1
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Glaser-Schmitt A, Ramnarine TJS, Parsch J. Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster. Mol Ecol 2024; 33:e17024. [PMID: 37222070 DOI: 10.1111/mec.17024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
Allele frequencies can shift rapidly within natural populations. Under certain conditions, repeated rapid allele frequency shifts can lead to the long-term maintenance of polymorphism. In recent years, studies of the model insect Drosophila melanogaster have suggested that this phenomenon is more common than previously believed and is often driven by some form of balancing selection, such as temporally fluctuating or sexually antagonistic selection. Here we discuss some of the general insights into rapid evolutionary change revealed by large-scale population genomic studies, as well as the functional and mechanistic causes of rapid adaptation uncovered by single-gene studies. As an example of the latter, we consider a regulatory polymorphism of the D. melanogaster fezzik gene. Polymorphism at this site has been maintained at intermediate frequency over an extended period of time. Regular observations from a single population over a period of 7 years revealed significant differences in the frequency of the derived allele and its variance across collections between the sexes. These patterns are highly unlikely to arise from genetic drift alone or from the action of sexually antagonistic or temporally fluctuating selection individually. Instead, the joint action of sexually antagonistic and temporally fluctuating selection can best explain the observed rapid and repeated allele frequency shifts. Temporal studies such as those reviewed here further our understanding of how rapid changes in selection can lead to the long-term maintenance of polymorphism as well as improve our knowledge of the forces driving and limiting adaptation in nature.
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Affiliation(s)
- Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timothy J S Ramnarine
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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2
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Fluctuating selection and the determinants of genetic variation. Trends Genet 2023; 39:491-504. [PMID: 36890036 DOI: 10.1016/j.tig.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.
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3
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Linder RA, Zabanavar B, Majumder A, Hoang HCS, Delgado VG, Tran R, La VT, Leemans SW, Long AD. Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes. Mol Biol Evol 2022; 39:msac248. [PMID: 36366952 PMCID: PMC9728589 DOI: 10.1093/molbev/msac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.
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Affiliation(s)
- Robert A Linder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Behzad Zabanavar
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Hannah Chiao-Shyan Hoang
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vanessa Genesaret Delgado
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Ryan Tran
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vy Thoai La
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Simon William Leemans
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
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4
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Busch JW, Bodbyl‐Roels S, Tusuubira S, Kelly JK. Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability. Evolution 2022; 76:2130-2144. [PMID: 35852008 PMCID: PMC9543508 DOI: 10.1111/evo.14572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/23/2022] [Accepted: 04/20/2022] [Indexed: 01/22/2023]
Abstract
Although selfing populations harbor little genetic variation limiting evolutionary potential, the causes are unclear. We experimentally evolved large, replicate populations of Mimulus guttatus for nine generations in greenhouses with or without pollinating bees and studied DNA polymorphism in descendants. Populations without bees adapted to produce more selfed seed yet exhibited striking reductions in DNA polymorphism despite large population sizes. Importantly, the genome-wide pattern of variation cannot be explained by a simple reduction in effective population size, but instead reflects the complicated interaction between selection, linkage, and inbreeding. Simulations demonstrate that the spread of favored alleles at few loci depresses neutral variation genome wide in large populations containing fully selfing lineages. It also generates greater heterogeneity among chromosomes than expected with neutral evolution in small populations. Genome-wide deviations from neutrality were documented in populations with bees, suggesting widespread influences of background selection. After applying outlier tests to detect loci under selection, two genome regions were found in populations with bees, yet no adaptive loci were otherwise mapped. Large amounts of stochastic change in selfing populations compromise evolutionary potential and undermine outlier tests for selection. This occurs because genetic draft in highly selfing populations makes even the largest changes in allele frequency unremarkable.
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Affiliation(s)
- Jeremiah W. Busch
- School of Biological SciencesWashington State UniversityPullmanWashington99164
| | - Sarah Bodbyl‐Roels
- Trefny Innovative Instruction CenterColorado School of MinesGoldenColorado80401
| | - Sharif Tusuubira
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas66045
| | - John K. Kelly
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas66045
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5
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Phillips MA, Kutch IC, McHugh KM, Taggard SK, Burke MK. Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae. Sci Rep 2021; 11:19551. [PMID: 34599243 PMCID: PMC8486856 DOI: 10.1038/s41598-021-99026-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
"Synthetic recombinant" populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In the latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.
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Affiliation(s)
- Mark A Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Ian C Kutch
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Kaitlin M McHugh
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Savannah K Taggard
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA.
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6
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Genetic Diversity and Divergence among Bighorn Sheep from Reintroduced Herds in Washington and Idaho. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Henry LP, Ayroles JF. Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster. BMC Microbiol 2021; 21:108. [PMID: 33836662 PMCID: PMC8034159 DOI: 10.1186/s12866-021-02168-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also respond to selection. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiments in Drosophila melanogaster to determine how the microbiome changed in response to host selection. RESULTS Bacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. CONCLUSIONS Our genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.
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Affiliation(s)
- Lucas P Henry
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Julien F Ayroles
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
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8
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Burny C, Nolte V, Nouhaud P, Dolezal M, Schlötterer C. Secondary Evolve and Resequencing: An Experimental Confirmation of Putative Selection Targets without Phenotyping. Genome Biol Evol 2021; 12:151-159. [PMID: 32159748 PMCID: PMC7144549 DOI: 10.1093/gbe/evaa036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Evolve and resequencing (E&R) studies investigate the genomic responses of adaptation during experimental evolution. Because replicate populations evolve in the same controlled environment, consistent responses to selection across replicates are frequently used to identify reliable candidate regions that underlie adaptation to a new environment. However, recent work demonstrated that selection signatures can be restricted to one or a few replicate(s) only. These selection signatures frequently have weak statistical support, and given the difficulties of functional validation, additional evidence is needed before considering them as candidates for functional analysis. Here, we introduce an experimental procedure to validate candidate loci with weak or replicate-specific selection signature(s). Crossing an evolved population from a primary E&R experiment to the ancestral founder population reduces the frequency of candidate alleles that have reached a high frequency. We hypothesize that genuine selection targets will experience a repeatable frequency increase after the mixing with the ancestral founders if they are exposed to the same environment (secondary E&R experiment). Using this approach, we successfully validate two overlapping selection targets, which showed a mutually exclusive selection signature in a primary E&R experiment of Drosophila simulans adapting to a novel temperature regime. We conclude that secondary E&R experiments provide a reliable confirmation of selection signatures that either are not replicated or show only a low statistical significance in a primary E&R experiment unless epistatic interactions predominate. Such experiments are particularly helpful to prioritize candidate loci for time-consuming functional follow-up investigations.
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Affiliation(s)
- Claire Burny
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria.,Vienna Graduate school of Population Genetics, Vetmeduni Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | - Pierre Nouhaud
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | - Marlies Dolezal
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria.,Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Austria
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9
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Phillips MA, Kutch IC, Long AD, Burke MK. Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change. Mol Ecol 2020; 29:4898-4912. [PMID: 33135198 DOI: 10.1111/mec.15687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/28/2022]
Abstract
"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms such as bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling-the number of discrete time points sequence data are collected from evolving populations. Using data from an E&R experiment with outcrossing Saccharomyces cerevisiae in which populations were sequenced 17 times over ~540 generations, we address the following questions: (a) Do more time points improve the ability to identify candidate regions underlying selection? And (b) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e., models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e., models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling eight or more time points has clear benefits for studying complex evolutionary dynamics.
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Affiliation(s)
- Mark A Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Ian C Kutch
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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10
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Langmüller AM, Schlötterer C. Low concordance of short-term and long-term selection responses in experimental Drosophila populations. Mol Ecol 2020; 29:3466-3475. [PMID: 32762052 PMCID: PMC7540288 DOI: 10.1111/mec.15579] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022]
Abstract
Experimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study in Drosophila simulans to compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10% of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.
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Affiliation(s)
- Anna Maria Langmüller
- Vienna Graduate School of Population GeneticsViennaAustria
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
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11
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Farzaneh F, Salimi S, Razavi M, Rezaei M, Saravani M. Association of H19 rs3741219 polymorphism with the susceptibility to uterine leiomyomas. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Bono LM, Draghi JA, Turner PE. Evolvability Costs of Niche Expansion. Trends Genet 2019; 36:14-23. [PMID: 31699305 DOI: 10.1016/j.tig.2019.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/22/2019] [Accepted: 10/07/2019] [Indexed: 01/31/2023]
Abstract
What prevents generalists from displacing specialists, despite obvious competitive advantages of utilizing a broad niche? The classic genetic explanation is antagonistic pleiotropy: genes underlying the generalism produce 'jacks-of-all-trades' that are masters of none. However, experiments challenge this assumption that mutations enabling niche expansion must reduce fitness in other environments. Theory suggests an alternative cost of generalism: decreased evolvability, or the reduced capacity to adapt. Generalists using multiple environments experience relaxed selection in any one environment, producing greater relative lag load. Additionally, mutations fixed by generalist lineages early during their evolution that avoid or compensate for antagonistic pleiotropy may limit access to certain future evolutionary trajectories. Hypothesized evolvability costs of generalism warrant further exploration, and we suggest outstanding questions meriting attention.
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Affiliation(s)
- Lisa M Bono
- Department of Ecology, Evolution, and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jeremy A Draghi
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210, USA; Program in Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, NY 10016, USA
| | - Paul E Turner
- Microbiology Program, Yale School of Medicine, New Haven, CT 06510, USA; Yale University, Department of Ecology and Evolutionary Biology, New Haven, CT 06511, USA.
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13
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Wang A, Singh A, Huang Y, Agrawal AF. Ecological specialization in populations adapted to constant versus heterogeneous environments. Evolution 2019; 73:1309-1317. [PMID: 30912125 DOI: 10.1111/evo.13725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/26/2019] [Indexed: 11/27/2022]
Abstract
Populations vary in their degree of ecological specialization. An intuitive, but often untested, hypothesis is that populations evolving under greater environmental heterogeneity will evolve to be less specialized. How important is environmental heterogeneity in explaining among-population variation in specialization? We assessed juvenile viability of 20 Drosophila melanogaster populations evolving under one of four regimes: (1) a salt-enriched environment, (2) a cadmium-enriched environment, (3) a temporally varying environment, and (4) a spatially varying environment. Juvenile viability was tested in both the original selective environments and a set of novel environments. In both the original and novel environments, populations from the constant cadmium regime had the lowest average viability and the highest variance in viability across environments but populations from the other three regimes were similar. Our results suggest that variation in specialization among these populations is most simply explained as a pleiotropic by-product of adaptation to specific environments rather than resulting from a history of exposure to environmental heterogeneity.
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Affiliation(s)
- Ao Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Amardeep Singh
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Yuheng Huang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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14
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Kelly JK, Hughes KA. Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans. Genetics 2019; 211:943-961. [PMID: 30593495 PMCID: PMC6404262 DOI: 10.1534/genetics.118.301824] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/15/2018] [Indexed: 11/18/2022] Open
Abstract
We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30-70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.
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Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Kimberly A Hughes
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
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15
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Phillips MA, Rutledge GA, Kezos JN, Greenspan ZS, Talbott A, Matty S, Arain H, Mueller LD, Rose MR, Shahrestani P. Effects of evolutionary history on genome wide and phenotypic convergence in Drosophila populations. BMC Genomics 2018; 19:743. [PMID: 30305018 PMCID: PMC6180417 DOI: 10.1186/s12864-018-5118-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies combining experimental evolution and next-generation sequencing have found that adaptation in sexually reproducing populations is primarily fueled by standing genetic variation. Consequently, the response to selection is rapid and highly repeatable across replicate populations. Some studies suggest that the response to selection is highly repeatable at both the phenotypic and genomic levels, and that evolutionary history has little impact. Other studies suggest that even when the response to selection is repeatable phenotypically, evolutionary history can have significant impacts at the genomic level. Here we test two hypotheses that may explain this discrepancy. Hypothesis 1: Past intense selection reduces evolutionary repeatability at the genomic and phenotypic levels when conditions change. Hypothesis 2: Previous intense selection does not reduce evolutionary repeatability, but other evolutionary mechanisms may. We test these hypotheses using D. melanogaster populations that were subjected to 260 generations of intense selection for desiccation resistance and have since been under relaxed selection for the past 230 generations. RESULTS We find that, with the exception of longevity and to a lesser extent fecundity, 230 generations of relaxed selection has erased the extreme phenotypic differentiation previously found. We also find no signs of genetic fixation, and only limited evidence of genetic differentiation between previously desiccation resistance selected populations and their controls. CONCLUSION Our findings suggest that evolution in our system is highly repeatable even when populations have been previously subjected to bouts of extreme selection. We therefore conclude that evolutionary repeatability can overcome past bouts of extreme selection in Drosophila experimental evolution, provided experiments are sufficiently long and populations are not inbred.
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Affiliation(s)
- Mark A Phillips
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, USA.
| | - Grant A Rutledge
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, USA
| | - James N Kezos
- Department of Development, Aging, and Regeneration, Sanford Burnham Prebys Medical Discovery Institute, San Diego, USA
| | - Zachary S Greenspan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, USA
| | - Andrew Talbott
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Sara Matty
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Hamid Arain
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Laurence D Mueller
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, USA
| | - Michael R Rose
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, USA
| | - Parvin Shahrestani
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
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16
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nat Ecol Evol 2018; 2:1128-1138. [PMID: 29942074 PMCID: PMC6519129 DOI: 10.1038/s41559-018-0581-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Abstract
A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages adapted to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-years selection experiment, we let giant stickleback from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the adaptive genomic change between 12,000 years old ecotypes. Adaptive genomic change was as fast as phenotypic change in defence and trophic morphology and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived adaptive radiation members, allowing adaptive radiations to unfold very rapidly.
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Affiliation(s)
- David A Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada. .,Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.
| | - Felicity C Jones
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK.,Department of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David M Kingsley
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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17
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Culumber ZW, Kraft B, Lemakos V, Hoffner E, Travis J, Hughes KA. GxG epistasis in growth and condition and the maintenance of genetic polymorphism in
Gambusia holbrooki. Evolution 2018; 72:1146-1154. [DOI: 10.1111/evo.13474] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Zachary W. Culumber
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee FL 32306
| | - Brittany Kraft
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee FL 32306
| | - Valerie Lemakos
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee FL 32306
| | - Erika Hoffner
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee FL 32306
| | - Joseph Travis
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee FL 32306
| | - Kimberly A. Hughes
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee FL 32306
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18
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Leale AM, Kassen R. The emergence, maintenance, and demise of diversity in a spatially variable antibiotic regime. Evol Lett 2018; 2:134-143. [PMID: 30283671 PMCID: PMC6121846 DOI: 10.1002/evl3.43] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/15/2018] [Accepted: 01/29/2018] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a growing global threat that, in the absence of new antibiotics, requires effective management of existing drugs. Here, we use experimental evolution of the opportunistic human pathogen Pseudomonas aeruginosa to explore how changing patterns of drug delivery modulates the spread of resistance in a population. Resistance evolves readily under both temporal and spatial variation in drug delivery and fixes rapidly under temporal, but not spatial, variation. Resistant and sensitive genotypes coexist in spatially varying conditions due to a resistance‐growth rate trade‐off which, when coupled to dispersal, generates negative frequency‐dependent selection and a quasi‐protected polymorphism. Coexistence is ultimately lost, however, because resistant types with improved growth rates in the absence of drug spread through the population. These results suggest that spatially variable drug prescriptions can delay but not prevent the spread of resistance and provide a striking example of how the emergence and eventual demise of biodiversity is underpinned by evolving fitness trade‐offs.
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Affiliation(s)
- Alanna M Leale
- Department of Biology University of Ottawa Ottawa Ontario K1N 6N5 Canada
| | - Rees Kassen
- Department of Biology University of Ottawa Ottawa Ontario K1N 6N5 Canada
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19
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Wright AE, Fumagalli M, Cooney CR, Bloch NI, Vieira FG, Buechel SD, Kolm N, Mank JE. Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture. Evol Lett 2018; 2:52-61. [PMID: 30283664 PMCID: PMC6089503 DOI: 10.1002/evl3.39] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome‐resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and intersexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male‐biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn lead to specific alleles influencing sex‐specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.
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Affiliation(s)
- Alison E Wright
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus Imperial College London London United Kingdom
| | - Christopher R Cooney
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Natasha I Bloch
- Department of Genetics, Evolution and Environment University College London London United Kingdom
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | | | - Niclas Kolm
- Department of Zoology Stockholm University Stockholm Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment University College London London United Kingdom.,Department of Organismal Biology Uppsala University Uppsala Sweden
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20
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21
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Schou MF, Loeschcke V, Bechsgaard J, Schlötterer C, Kristensen TN. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance. Mol Ecol 2017; 26:6510-6523. [PMID: 28746770 DOI: 10.1111/mec.14262] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/17/2022]
Abstract
The effective population size (Ne ) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on Ne , with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between Ne and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long-term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X-chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X-chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations.
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Affiliation(s)
- Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | | | | | | | - Torsten N Kristensen
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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22
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Drosophila simulans: A Species with Improved Resolution in Evolve and Resequence Studies. G3-GENES GENOMES GENETICS 2017; 7:2337-2343. [PMID: 28546383 PMCID: PMC5499140 DOI: 10.1534/g3.117.043349] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The combination of experimental evolution with high-throughput sequencing of pooled individuals—i.e., evolve and resequence (E&R)—is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E&R studies in Drosophila melanogaster have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ∼60 generations in a novel hot environment for D. melanogaster and D. simulans. For D. simulans, the regions carrying putatively selected loci were far more distinct, and thus harbored fewer false positives, than those in D. melanogaster. We propose that species without segregating inversions and higher recombination rates, such as D. simulans, are better suited for E&R studies that aim to characterize the genetic variants underlying the adaptive response.
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23
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Wiberg RAW, Gaggiotti OE, Morrissey MB, Ritchie MG. Identifying consistent allele frequency differences in studies of stratified populations. Methods Ecol Evol 2017; 8:1899-1909. [PMID: 29263778 PMCID: PMC5726381 DOI: 10.1111/2041-210x.12810] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/02/2017] [Indexed: 12/02/2022]
Abstract
With increasing application of pooled‐sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used, which means that underlying assumptions about the data are frequently violated. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including Generalised Linear Models [GLMs] with quasibinomial error structure) with attractive properties for the analysis of allele frequency differences and re‐analyse a published dataset. The simulations show that common statistical tests for consistent allele frequency differences perform poorly, with high false positive rates. Applying tests that do not confound heterogeneity and main effects significantly improves inference. Variation in sequencing coverage likely produces many false positives and re‐scaling allele frequencies to counts out of a common value or an effective sample size reduces this effect. Many researchers are interested in identifying allele frequencies that vary consistently across replicates to identify loci underlying phenotypic responses to selection or natural variation in phenotypes. Popular methods that have been suggested for this task perform poorly in simulations. Overall, quasibinomial GLMs perform better and also have the attractive feature of allowing correction for multiple testing by standard procedures and are easily extended to other designs.
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Affiliation(s)
- R Axel W Wiberg
- Centre for Biological Diversity Sir Harold Mitchell Building University of St Andrews St Andrews, Scotland United Kingdom
| | - Oscar E Gaggiotti
- Scottish Oceans Institute Gatty Marine Laboratory University of St Andrews East Sands St Andrews, Scotland United Kingdom
| | - Michael B Morrissey
- Centre for Biological Diversity Sir Harold Mitchell Building University of St Andrews St Andrews, Scotland United Kingdom
| | - Michael G Ritchie
- Centre for Biological Diversity Sir Harold Mitchell Building University of St Andrews St Andrews, Scotland United Kingdom
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24
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25
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Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P. Multilocus approaches for the measurement of selection on correlated genetic loci. Mol Ecol 2016; 26:365-382. [DOI: 10.1111/mec.13867] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 02/02/2023]
Affiliation(s)
| | - Scott P. Egan
- Department of BioSciences Rice University Houston TX 77005 USA
| | | | - Jeffrey L. Feder
- Department of Biological Science University of Notre Dame South Bend IN 46556 USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences University of Sheffield Sheffield S10 2TN UK
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26
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Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes. PLoS Genet 2016; 12:e1006336. [PMID: 27661078 PMCID: PMC5035091 DOI: 10.1371/journal.pgen.1006336] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/01/2016] [Indexed: 11/23/2022] Open
Abstract
Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental heterogeneity are expected to show adaptive evolution of plasticity. We measured the transcriptome in a cadmium-enriched diet and a salt-enriched diet for experimental populations of Drosophila melanogaster that evolved for ~130 generations in one of four selective regimes: two constant regimes maintained in either cadmium or salt diets and two heterogeneous regimes that varied either temporally or spatially between the two diets. For populations evolving in constant regimes, we find a strong signature of counter-gradient evolution; the evolved expression differences between populations adapted to alternative diets is opposite to the plastic response of the ancestral population that is naïve to both diets. Based on expression patterns in the ancestral populations, we identify a set of genes for which we predict selection in heterogeneous regimes to result in increases in plasticity and we find the expected pattern. In contrast, a set of genes where we predicted reduced plasticity did not follow expectation. Nonetheless, both gene sets showed a pattern consistent with adaptive expression evolution in heterogeneous regimes, highlighting the difference between observing “optimal” plasticity and improvements in environment-specific expression. Looking across all genes, there is evidence in all regimes of differences in biased allele expression across environments (“allelic plasticity”) and this is more common among genes with plasticity in total expression. Different developmental environments change how genes are expressed and what phenotypes are produced. Here we examine how the responsiveness of gene expression to different environments (“expression plasticity”) evolves in populations adapted to constant environments or heterogeneous ones (temporal or spatial heterogeneity) using experimental populations of D. melanogaster. We find the plastic response of the ancestral population that is naïve to both environments is generally opposed by the evolved differences between populations adapted to alternative environments. Populations that live in heterogeneous environments show evidence of adaptive expression evolution in genes predicted to evolve changes in plasticity.
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27
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Rendueles O, Velicer GJ. Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes. ISME JOURNAL 2016; 11:555-568. [PMID: 27662568 PMCID: PMC5270557 DOI: 10.1038/ismej.2016.115] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/19/2016] [Accepted: 07/03/2016] [Indexed: 01/16/2023]
Abstract
Evolutionary adaptation can be achieved by mechanisms accessible to all organisms, including faster growth and interference competition, but self-generated motility offers additional possibilities. We tested whether 55 populations of the bacterium Myxococcus xanthus that underwent selection for increased fitness at the leading edge of swarming colonies adapted by swarming faster toward unused resources or by other means. Populations adapted greatly but diversified markedly in both swarming phenotypes and apparent mechanisms of adaptation. Intriguingly, although many adapted populations swarm intrinsically faster than their ancestors, numerous others do not. Some populations evolved interference competition toward their ancestors, whereas others gained the ability to facultatively increase swarming rate specifically upon direct interaction with ancestral competitors. Our results both highlight the diverse range of mechanisms by which actively motile organisms can adapt evolutionarily and help to explain the high levels of swarming-phenotype diversity found in local soil populations of M. xanthus.
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Affiliation(s)
- Olaya Rendueles
- Institute for Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich, Switzerland
| | - Gregory J Velicer
- Institute for Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich, Switzerland
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28
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Abstract
Combining modern transgenic techniques with fitness measurements and enzyme activity assays, a new study demonstrates a habitat-dependent tradeoff between two alleles of a key detoxification enzyme in fruit flies. The elegant findings provide concrete, elusive evidence supporting a foundational and controversial theory about the maintenance of genetic variation.
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Affiliation(s)
- Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, BioSciences West, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Noah K Whiteman
- Department of Ecology and Evolutionary Biology, University of Arizona, BioSciences West, 1041 East Lowell Street, Tucson, AZ 85721, USA.
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29
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Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution. Genetics 2016; 204:723-735. [PMID: 27542959 PMCID: PMC5068858 DOI: 10.1534/genetics.116.191197] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/30/2016] [Indexed: 01/22/2023] Open
Abstract
The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.
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30
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Gompert Z, Messina FJ. Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle. Evolution 2016; 70:1249-64. [DOI: 10.1111/evo.12933] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/15/2016] [Indexed: 01/12/2023]
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31
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Huang Y, Tran I, Agrawal AF. Does Genetic Variation Maintained by Environmental Heterogeneity Facilitate Adaptation to Novel Selection? Am Nat 2016; 188:27-37. [PMID: 27322119 DOI: 10.1086/686889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Environmental heterogeneity helps maintain genetic variation in fitness. Therefore, one might predict that populations living in heterogeneous environments have higher adaptive potential than populations living in homogeneous environments. Such a prediction could be useful in guiding conservation priorities without requiring detailed genetic studies. However, this prediction will be true only if the additional genetic variation maintained by environmental heterogeneity can be used to respond to novel selection. Here we examine the effect of environmental heterogeneity on future adaptability using replicated experimental Drosophila melanogaster populations that had previously evolved for ∼100 generations under one of four selective regimes: constant salt-enriched larvae medium, constant cadmium-enriched larvae medium, and two heterogeneous regimes that vary either temporally or spatially between the two media. Replicates of these experimental populations were subjected to a novel heat stress while being maintained in their original larval diet selection regimes. Adaptation to increased temperature was measured with respect to female productivity and male siring success after ∼20 generations. For female productivity, there was evidence of adaptation overall and heterogeneous populations had a larger adaptive response than homogeneous populations. There was less evidence of adaptation overall for male siring success and no support for faster adaptation in heterogeneous populations.
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32
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Bailey SF, Bataillon T. Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Mol Ecol 2016; 25:203-18. [PMID: 26346808 PMCID: PMC5019151 DOI: 10.1111/mec.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/26/2015] [Accepted: 09/04/2015] [Indexed: 02/04/2023]
Abstract
There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions--that is simple environments, a small range of usually asexual species, relatively short timescales--the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches.
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Affiliation(s)
- Susan F. Bailey
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
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33
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Kain JS, Zhang S, Akhund-Zade J, Samuel ADT, Klein M, de Bivort BL. Variability in thermal and phototactic preferences in Drosophila may reflect an adaptive bet-hedging strategy. Evolution 2015; 69:3171-85. [PMID: 26531165 PMCID: PMC5063146 DOI: 10.1111/evo.12813] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 10/18/2015] [Accepted: 10/21/2015] [Indexed: 01/18/2023]
Abstract
Organisms use various strategies to cope with fluctuating environmental conditions. In diversified bet‐hedging, a single genotype exhibits phenotypic heterogeneity with the expectation that some individuals will survive transient selective pressures. To date, empirical evidence for bet‐hedging is scarce. Here, we observe that individual Drosophila melanogaster flies exhibit striking variation in light‐ and temperature‐preference behaviors. With a modeling approach that combines real world weather and climate data to simulate temperature preference‐dependent survival and reproduction, we find that a bet‐hedging strategy may underlie the observed interindividual behavioral diversity. Specifically, bet‐hedging outcompetes strategies in which individual thermal preferences are heritable. Animals employing bet‐hedging refrain from adapting to the coolness of spring with increased warm‐seeking that inevitably becomes counterproductive in the hot summer. This strategy is particularly valuable when mean seasonal temperatures are typical, or when there is considerable fluctuation in temperature within the season. The model predicts, and we experimentally verify, that the behaviors of individual flies are not heritable. Finally, we model the effects of historical weather data, climate change, and geographic seasonal variation on the optimal strategies underlying behavioral variation between individuals, characterizing the regimes in which bet‐hedging is advantageous.
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Affiliation(s)
- Jamey S Kain
- Rowland Institute at Harvard, Cambridge, Massachusetts, 02142
| | - Sarah Zhang
- Rowland Institute at Harvard, Cambridge, Massachusetts, 02142
| | - Jamilla Akhund-Zade
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, 02138.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Aravinthan D T Samuel
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, 02138.,Department of Physics, Harvard University, Cambridge, Massachusetts, 02138
| | - Mason Klein
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, 02138.,Department of Physics, Harvard University, Cambridge, Massachusetts, 02138.,Department of Physics, University of Miami, Coral Gables, Florida, 33124
| | - Benjamin L de Bivort
- Rowland Institute at Harvard, Cambridge, Massachusetts, 02142. .,Center for Brain Science, Harvard University, Cambridge, Massachusetts, 02138. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138.
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34
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Huang Y, Stinchcombe JR, Agrawal AF. Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity. Evolution 2015; 69:2735-46. [DOI: 10.1111/evo.12771] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 07/09/2015] [Accepted: 08/26/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Yuheng Huang
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - John R. Stinchcombe
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Aneil F. Agrawal
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
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35
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Gompert Z. Bayesian inference of selection in a heterogeneous environment from genetic time-series data. Mol Ecol 2015; 25:121-34. [PMID: 26184577 DOI: 10.1111/mec.13323] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 12/14/2022]
Abstract
Evolutionary geneticists have sought to characterize the causes and molecular targets of selection in natural populations for many years. Although this research programme has been somewhat successful, most statistical methods employed were designed to detect consistent, weak to moderate selection. In contrast, phenotypic studies in nature show that selection varies in time and that individual bouts of selection can be strong. Measurements of the genomic consequences of such fluctuating selection could help test and refine hypotheses concerning the causes of ecological specialization and the maintenance of genetic variation in populations. Herein, I proposed a Bayesian nonhomogeneous hidden Markov model to estimate effective population sizes and quantify variable selection in heterogeneous environments from genetic time-series data. The model is described and then evaluated using a series of simulated data, including cases where selection occurs on a trait with a simple or polygenic molecular basis. The proposed method accurately distinguished neutral loci from non-neutral loci under strong selection, but not from those under weak selection. Selection coefficients were accurately estimated when selection was constant or when the fitness values of genotypes varied linearly with the environment, but these estimates were less accurate when fitness was polygenic or the relationship between the environment and the fitness of genotypes was nonlinear. Past studies of temporal evolutionary dynamics in laboratory populations have been remarkably successful. The proposed method makes similar analyses of genetic time-series data from natural populations more feasible and thereby could help answer fundamental questions about the causes and consequences of evolution in the wild.
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Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One 2014; 9:e112332. [PMID: 25383542 PMCID: PMC4226552 DOI: 10.1371/journal.pone.0112332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scale, thus leads to low levels of divergence between populations at selected loci. However, little is known about the relative importance of these two selective forces in shaping genomic diversity, partly due to difficulties in recognizing balancing selection in species showing low levels of differentiation. Here we address this problem by studying genomic diversity in the European common vole (Microtus arvalis) presenting high levels of differentiation between populations (average FST = 0.31). We studied 3,839 Amplified Fragment Length Polymorphism (AFLP) markers genotyped in 444 individuals from 21 populations distributed across the European continent and hence over different environmental conditions. Our statistical approach to detect markers under selection is based on a Bayesian method specifically developed for AFLP markers, which treats AFLPs as a nearly codominant marker system, and therefore has increased power to detect selection. The high number of screened populations allowed us to detect the signature of balancing selection across a large geographic area. We detected 33 markers potentially under balancing selection, hence strong evidence of stabilizing selection in 21 populations across Europe. However, our analyses identified four-times more markers (138) being under positive selection, and geographical patterns suggest that some of these markers are probably associated with alpine regions, which seem to have environmental conditions that favour adaptation. We conclude that despite favourable conditions in this study for the detection of balancing selection, this evolutionary force seems to play a relatively minor role in shaping the genomic diversity of the common vole, which is more influenced by positive selection and neutral processes like drift and demographic history.
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