to specify a function linking costs to benefits. The choice of trade-off function is often consequential; functions that assume diminishing returns (accelerating costs) typically lead to single equilibrium genotypes, while decelerating costs often lead to evolutionary branching. Despite their importance, we still lack a strong theoretical foundation to base the choice of trade-off function. To address this gap, we explore how trade-off functions can emerge from the genetic architecture of a quantitative trait. We developed a multi-locus model of disease resistance, assuming each locus had random antagonistic pleiotropic effects on resistance and fecundity. We used this model to generate genotype landscapes and explored how additive versus epistatic genetic architectures influenced the shape of the trade-off function. Regardless of epistasis, our model consistently led to accelerating costs. We then used our genotype landscapes to build an evolutionary model of disease resistance. Unlike other models with accelerating costs, our approach often led to genetic polymorphisms at equilibrium. Our results suggest that accelerating costs are a strong null model for evolutionary trade-offs and that the eco-evolutionary conditions required for polymorphism may be more nuanced than previously believed.
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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Morgan C, Knight E, Bomblies K. The meiotic cohesin subunit REC8 contributes to multigenic adaptive evolution of autopolyploid meiosis in Arabidopsis arenosa. PLoS Genet 2022; 18:e1010304. [PMID: 35830475 PMCID: PMC9312919 DOI: 10.1371/journal.pgen.1010304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/25/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
Genome duplication, which leads to polyploidy, poses challenges to the meiotic segregation of the now-multiple homologous chromosome copies. Genome scan data showed previously that adaptation to polyploid meiosis in autotetraploid Arabidopsis arenosa is likely multigenic, involving genes encoding interacting proteins. But what does this really mean? Functional follow-up studies to genome scans for multigenic traits remain rare in most systems, and thus many mysteries remain about the "functional architecture" of polygenic adaptations. Do different genes all contribute subtle and additive progression towards a fitness optimum, or are there more complex interactions? We previously showed that derived alleles of genes encoding two interacting meiotic axis proteins (ASY1 and ASY3) have additive functional consequences for meiotic adaptation. Here we study derived versus ancestral alleles of the meiotic cohesin subunit REC8, which has roles in chromatin condensation, recruiting the axes, and other critical functions in meiosis. We use genetic and cytological approaches to assess the functional effects of REC8 diploid versus tetraploid alleles, as well as their interaction with ancestral versus derived alleles of ASY1 and ASY3. We show that homozygotes for derived (tetraploid) REC8 alleles have significantly fewer unpaired univalents, a common problem in neotetraploids. Interactions with ASY1 and ASY3 are complex, with the genes in some cases affecting distinct traits, and additive or even antagonistic effects on others. These findings suggest that the road to meiotic adaptation in A. arenosa was perhaps neither straight nor smooth.
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Affiliation(s)
| | | | - Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Plant Molecular Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
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4
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Whiteman NK. Evolution in small steps and giant leaps. Evolution 2022; 76:67-77. [PMID: 35040122 PMCID: PMC9387839 DOI: 10.1111/evo.14432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 02/03/2023]
Abstract
The first Editor of Evolution was Ernst Mayr. His foreword to the first issue of Evolution published in 1947 framed evolution as a "problem of interaction" that was just beginning to be studied in this broad context. First, I explore progress and prospects on understanding the subsidiary interactions identified by Mayr, including interactions between parts of organisms, between individuals and populations, between species, and between the organism and its abiotic environment. Mayr's overall "problem of interaction" framework is examined in the context of coevolution within and among levels of biological organization. This leads to a comparison in the relative roles of biotic versus abiotic agents of selection and fluctuating versus directional selection, followed by stabilizing selection in shaping the genomic architecture of adaptation. Oligogenic architectures may be typical for traits shaped more by fluctuating selection and biotic selection. Conversely, polygenic architectures may be typical for traits shaped more by directional followed by stabilizing selection and abiotic selection. The distribution of effect sizes and turnover dynamics of adaptive alleles in these scenarios deserves further study. Second, I review two case studies on the evolution of acquired toxicity in animals, one involving cardiac glycosides obtained from plants and one involving bacterial virulence factors horizontally transferred to animals. The approaches used in these studies and the results gained directly flow from Mayr's vision of an evolutionary biology that revolves around the "problem of interaction."
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Affiliation(s)
- Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, California 94720,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720,
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5
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Connallon T, Hodgins KA. Allen Orr and the genetics of adaptation. Evolution 2021; 75:2624-2640. [PMID: 34606622 DOI: 10.1111/evo.14372] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023]
Abstract
Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro-mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well-known examples of large-effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small- and large-effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large-effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro-mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
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Kay KM, Surget-Groba Y. The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understorey herbs. Mol Ecol 2021; 31:4351-4363. [PMID: 34487383 DOI: 10.1111/mec.16165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many co-adapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.
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Affiliation(s)
- Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yann Surget-Groba
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Département de Biologie, Université du Québec en Outaouais, Ripon, QC, Canada
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7
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Esfeld K, Berardi AE, Moser M, Bossolini E, Freitas L, Kuhlemeier C. Pseudogenization and Resurrection of a Speciation Gene. Curr Biol 2018; 28:3776-3786.e7. [PMID: 30472000 DOI: 10.1016/j.cub.2018.10.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/05/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
Abstract
A persistent question in evolutionary biology is how complex phenotypes evolve and whether phenotypic transitions are reversible. Multiple losses of floral pigmentation have been documented in the angiosperms, but color re-gain has not yet been described, supporting that re-gain is unlikely. Pollinator-mediated selection in Petunia has resulted in several color shifts comprised of both losses and gains of color. The R2R3-MYB transcription factor AN2 has been identified as a major locus responsible for shifts in pollinator preference. Whereas the loss of visible color has previously been attributed to repeated pseudogenization of AN2, here, we describe the mechanism of an independent re-gain of floral color via AN2 evolution. In P. secreta, purple color is restored through the improbable resurrection of AN2 gene function from a non-functional AN2-ancestor by a single reading-frame-restoring mutation. Thus, floral color evolution in Petunia is mechanistically dependent on AN2 functionality, highlighting its role as a hotspot in color transitions and a speciation gene for the genus.
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Affiliation(s)
- Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Andrea E Berardi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Eligio Bossolini
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Loreta Freitas
- Department of Genetics, University Fed Rio Grande do Sul, POB 15053, Porto Alegre, 91501970 Rio Grande do Sul, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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8
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Abstract
Evolutionary conflict occurs when two parties can each affect a joint phenotype, but they gain from pushing it in opposite directions. Conflicts occur across many biological levels and domains but share many features. They are a major source of biological maladaptation. They affect biological diversity, often increasing it, at almost every level. Because opponents create selection that can be strong, persistent, and malevolent, conflict often leads to accelerated evolution and arms races. Conflicts might even drive the majority of adaptation, with pathogens leading the way as selective forces. The evolution of conflicts is complex, with outcomes determined partly by the relative evolvability of each party and partly by the kinds of power that each evolves. Power is a central issue in biology. In addition to physical strength and weapons, it includes strength from numbers and complexity; abilities to bind and block; advantageous timing; and abilities to acquire, use, and distort information.
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Affiliation(s)
- David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;,
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;,
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9
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Lamara M, Parent GJ, Giguère I, Beaulieu J, Bousquet J, MacKay JJ. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC PLANT BIOLOGY 2018; 18:231. [PMID: 30309315 PMCID: PMC6182838 DOI: 10.1186/s12870-018-1434-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Outbreaks of spruce budworm (SBW, Choristoneura fumiferana Clem.) cause major recurrent damage in boreal conifers such as white spruce (Picea glauca [Moench] Voss) and large losses of forest biomass in North America. Although defensive phenolic compounds have recently been linked to chemical resistance against SBW, their genetic basis remains poorly understood in forest trees, especially in conifers. Here, we used diverse association genetics approaches to discover genes and their variants that may control the accumulation of acetophenones, and dissect the genetic architecture of these defence compounds against SBW in white spruce mature trees. RESULTS Out of 4747 single nucleotide polymorphisms (SNPs) from 2312 genes genotyped in a population of 211 unrelated individuals, genetic association analyses identified 35 SNPs in 33 different genes that were significantly associated with the defence traits by using single-locus, multi-locus and multi-trait approaches. The multi-locus approach was particularly effective at detecting SNP-trait associations that explained a large fraction of the phenotypic variance (from 20 to 43%). Significant genes were regulatory including the NAC transcription factor, or they were involved in carbohydrate metabolism, falling into the binding, catalytic or transporter activity functional classes. Most of them were highly expressed in foliage. Weak positive phenotypic correlations were observed between defence and growth traits, indicating little or no evidence of defence-growth trade-offs. CONCLUSIONS This study provides new insights on the genetic architecture of tree defence traits, contributing to our understanding of the physiology of resistance mechanisms to biotic factors and providing a basis for the genetic improvement of the constitutive defence of white spruce against SBW.
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Affiliation(s)
- Mebarek Lamara
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | | | - Isabelle Giguère
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Beaulieu
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Bousquet
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - John J. MacKay
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
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11
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Cirilli M, Rossini L, Geuna F, Palmisano F, Minafra A, Castrignanò T, Gattolin S, Ciacciulli A, Babini AR, Liverani A, Bassi D. Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). BMC PLANT BIOLOGY 2017; 17:192. [PMID: 29100531 PMCID: PMC5670703 DOI: 10.1186/s12870-017-1117-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the lack of resistant sources, while suggesting the presence of a quantitative disease resistance, expressed as reduction in the intensity of symptoms. Unravelling the genetic architecture of peach response to PPV infection is essential for pyramiding resistant genes and for developing more tolerant varieties. For this purpose, a genome-wide association (GWA) approach was applied in a panel of accessions phenotyped for virus susceptibility and genotyped with the IPSC peach 9 K SNP Array, and coupled with an high-coverage resequencing of the tolerant accession 'Kamarat'. RESULTS Genome-wide association identified three highly significant associated loci on chromosome 2 and 3, accounting for most of the reduction in PPV-M susceptibility within the analysed peach population. The exploration of associated intervals through whole-genome comparison of the tolerant accession 'Kamarat' and other susceptible accessions, including the PPV-resistant wild-related species P. davidiana, allow the identification of allelic variants in promising candidate genes, including an RTM2-like gene already characterized in A. thaliana. CONCLUSIONS The present study is the first effort to identify genetic factors involved in Sharka disease in peach germplasm through a GWA approach. We provide evidence of the presence of quantitative resistant loci in a collection of peach accessions, identifying major loci and highly informative SNPs that could be useful for marker assisted selection. These results could serve as reference bases for future research aimed at the comprehension of genetic mechanism regulating the complex peach-PPV interaction.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura Basile-Caramia (CRSFA), via Cisternino, 281 Locorotondo, Bari, Italy
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), via Amendola 122/D, Bari, Italy
| | - Tiziana Castrignanò
- CINECA, SCAI Super Computing Applications and Innovation, via dei Tizii 6, Rome, Italy
| | - Stefano Gattolin
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | | | - Alessandro Liverani
- CREA, Research Centre for Olive, Citrus and Tree Fruit, via La Canapona 1 bis, Forlì, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
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12
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Martin CH, Erickson PA, Miller CT. The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation. Mol Ecol 2016; 26:624-638. [PMID: 27873369 DOI: 10.1111/mec.13935] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, Campus Box 3280, 120 South Rd, Chapel Hill, NC 27599-3280, USA
| | - Priscilla A Erickson
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA.,Department of Biology, University of Virginia, 229 Gilmer Hall, 485 McCormick Road, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Craig T Miller
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA
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Gloss AD, Groen SC, Whiteman NK. A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016; 47:165-187. [PMID: 28736510 DOI: 10.1146/annurev-ecolsys-121415-032220] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.
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Affiliation(s)
- Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Simon C Groen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Noah K Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California
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14
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Roux F, Bergelson J. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology. Curr Top Dev Biol 2016; 119:111-56. [PMID: 27282025 DOI: 10.1016/bs.ctdb.2016.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity.
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Affiliation(s)
- F Roux
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
| | - J Bergelson
- University of Chicago, Chicago, IL, United States
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15
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Dittmar EL, Oakley CG, Conner JK, Gould BA, Schemske DW. Factors influencing the effect size distribution of adaptive substitutions. Proc Biol Sci 2016; 283:20153065. [PMID: 27053750 PMCID: PMC4843649 DOI: 10.1098/rspb.2015.3065] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/15/2016] [Indexed: 12/17/2022] Open
Abstract
The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature.
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Affiliation(s)
- Emily L Dittmar
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Christopher G Oakley
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jeffrey K Conner
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
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Dixit S, Kumar Biswal A, Min A, Henry A, Oane RH, Raorane ML, Longkumer T, Pabuayon IM, Mutte SK, Vardarajan AR, Miro B, Govindan G, Albano-Enriquez B, Pueffeld M, Sreenivasulu N, Slamet-Loedin I, Sundarvelpandian K, Tsai YC, Raghuvanshi S, Hsing YIC, Kumar A, Kohli A. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL. Sci Rep 2015; 5:15183. [PMID: 26507552 PMCID: PMC4623671 DOI: 10.1038/srep15183] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/21/2015] [Indexed: 02/06/2023] Open
Abstract
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.
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Affiliation(s)
- Shalabh Dixit
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Akshaya Kumar Biswal
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Aye Min
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Amelia Henry
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Rowena H. Oane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Manish L. Raorane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Toshisangba Longkumer
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Isaiah M. Pabuayon
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Sumanth K. Mutte
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Adithi R. Vardarajan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Berta Miro
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ganesan Govindan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Blesilda Albano-Enriquez
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Mandy Pueffeld
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Nese Sreenivasulu
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Inez Slamet-Loedin
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | | | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Yue-Ie C. Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
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Cutler DJ, Zwick ME, Okou DT, Prahalad S, Walters T, Guthery SL, Dubinsky M, Baldassano R, Crandall WV, Rosh J, Markowitz J, Stephens M, Kellermayer R, Pfefferkorn M, Heyman MB, LeLeiko N, Mack D, Moulton D, Kappelman MD, Kumar A, Prince J, Bose P, Mondal K, Ramachandran D, Bohnsack JF, Griffiths AM, Haberman Y, Essers J, Thompson SD, Aronow B, Keljo DJ, Hyams JS, Denson LA, Kugathasan S. Dissecting Allele Architecture of Early Onset IBD Using High-Density Genotyping. PLoS One 2015; 10:e0128074. [PMID: 26098103 PMCID: PMC4476779 DOI: 10.1371/journal.pone.0128074] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/23/2015] [Indexed: 01/15/2023] Open
Abstract
Background The inflammatory bowel diseases (IBD) are common, complex disorders in which genetic and environmental factors are believed to interact leading to chronic inflammatory responses against the gut microbiota. Earlier genetic studies performed in mostly adult population of European descent identified 163 loci affecting IBD risk, but most have relatively modest effect sizes, and altogether explain only ~20% of the genetic susceptibility. Pediatric onset represents about 25% of overall incident cases in IBD, characterized by distinct disease physiology, course and risks. The goal of this study is to compare the allelic architecture of early onset IBD with adult onset in population of European descent. Methods We performed a fine mapping association study of early onset IBD using high-density Immunochip genotyping on 1008 pediatric-onset IBD cases (801 Crohn’s disease; 121 ulcerative colitis and 86 IBD undetermined) and 1633 healthy controls. Of the 158 SNP genotypes obtained (out of the 163 identified in adult onset), this study replicated 4% (5 SNPs out of 136) of the SNPs identified in the Crohn’s disease (CD) cases and 0.8% (1 SNP out of 128) in the ulcerative colitis (UC) cases. Replicated SNPs implicated the well known NOD2 and IL23R. The point estimate for the odds ratio (ORs) for NOD2 was above and outside the confidence intervals reported in adult onset. A polygenic liability score weakly predicted the age of onset for a larger collection of CD cases (p< 0.03, R2= 0.007), but not for the smaller number of UC cases. Conclusions The allelic architecture of common susceptibility variants for early onset IBD is similar to that of adult onset. This immunochip genotyping study failed to identify additional common variants that may explain the distinct phenotype that characterize early onset IBD. A comprehensive dissection of genetic loci is necessary to further characterize the genetic architecture of early onset IBD.
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Affiliation(s)
- David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Michael E. Zwick
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - David T. Okou
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Sampath Prahalad
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | | | - Stephen L. Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Marla Dubinsky
- Icahn School of Medicine, Mount Sinai Hospital, New York, New York, United States of America
| | - Robert Baldassano
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | | | - Joel Rosh
- Goryeb Children’s Hospital, Morristown, New Jersey, United States of America
| | - James Markowitz
- Cohen Children’s Medical Center, New Hyde Park, New York, United States of America
| | - Michael Stephens
- Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard Kellermayer
- Baylor College School of Medicine, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Marian Pfefferkorn
- Riley Children’s Hospital, Indiannapolis, Indianapolis, United States of America
| | - Melvin B. Heyman
- University of California, San Francisco, California, United States of America
| | - Neal LeLeiko
- Hasbro Children’s Hospital, Providence, Rhode Island, United States of America
| | - David Mack
- Children’s Hospital of Eastern Ontario, Ottawa, Canada
| | - Dedrick Moulton
- Vanderbilt Children’s Hospital, Nashville, Tennessee, United States of America
| | - Michael D. Kappelman
- University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Archana Kumar
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Jarod Prince
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Promita Bose
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Kajari Mondal
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Dhanya Ramachandran
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - John F. Bohnsack
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | | | - Yael Haberman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jonah Essers
- Children’s Hospital of Boston, Boston, Massachusetts, United States of America
| | - Susan D. Thompson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Bruce Aronow
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - David J. Keljo
- Children Hospital of Pittsburgh, Pittsburg, Pennsylvania, United States of America
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut, United States of America
| | - Lee A. Denson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Subra Kugathasan
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Dlugosch KM, Anderson SR, Braasch J, Cang FA, Gillette HD. The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Mol Ecol 2015; 24:2095-111. [PMID: 25846825 DOI: 10.1111/mec.13183] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/14/2022]
Abstract
The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself.
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Affiliation(s)
- Katrina M Dlugosch
- Department of Ecology & Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
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Soliveres S, Smit C, Maestre FT. Moving forward on facilitation research: response to changing environments and effects on the diversity, functioning and evolution of plant communities. Biol Rev Camb Philos Soc 2015; 90:297-313. [PMID: 24774563 PMCID: PMC4407973 DOI: 10.1111/brv.12110] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 04/02/2014] [Accepted: 04/04/2014] [Indexed: 12/22/2022]
Abstract
Once seen as anomalous, facilitative interactions among plants and their importance for community structure and functioning are now widely recognized. The growing body of modelling, descriptive and experimental studies on facilitation covers a wide variety of terrestrial and aquatic systems throughout the globe. However, the lack of a general body of theory linking facilitation among different types of organisms and biomes and their responses to environmental changes prevents further advances in our knowledge regarding the evolutionary and ecological implications of facilitation in plant communities. Moreover, insights gathered from alternative lines of inquiry may substantially improve our understanding of facilitation, but these have been largely neglected thus far. Despite over 15 years of research and debate on this topic, there is no consensus on the degree to which plant-plant interactions change predictably along environmental gradients (i.e. the stress-gradient hypothesis), and this hinders our ability to predict how plant-plant interactions may affect the response of plant communities to ongoing global environmental change. The existing controversies regarding the response of plant-plant interactions across environmental gradients can be reconciled when clearly considering and determining the species-specificity of the response, the functional or individual stress type, and the scale of interest (pairwise interactions or community-level response). Here, we introduce a theoretical framework to do this, supported by multiple lines of empirical evidence. We also discuss current gaps in our knowledge regarding how plant-plant interactions change along environmental gradients. These include the existence of thresholds in the amount of species-specific stress that a benefactor can alleviate, the linearity or non-linearity of the response of pairwise interactions across distance from the ecological optimum of the beneficiary, and the need to explore further how frequent interactions among multiple species are and how they change across different environments. We review the latest advances in these topics and provide new approaches to fill current gaps in our knowledge. We also apply our theoretical framework to advance our knowledge on the evolutionary aspects of plant facilitation, and the relative importance of facilitation, in comparison with other ecological processes, for maintaining ecosystem structure, functioning and dynamics. We build links between these topics and related fields, such as ecological restoration, woody encroachment, invasion ecology, ecological modelling and biodiversity-ecosystem-functioning relationships. By identifying commonalities and insights from alternative lines of research, we further advance our understanding of facilitation and provide testable hypotheses regarding the role of (positive) biotic interactions in the maintenance of biodiversity and the response of ecological communities to ongoing environmental changes.
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Affiliation(s)
- Santiago Soliveres
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933 Móstoles, Spain
| | - Christian Smit
- Community and Conservation Ecology group, Centre for Evolutionary and Ecological Studies, University of Groningen, P.O. Box 11103, Nijenborg 7, 9700 CC Groningen, the Netherland
| | - Fernando T. Maestre
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933 Móstoles, Spain
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20
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Twyford AD, Ennos RA, White CD, Ali MS, Kidner CA. The evolution of sex ratio differences and inflorescence architectures in Begonia (Begoniaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:308-317. [PMID: 24491344 DOI: 10.3732/ajb.1300090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY A major benefit conferred by monoecy is the ability to alter floral sex ratio in response to selection. In monoecious species that produce flowers of a given sex at set positions on the inflorescence, floral sex ratio may be related to inflorescence architecture. We studied the loci underlying differences in inflorescence architecture between two monoecious Begonia species and related this to floral sex ratios. METHODS We performed trait comparisons and quantitative trait locus (QTL) mapping in a segregating backcross population between Central American Begonia plebeja and B. conchifolia. We focused on traits related to inflorescence architecture, sex ratios, and other reproductive traits. KEY RESULTS The inflorescence branching pattern of B. conchifolia was more asymmetric than B. plebeja, which in turn affects the floral sex ratio. Colocalizing QTLs of moderate effect influenced both the number of male flowers and the fate decisions of axillary meristems, demonstrating the close link between inflorescence architecture and sex ratio. Additional QTLs were found for stamen number (30% variance explained, VE) and pollen sterility (12.3% VE). CONCLUSIONS One way in which Begonia species develop different floral sex ratios is through modifications of their inflorescence architecture. The potential pleiotropic action of QTL on inflorescence branching and floral sex ratios may have major implications for trait evolution and responses to selection. The presence of a single QTL of large effect on stamen number may allow rapid divergence for this key floral trait. We propose candidate loci for stamen number and inflorescence branching for future characterization.
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Affiliation(s)
- Alex D Twyford
- Department of Biology, Syracuse University, 107 College Place, Room 110 LSC, Syracuse, New York 13244 USA
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21
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Gloss AD, Dittrich ACN, Goldman-Huertas B, Whiteman NK. Maintenance of genetic diversity through plant-herbivore interactions. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:443-50. [PMID: 23834766 PMCID: PMC4059408 DOI: 10.1016/j.pbi.2013.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 06/01/2013] [Accepted: 06/07/2013] [Indexed: 05/10/2023]
Abstract
Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains genome-wide functionally important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to address this hypothesis. Population genomic studies of Arabidopsis thaliana and its relatives suggest spatial variation in herbivory maintains adaptive genetic variation controlling defense phenotypes, both within and among populations. Conversely, inter-species variation in plant defenses promotes adaptive genetic variation in herbivores. Emerging genomic model herbivores of Arabidopsis could illuminate how genetic variation in herbivores and plants interact simultaneously.
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Affiliation(s)
- Andrew D. Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA,
| | - Anna C. Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA,
| | | | - Noah K. Whiteman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA,
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22
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Nakazato T, Rieseberg LH, Wood TE. The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae). Heredity (Edinb) 2013; 111:227-37. [PMID: 23652565 DOI: 10.1038/hdy.2013.41] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 03/27/2013] [Accepted: 04/02/2013] [Indexed: 12/29/2022] Open
Abstract
One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL) analyses of floral traits and other variable phenotypes. We detected one to six QTLs per trait, with each QTL generally explaining small to modest amounts of the phenotypic variance of a backcross hybrid population. In contrast, flowering time and anthocyanin abundance (a metric of color variation) were controlled by a few QTLs of relatively large effect. QTLs were strongly clustered within linkage groups, with 26 of 37 QTLs localized to six marker-interval 'hotspots,' all of which harbored pleiotropic QTLs. In contrast to other studies that have examined the genetic basis of pollinator shifts, our results indicate that, in general, mutations of small to modest effect on phenotype were involved. Thus, the evolutionary transition between the distinct pollination modes of I. guttata and I. tenuifolia likely proceeded incrementally, rather than saltationally.
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Affiliation(s)
- T Nakazato
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
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23
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The evolution of quantitative traits in complex environments. Heredity (Edinb) 2013; 112:4-12. [PMID: 23612691 DOI: 10.1038/hdy.2013.33] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/12/2013] [Accepted: 03/14/2013] [Indexed: 02/01/2023] Open
Abstract
Species inhabit complex environments and respond to selection imposed by numerous abiotic and biotic conditions that vary in both space and time. Environmental heterogeneity strongly influences trait evolution and patterns of adaptive population differentiation. For example, heterogeneity can favor local adaptation, or can promote the evolution of plastic genotypes that alter their phenotypes based on the conditions they encounter. Different abiotic and biotic agents of selection can act synergistically to either accelerate or constrain trait evolution. The environmental context has profound effects on quantitative genetic parameters. For instance, heritabilities measured in controlled conditions often exceed those measured in the field; thus, laboratory experiments could overestimate the potential for a population to respond to selection. Nevertheless, most studies of the genetic basis of ecologically relevant traits are conducted in simplified laboratory environments, which do not reflect the complexity of nature. Here, we advocate for manipulative field experiments in the native ranges of plant species that differ in mating system, life-history strategy and growth form. Field studies are vital to evaluate the roles of disparate agents of selection, to elucidate the targets of selection and to develop a nuanced perspective on the evolution of quantitative traits. Quantitative genetics field studies will also shed light on the potential for natural populations to adapt to novel climates in highly fragmented landscapes. Drawing from our experience with the ecological model system Boechera (Brassicaceae), we discuss advancements possible through dedicated field studies, highlight future research directions and examine the challenges associated with field studies.
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Korte A, Farlow A. The advantages and limitations of trait analysis with GWAS: a review. PLANT METHODS 2013; 9:29. [PMID: 23876160 PMCID: PMC3750305 DOI: 10.1186/1746-4811-9-29] [Citation(s) in RCA: 803] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 06/13/2013] [Indexed: 05/17/2023]
Abstract
Over the last 10 years, high-density SNP arrays and DNA re-sequencing have illuminated the majority of the genotypic space for a number of organisms, including humans, maize, rice and Arabidopsis. For any researcher willing to define and score a phenotype across many individuals, Genome Wide Association Studies (GWAS) present a powerful tool to reconnect this trait back to its underlying genetics. In this review we discuss the biological and statistical considerations that underpin a successful analysis or otherwise. The relevance of biological factors including effect size, sample size, genetic heterogeneity, genomic confounding, linkage disequilibrium and spurious association, and statistical tools to account for these are presented. GWAS can offer a valuable first insight into trait architecture or candidate loci for subsequent validation.
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Affiliation(s)
- Arthur Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Ashley Farlow
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
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25
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Olson-Manning CF, Wagner MR, Mitchell-Olds T. Adaptive evolution: evaluating empirical support for theoretical predictions. Nat Rev Genet 2012; 13:867-77. [PMID: 23154809 PMCID: PMC3748133 DOI: 10.1038/nrg3322] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adaptive evolution is shaped by the interaction of population genetics, natural selection and underlying network and biochemical constraints. Variation created by mutation, the raw material for evolutionary change, is translated into phenotypes by flux through metabolic pathways and by the topography and dynamics of molecular networks. Finally, the retention of genetic variation and the efficacy of selection depend on population genetics and demographic history. Emergent high-throughput experimental methods and sequencing technologies allow us to gather more evidence and to move beyond the theory in different systems and populations. Here we review the extent to which recent evidence supports long-established theoretical principles of adaptation.
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Affiliation(s)
- Carrie F. Olson-Manning
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| | - Maggie R. Wagner
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| | - Thomas Mitchell-Olds
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
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26
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Colautti RI, Lee CR, Mitchell-Olds T. Origin, fate, and architecture of ecologically relevant genetic variation. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:199-204. [PMID: 22341792 PMCID: PMC3413448 DOI: 10.1016/j.pbi.2012.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/11/2012] [Accepted: 01/23/2012] [Indexed: 05/08/2023]
Abstract
Recent advances in molecular genetics combined with field manipulations are yielding new insight into the origin, evolutionary fate, and genetic architecture of phenotypic variation in natural plant populations, with two surprising implications for the evolution of plant genomes. First, genetic loci exhibiting antagonistic pleiotropy across natural environments appear rare relative to loci that are adaptive in one or more environments and neutral elsewhere. These 'conditionally neutral' alleles should sweep to fixation when they arise, yet genome comparisons find little evidence for such selective sweeps. Second, genes under biotic selection tend to be of larger effect than genes under abiotic selection. Recent theory suggests this may be a consequence of high gene flow among populations under selection for local adaptation.
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Affiliation(s)
- Robert I Colautti
- Biology Department, Duke University, Durham, NC 27708, United States.
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