1
|
Lai WY, Nolte V, Jakšić AM, Schlötterer C. Evolution of Phenotypic Variance Provides Insights into the Genetic Basis of Adaptation. Genome Biol Evol 2024; 16:evae077. [PMID: 38620076 PMCID: PMC11057206 DOI: 10.1093/gbe/evae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Most traits are polygenic, and the contributing loci can be identified by genome-wide association studies. The genetic basis of adaptation (adaptive architecture) is, however, difficult to characterize. Here, we propose to study the adaptive architecture of traits by monitoring the evolution of their phenotypic variance during adaptation to a new environment in well-defined laboratory conditions. Extensive computer simulations show that the evolution of phenotypic variance in a replicated experimental evolution setting can distinguish between oligogenic and polygenic adaptive architectures. We compared gene expression variance in male Drosophila simulans before and after 100 generations of adaptation to a novel hot environment. The variance change in gene expression was indistinguishable for genes with and without a significant change in mean expression after 100 generations of evolution. We suggest that the majority of adaptive gene expression evolution can be explained by a polygenic architecture. We propose that tracking the evolution of phenotypic variance across generations can provide an approach to characterize the adaptive architecture.
Collapse
Affiliation(s)
- Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
- Present address: École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
2
|
Schlötterer C. Unraveling the Molecular Basis of Stabilizing Selection by Experimental Evolution. Genome Biol Evol 2023; 15:evad220. [PMID: 38092037 PMCID: PMC10718812 DOI: 10.1093/gbe/evad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Stabilizing selection provides a challenge to molecular population genetics. Although stabilizing selection is ubiquitous, its genomic signature is difficult to distinguish from demographic signals. Experimental evolution provides a promising approach to characterize genomic regions exposed to stabilizing selection. A recent experimental evolution study of Aedes aegypti populations evolving either with or without sexual selection found a pattern of genetic differentiation suggestive of relaxed stabilizing selection. I argue that this study could not have detected the signal of relaxed stabilizing selection. I highlight why incorrect statistical methods resulted in a high number of false positive candidate single nucleotide polymorphism (SNPs) and discuss the fallacy of functional validation of candidate SNPs for polygenic traits by RNA-mediated knockdown.
Collapse
|
3
|
Xiao C, Duarri‐Redondo S, Thorhölludottir DAV, Chen Y, Schlötterer C. Non-additive effects between genotypes: Implications for competitive fitness assays. Ecol Evol 2023; 13:e10713. [PMID: 37941737 PMCID: PMC10630047 DOI: 10.1002/ece3.10713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/22/2023] [Indexed: 11/10/2023] Open
Abstract
Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged Drosophila simulans populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: (1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. (2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype × environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.
Collapse
Affiliation(s)
- Changyi Xiao
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Sara Duarri‐Redondo
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Dagny A. V. Thorhölludottir
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Yiwen Chen
- Institut für PopulationsgenetikVetmeduni ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | | |
Collapse
|
4
|
Buchner S, Hsu S, Nolte V, Otte KA, Schlötterer C. Effects of larval crowding on the transcriptome of Drosophila simulans. Evol Appl 2023; 16:1671-1679. [PMID: 38020870 PMCID: PMC10660784 DOI: 10.1111/eva.13592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 08/21/2023] [Indexed: 12/01/2023] Open
Abstract
Larval crowding is one common ecological stressor for many insect species. In Drosophila, high larval density alters multiple widely-studied phenotypes including life-history traits, morphology and behavior. Nevertheless, we still miss a holistic view of the full range of phenotypic changes and the underlying molecular mechanisms. In this study, we analyzed the adult transcriptomes of high and low larval density fly cohorts, and highlighted the molecular basis of the plastic traits. Increased cellular energy metabolism and locomotion, along with reduced reproductive investment, are key responses to high larval density. Moreover, we compared the expression changes among cohorts with different developmental delays caused by larval crowding. The majority of genes induced by larval crowding showed the strongest expression alterations in cohorts with intermediate delay. Furthermore, linear expression changes were observed in genes related to nutrition and detoxification. Comparing different high-density cohorts could provide insights into the varied responses to distinct larval crowding-induced stresses such as space competition, food degradation and waste accumulation.
Collapse
Affiliation(s)
- Stephan Buchner
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
| | - Sheng‐Kai Hsu
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsVetmeduni ViennaViennaAustria
| | - Viola Nolte
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
| | - Kathrin A. Otte
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Present address:
Institute for ZoologyUniversity of CologneCologneGermany
| | | |
Collapse
|
5
|
Langmüller AM, Nolte V, Dolezal M, Schlötterer C. The genomic distribution of transposable elements is driven by spatially variable purifying selection. Nucleic Acids Res 2023; 51:9203-9213. [PMID: 37560917 PMCID: PMC10516647 DOI: 10.1093/nar/gkad635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
It is widely accepted that the genomic distribution of transposable elements (TEs) mainly reflects the outcome of purifying selection and insertion bias (1). Nevertheless, the relative importance of these two evolutionary forces could not be tested thoroughly. Here, we introduce an experimental system, which allows separating purifying selection from TE insertion bias. We used experimental evolution to study the TE insertion patterns in Drosophila simulans founder populations harboring 1040 insertions of an active P-element. After 10 generations at a large population size, we detected strong selection against P-element insertions. The exception were P-element insertions in genomic regions for which a strong insertion bias has been proposed (2-4). Because recurrent P-element insertions cannot explain this pattern, we conclude that purifying selection, with variable strength along the chromosomes, is the major determinant of the genomic distribution of P-elements. Genomic regions with relaxed purifying selection against P-element insertions exhibit normal levels of purifying selection against base substitutions. This suggests that different types of purifying selection operate on base substitutions and P-element insertions. Our results highlight the power of experimental evolution to understand basic evolutionary processes, which are difficult to infer from patterns of natural variation alone.
Collapse
Affiliation(s)
- Anna M Langmüller
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| |
Collapse
|
6
|
Thorhölludottir DAV, Nolte V, Schlötterer C. Temperature-driven gene expression evolution in natural and laboratory populations highlights the crucial role of correlated fitness effects for polygenic adaptation. Evolution 2023; 77:2081-2089. [PMID: 37455661 DOI: 10.1093/evolut/qpad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/14/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
The influence of pleiotropy on adaptive responses is a highly controversial topic, with limited empirical evidence available. Recognizing the pivotal role of the correlation of fitness effects, we designed an experiment to compare the adaptive gene expression evolution of natural and experimental populations. To test this, we studied the evolution of gene expression in response to temperature in two Drosophila species on a natural temperature cline in North America and replicated populations evolving in hot- and cold-temperature regimes. If fitness effects of affected traits are independent, pleiotropy is expected to constrain the adaptive response in both settings, laboratory and natural populations. However, when fitness effects are more correlated in natural populations, adaptation in the wild will be facilitated by pleiotropy. Remarkably, we find evidence for both predicted effects. In both settings, genes with strong pleiotropic effects contribute less to adaptation, indicating that the majority of fitness effects are not correlated. In addition, we discovered that genes involved in adaptation exhibited more pleiotropic effects in natural populations. We propose that this pattern can be explained by a stronger correlation of fitness effects in nature. More insights into the dual role of pleiotropy will be crucial for the understanding of polygenic adaptation.
Collapse
Affiliation(s)
- Dagny A V Thorhölludottir
- Vienna Graduate School of Population Genetics, Vienna, Austria
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
7
|
Lai WY, Otte KA, Schlötterer C. Evolution of metabolome and transcriptome support a hierarchical organization of adaptive traits. Genome Biol Evol 2023:7180075. [PMID: 37232360 DOI: 10.1093/gbe/evad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/07/2023] [Accepted: 05/25/2023] [Indexed: 05/27/2023] Open
Abstract
Most organismal phenotypes have a polygenic basis, which enables adaptive phenotypic responses on ecological time scales. While adaptive phenotypic changes are highly parallel in replicate populations, this does not apply to the contributing loci. In particular for small populations, the same phenotypic shift can be fueled by different sets of alleles at alternative loci (genetic redundancy). Although this phenomenon is empirically well supported, the molecular basis of the genetic redundancy is not yet understood. To fill this gap, we compared the heterogeneity of the evolutionary transcriptomic and metabolomic response in 10 Drosophila simulans populations which evolved parallel high level phenotypic changes in a novel temperature environment but used different allelic combinations of alternative loci. We showed that the metabolome evolved more parallel than the transcriptome, confirming a hierarchical organization of molecular phenotypes. Different sets of genes responded in each evolved population but led to the enrichment of similar biological functions and a consistent metabolic profile. Since even the metabolomic response was still highly heterogeneous across evolved populations, we propose that selection may operate on pathways/networks.
Collapse
Affiliation(s)
- Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Kathrin A Otte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Aquatic Chemical Ecology, University of Cologne, Cologne, Germany
| | | |
Collapse
|
8
|
Schlötterer C. How predictable is adaptation from standing genetic variation? Experimental evolution in Drosophila highlights the central role of redundancy and linkage disequilibrium. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220046. [PMID: 37004724 PMCID: PMC10067264 DOI: 10.1098/rstb.2022.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Experimental evolution is well-suited to test the predictability of evolution without the confounding effects of inaccurate forecasts about future environments. Most of the literature about parallel (and thus predictable) evolution has been carried out in asexual microorganisms, which adapt by de novo mutations. Nevertheless, parallel evolution has also been studied in sexual species at the genomic level. Here, I review the evidence for parallel evolution in Drosophila, the best-studied obligatory outcrossing model for adaptation from standing genetic variation in the laboratory. Similar to asexual microorganisms, evidence for parallel evolution varies between the focal hierarchical levels. Selected phenotypes consistently respond in a very predicable way, but the underlying allele frequency changes are much less predictable. The most important insight is that the predictability of the genomic selection response for polygenic traits depends highly on the founder population and to a much lesser extent on the selection regime. This implies that predicting adaptive genomic response is challenging and requires a good understanding of the adaptive architecture (including linkage disequilibrium) in the ancestral populations. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
Collapse
Affiliation(s)
- Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| |
Collapse
|
9
|
Burny C, Nolte V, Dolezal M, Schlötterer C. Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster. Proc Biol Sci 2022; 289:20221857. [PMID: 36259211 PMCID: PMC9579754 DOI: 10.1098/rspb.2022.1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Experimental evolution combined with whole-genome sequencing (evolve and resequence (E&R)) is a powerful approach to study the adaptive architecture of selected traits. Nevertheless, so far the focus has been on the selective response triggered by a single stressor. Building on the highly parallel selection response of founder populations with reduced variation, we evaluated how the presence of a second stressor affects the genomic selection response. After 20 generations of adaptation to laboratory conditions at either 18°C or 29°C, strong genome-wide selection signatures were observed. Only 38% of the selection signatures can be attributed to laboratory adaptation (no difference between temperature regimes). The remaining selection responses are either caused by temperature-specific effects, or reflect the joint effects of temperature and laboratory adaptation (same direction, but the magnitude differs between temperatures). The allele frequency changes resulting from the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions-indicating widespread synergistic effects of the two stressors. We conclude that E&R with reduced genetic variation is a powerful approach to study genome-wide fitness consequences driven by the combined effects of multiple environmental factors.
Collapse
Affiliation(s)
- Claire Burny
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna 1210, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna 1210, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna 1210, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Vienna 1210, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna 1210, Austria
| |
Collapse
|
10
|
Abstract
The popular trap model assumes that the invasions of transposable elements (TEs) in mammals and invertebrates are stopped by piRNAs that emerge after insertion of the TE into a piRNA cluster. It remains, however, still unclear which factors influence the dynamics of TE invasions. The activity of the TE (i.e., transposition rate) is one frequently discussed key factor. Here we take advantage of the temperature-dependent activity of the P-element, a widely studied eukaryotic TE, to test how TE activity affects the dynamics of a TE invasion. We monitored P-element invasion dynamics in experimental Drosophila simulans populations at hot and cold culture conditions. Despite marked differences in transposition rates, the P-element reached very similar copy numbers at both temperatures. The reduction of the insertion rate upon approaching the copy number plateau was accompanied by similar amounts of piRNAs against the P-element at both temperatures. Nevertheless, we also observed fewer P-element insertions in piRNA clusters than expected, which is not compatible with a simple trap model. The ping-pong cycle, which degrades TE transcripts, becomes typically active after the copy number plateaued. We generated a model, with few parameters, that largely captures the observed invasion dynamics. We conclude that the transposition rate has at the most only a minor influence on TE abundance, but other factors, such as paramutations or selection against TE insertions are shaping the TE composition.
Collapse
Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| |
Collapse
|
11
|
Christodoulaki E, Nolte V, Lai WY, Schlötterer C. Natural variation in Drosophila shows weak pleiotropic effects. Genome Biol 2022; 23:116. [PMID: 35578368 PMCID: PMC9109288 DOI: 10.1186/s13059-022-02680-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
Background Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is that empirical tests of pleiotropy are restricted to a small subset of all possible phenotypes. To overcome these limitations, we propose a new measurement of pleiotropy that integrates across many phenotypes and multiple generations to improve power. Results We infer pleiotropy from the fitness cost imposed by frequency changes of pleiotropic loci. Mixing Drosophila simulans populations, which adapted independently to the same new environment using different sets of genes, we show that the adaptive frequency changes have been accompanied by measurable fitness costs. Conclusions Unlike previous studies characterizing the molecular basis of pleiotropy, we show that many loci, each of weak effect, contribute to genome-wide pleiotropy. We propose that the costs of pleiotropy are reduced by the modular architecture of gene expression, which facilitates adaptive gene expression changes with low impact on other functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02680-4.
Collapse
Affiliation(s)
- Eirini Christodoulaki
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria
| | - Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | | |
Collapse
|
12
|
Lirakis M, Nolte V, Schlötterer C. Pool-GWAS on reproductive dormancy in Drosophila simulans suggests a polygenic architecture. G3 Genes|Genomes|Genetics 2022; 12:6523974. [PMID: 35137042 PMCID: PMC8895979 DOI: 10.1093/g3journal/jkac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/29/2021] [Indexed: 11/29/2022]
Abstract
The genetic basis of adaptation to different environments has been of long-standing interest to evolutionary biologists. Dormancy is a well-studied adaptation to facilitate overwintering. In Drosophila melanogaster, a moderate number of genes with large effects have been described, which suggests a simple genetic basis of dormancy. On the other hand, genome-wide scans for dormancy suggest a polygenic architecture in insects. In D. melanogaster, the analysis of the genetic architecture of dormancy is complicated by the presence of cosmopolitan inversions. Here, we performed a genome-wide scan to characterize the genetic basis of this ecologically extremely important trait in the sibling species of D. melanogaster, D. simulans that lacks cosmopolitan inversions. We performed Pool-GWAS in a South African D. simulans population for dormancy incidence at 2 temperature regimes (10 and 12°C, LD 10:14). We identified several genes with SNPs that showed a significant association with dormancy (P-value < 1e-13), but the overall modest response suggests that dormancy is a polygenic trait with many loci of small effect. Our results shed light on controversies on reproductive dormancy in Drosophila and have important implications for the characterization of the genetic basis of this trait.
Collapse
Affiliation(s)
- Manolis Lirakis
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
| | | |
Collapse
|
13
|
Mazzucco R, Schlötterer C. Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level. Proc Biol Sci 2021; 288:20212193. [PMID: 34905708 PMCID: PMC8670958 DOI: 10.1098/rspb.2021.2193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The influence of the microbiome on its host is well-documented, but the interplay of its members is not yet well-understood. Even for simple microbiomes, the interaction among members of the microbiome is difficult to study. Longitudinal studies provide a promising approach to studying such interactions through the temporal covariation of different taxonomic units. By contrast to most longitudinal studies, which span only a single host generation, we here present a post hoc analysis of a whole-genome dataset of 81 samples that follows microbiome composition for up to 180 host generations, which cover nearly 10 years. The microbiome diversity remained rather stable in replicated Drosophila melanogaster populations exposed to two different temperature regimes. The composition changed, however, systematically across replicates of the two temperature regimes. Significant associations between families, mostly specific to one temperature regime, indicate functional interdependence of different microbiome components. These associations also involve moderately abundant families, which emphasizes their functional importance, and highlights the importance of looking beyond the common constituents of the Drosophila microbiome.
Collapse
Affiliation(s)
- Rupert Mazzucco
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien 1210, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien 1210, Austria
| |
Collapse
|
14
|
Lai WY, Schlötterer C. Evolution of phenotypic variance in response to a novel hot environment. Mol Ecol 2021; 31:934-945. [PMID: 34775658 DOI: 10.1111/mec.16274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/21/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022]
Abstract
Shifts in trait means are widely considered as evidence for adaptive responses, but the impact on phenotypic variance remains largely unexplored. Classic quantitative genetics provides a theoretical framework to predict how selection on phenotypic mean affects the variance. In addition to this indirect effect, it is also possible that the variance of the trait is the direct target of selection, but experimentally characterized cases are rare. Here, we studied gene expression variance of Drosophila simulans males before and after 100 generations of adaptation to a novel hot laboratory environment. In each of the two independently evolved populations, the variance of 125 and 97 genes was significantly reduced. We propose that the drastic loss in environmental complexity from nature to the laboratory may have triggered selection for reduced variance. Our observation that selection could drive changes in the variance of gene expression could have important implications for studies of adaptation processes in natural and experimental populations.
Collapse
Affiliation(s)
- Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
15
|
Burny C, Nolte V, Dolezal M, Schlötterer C. Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation. Genome Biol Evol 2021; 13:6409861. [PMID: 34694407 PMCID: PMC8599828 DOI: 10.1093/gbe/evab239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Because genetic redundancy often results in nonparallel selection responses among replicates, we propose a modified evolve and resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29 °C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Because two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.
Collapse
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
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Wien, Austria
| | | |
Collapse
|
16
|
Otte KA, Nolte V, Mallard F, Schlötterer C. The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime. Genome Biol 2021; 22:211. [PMID: 34271951 PMCID: PMC8285869 DOI: 10.1186/s13059-021-02425-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 06/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence, which combines advantages of experimental evolution such as time series, replicate populations, and controlled environmental conditions, with whole genome sequencing. Recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures—either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Results Here, we expose the founder population from Portugal to a cold temperature regime. Although almost no selection targets are shared between the hot and cold selection regime, the adaptive architecture was similar. We identify a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. Conclusions These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02425-9.
Collapse
Affiliation(s)
- Kathrin A Otte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Present address: Institute for Zoology, University of Cologne, Cologne, Germany
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Present address: Institut de Biologie de l'École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, F-75005, Paris, France
| | | |
Collapse
|
17
|
Langmüller AM, Dolezal M, Schlötterer C. Fine Mapping without Phenotyping: Identification of Selection Targets in Secondary Evolve and Resequence Experiments. Genome Biol Evol 2021; 13:6311659. [PMID: 34190980 PMCID: PMC8358229 DOI: 10.1093/gbe/evab154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Evolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution setup. Despite the popularity of E&R, empirical studies in sexually reproducing organisms typically suffer from an excess of candidate loci due to linkage disequilibrium, and single gene or SNP resolution is the exception rather than the rule. Recently, so-called "secondary E&R" has been suggested as promising experimental follow-up procedure to confirm putatively selected regions from a primary E&R study. Secondary E&R provides also the opportunity to increase mapping resolution by allowing for additional recombination events, which separate the selection target from neutral hitchhikers. Here, we use computer simulations to assess the effect of different crossing schemes, population size, experimental duration, and number of replicates on the power and resolution of secondary E&R. We find that the crossing scheme and population size are crucial factors determining power and resolution of secondary E&R: A simple crossing scheme with few founder lines consistently outcompetes crossing schemes where evolved populations from a primary E&R experiment are mixed with a complex ancestral founder population. Regardless of the experimental design tested, a population size of at least 4,800 individuals, which is roughly five times larger than population sizes in typical E&R studies, is required to achieve a power of at least 75%. Our study provides an important step toward improved experimental designs aiming to characterize causative SNPs in Experimental Evolution studies.
Collapse
Affiliation(s)
- Anna Maria Langmüller
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
18
|
Fischer C, Koblmüller S, Börger C, Michelitsch G, Trajanoski S, Schlötterer C, Guelly C, Thallinger GG, Sturmbauer C. Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. Sci Rep 2021; 11:4309. [PMID: 33619328 PMCID: PMC7900123 DOI: 10.1038/s41598-021-81030-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023] Open
Abstract
With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3-9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.
Collapse
Affiliation(s)
- C Fischer
- Institute of Biology, University of Graz, Graz, Austria
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - S Koblmüller
- Institute of Biology, University of Graz, Graz, Austria
| | - C Börger
- Institute of Biology, University of Graz, Graz, Austria
| | - G Michelitsch
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - S Trajanoski
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - C Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - C Guelly
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - G G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - C Sturmbauer
- Institute of Biology, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| |
Collapse
|
19
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | |
Collapse
|
20
|
Hsu S, Belmouaden C, Nolte V, Schlötterer C. Parallel gene expression evolution in natural and laboratory evolved populations. Mol Ecol 2021; 30:884-894. [PMID: 32979867 PMCID: PMC7891358 DOI: 10.1111/mec.15649] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/19/2020] [Accepted: 09/11/2020] [Indexed: 01/01/2023]
Abstract
Ecological adaptation is frequently inferred by the comparison of natural populations from different environments. Nevertheless, inference of the selective forces suffers the challenge that many environmental factors covary. With well-controlled environmental conditions, experimental evolution provides a powerful approach to complement the analysis of natural populations. On the other hand, it is apparent that laboratory conditions differ in many ways from natural environments, which raises the question as to what extent selection responses in experimental evolution studies can inform us about adaptation processes in the wild. In this study, we compared the expression profiles of replicated Drosophila melanogaster populations which have been exposed to two distinct temperature regimes (18/28 and 10/20°C) in the laboratory for more than 80 generations. Using gene-wise differential expression analysis and co-expression network analysis, we identified 541 genes and three coregulated gene modules that evolved in the same direction in both temperature regimes, and most of these changes probably reflect an adaptation to the space constraint or diurnal temperature fluctuation that is common in both selection regimes. In total, 203 genes and seven modules evolved temperature-specific expression changes. Remarkably, we detected a significant overlap of these temperature-adaptive genes/modules from experimental evolution with temperature-adaptive genes inferred from natural Drosophila populations covering two different temperature clines. We conclude that well-designed experimental evolution studies are a powerful tool to dissect evolutionary responses.
Collapse
Affiliation(s)
- Sheng‐Kai Hsu
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsVetmeduni ViennaViennaAustria
| | - Chaimae Belmouaden
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Present address:
Faculty of Fundamental and Applied Sciences of PoitiersFrance
| | - Viola Nolte
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
| | | |
Collapse
|
21
|
Abstract
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to environmental variation. The importance of phenotypic plasticity in natural populations and its contribution to phenotypic evolution during rapid environmental change is widely debated. Here, we show that thermal plasticity of gene expression in natural populations is a key component of its adaptation: evolution to novel thermal environments increases ancestral plasticity rather than mean genetic expression. We determined the evolution of plasticity in gene expression by conducting laboratory natural selection on a Drosophila simulans population in hot and cold environments. After more than 60 generations in the hot environment, 325 genes evolved a change in plasticity relative to the natural ancestral population. Plasticity increased in 75% of these genes, which were strongly enriched for several well-defined functional categories (e.g., chitin metabolism, glycolysis, and oxidative phosphorylation). Furthermore, we show that plasticity in gene expression of populations exposed to different temperatures is rather similar across species. We conclude that most of the ancestral plasticity can evolve further in more extreme environments.
Collapse
Affiliation(s)
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | | |
Collapse
|
22
|
Langmüller AM, Nolte V, Galagedara R, Poupardin R, Dolezal M, Schlötterer C. Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature. BMC Biol 2020; 18:157. [PMID: 33121485 PMCID: PMC7597021 DOI: 10.1186/s12915-020-00882-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species, three amino acid replacements (I161V, G265A, and F330Y) provide resistance against several insecticides. Because temperature disturbs neuronal signaling homeostasis, we reasoned that the cost of insecticide resistance could be modulated by ambient temperature. RESULTS Experimental evolution of a natural Drosophila simulans population at hot and cold temperature regimes uncovered a surprisingly strong effect of ambient temperature. In the cold temperature regime, the resistance mutations were strongly counter selected (s = - 0.055), but in a hot environment, the fitness costs of resistance mutations were reduced by almost 50% (s = - 0.031). We attribute this unexpected observation to the advantage of the reduced enzymatic activity of resistance mutations in hot environments. CONCLUSION We show that fitness costs of insecticide resistance genes are temperature-dependent and suggest that the duration of insecticide-free periods need to be adjusted for different climatic regions to reflect these costs. We suggest that such environment-dependent fitness effects may be more common than previously assumed and pose a major challenge for modeling climate change.
Collapse
Affiliation(s)
- Anna Maria Langmüller
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Ruwansha Galagedara
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Rodolphe Poupardin
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Present Address: Paracelsus Medical University Salzburg, Strubergasse 21, 5020, Salzburg, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
| |
Collapse
|
23
|
Otte KA, Schlötterer C. Detecting selected haplotype blocks in evolve and resequence experiments. Mol Ecol Resour 2020; 21:93-109. [PMID: 32810339 PMCID: PMC7754423 DOI: 10.1111/1755-0998.13244] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022]
Abstract
Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of evolve and resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool‐seq data need a variety of data‐specific parameters that are typically defined ad hoc and require haplotype sequences for validation. Here, we introduce haplovalidate, a tool which detects selected haplotypes in Pool‐seq time series data without the need for sequenced haplotypes. Haplovalidate makes data‐driven choices of two key parameters for the clustering procedure, the minimum correlation between SNPs constituting a cluster and the window size. Applying haplovalidate to simulated E&R data reliably detects selected haplotype blocks with low false discovery rates. Importantly, our analyses identified a restriction of the haplotype block‐based approach to describe the genomic architecture of adaptation. We detected a substantial fraction of haplotypes containing multiple selection targets. These blocks were considered as one region of selection and therefore led to underestimation of the number of selection targets. We demonstrate that the separate analysis of earlier time points can significantly increase the separation of selection targets into individual haplotype blocks. We conclude that the analysis of selected haplotype blocks has great potential for the characterization of the adaptive architecture with E&R experiments.
Collapse
Affiliation(s)
- Kathrin A Otte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
24
|
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: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
Affiliation(s)
- Anna Maria Langmüller
- Vienna Graduate School of Population GeneticsViennaAustria
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
| | | |
Collapse
|
25
|
Leung K, Ras E, Ferguson KB, Ariëns S, Babendreier D, Bijma P, Bourtzis K, Brodeur J, Bruins MA, Centurión A, Chattington SR, Chinchilla-Ramírez M, Dicke M, Fatouros NE, González-Cabrera J, Groot TVM, Haye T, Knapp M, Koskinioti P, Le Hesran S, Lyrakis M, Paspati A, Pérez-Hedo M, Plouvier WN, Schlötterer C, Stahl JM, Thiel A, Urbaneja A, van de Zande L, Verhulst EC, Vet LEM, Visser S, Werren JH, Xia S, Zwaan BJ, Magalhães S, Beukeboom LW, Pannebakker BA. Next-generation biological control: the need for integrating genetics and genomics. Biol Rev Camb Philos Soc 2020; 95:1838-1854. [PMID: 32794644 PMCID: PMC7689903 DOI: 10.1111/brv.12641] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro‐ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker‐assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post‐release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.
Collapse
Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Erica Ras
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Kim B Ferguson
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Simone Ariëns
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | | | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Jacques Brodeur
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Quebec, Canada, H1X 2B2
| | - Margreet A Bruins
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Alejandra Centurión
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Sophie R Chattington
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Milena Chinchilla-Ramírez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Joel González-Cabrera
- Department of Genetics, Estructura de Recerca Interdisciplinar en Biotecnología i Biomedicina (ERI-BIOTECMED), Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Universitat de València, Dr Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Thomas V M Groot
- Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Tim Haye
- CABI, Rue des Grillons 1, 2800, Delémont, Switzerland
| | - Markus Knapp
- Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Panagiota Koskinioti
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Sophie Le Hesran
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Manolis Lyrakis
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Angeliki Paspati
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Meritxell Pérez-Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Wouter N Plouvier
- INRA, CNRS, UMR 1355-7254, 400 Route des Chappes, BP 167 06903, Sophia Antipolis Cedex, France
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Judith M Stahl
- CABI, Rue des Grillons 1, 2800, Delémont, Switzerland.,Kearney Agricultural Research and Extension Center, University of California Berkeley, 9240 South Riverbend Avenue, Parlier, CA, 93648, USA
| | - Andra Thiel
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Eveline C Verhulst
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Louise E M Vet
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Sander Visser
- Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Shuwen Xia
- Animal Breeding and Genomics, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016, Lisbon, Portugal
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Bart A Pannebakker
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
26
|
Abstract
In molecular population genetics, adaptation is typically thought to occur via selective sweeps, where targets of selection have independent effects on the phenotype and rise to fixation, whereas in quantitative genetics, many loci contribute to the phenotype and subtle frequency changes occur at many loci during polygenic adaptation. The sweep model makes specific predictions about frequency changes of beneficial alleles and many test statistics have been developed to detect such selection signatures. Despite polygenic adaptation is probably the prevalent mode of adaptation, because of the traditional focus on the phenotype, we are lacking a solid understanding of the similarities and differences of selection signatures under the two models. Recent theoretical and empirical studies have shown that both selective sweep and polygenic adaptation models could result in a sweep-like genomic signature; therefore, additional criteria are needed to distinguish the two models. With replicated populations and time series data, experimental evolution studies have the potential to identify the underlying model of adaptation. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles for two models: 1) adaptation of a trait via independent beneficial mutations that are conditioned for fixation, that is, selective sweep model and 2) trait optimum model (polygenic adaptation), that is adaptation of a quantitative trait under stabilizing selection after a sudden shift in trait optimum. We identify several distinct patterns of selective sweep and trait optimum models in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two models.
Collapse
Affiliation(s)
- Neda Barghi
- Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | | |
Collapse
|
27
|
Mazzucco R, Nolte V, Vijayan T, Schlötterer C. Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts. Front Genet 2020; 11:482. [PMID: 32477411 PMCID: PMC7241558 DOI: 10.3389/fgene.2020.00482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
Climate change is a major evolutionary force triggering thermal adaptation in a broad range of species. While the consequences of global warming are being studied for an increasing number of species, limited attention has been given to the evolutionary dynamics of endosymbionts in response to climate change. Here, we address this question by studying the dynamics of Wolbachia, a well-studied endosymbiont of Drosophila melanogaster. D. melanogaster populations infected with 13 different Wolbachia strains were exposed to novel hot and cold laboratory environments for up to 180 generations. The short-term dynamics suggested a temperature-related fitness difference resulting in the increase of clade V strains in the cold environment only. Our long-term analysis now uncovers that clade V dominates in all replicates after generation 60 irrespective of temperature treatment. We propose that adaptation of the Drosophila host to either temperature or Drosophila C virus (DCV) infection are the cause of the replicated, temporally non-concordant Wolbachia dynamics. Our study provides an interesting case demonstrating that even simple, well-controlled experiments can result in complex, but repeatable evolutionary dynamics, thus providing a cautionary note on too simple interpretations on the impact of climate change.
Collapse
Affiliation(s)
- Rupert Mazzucco
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Thapasya Vijayan
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Wien, Austria
| |
Collapse
|
28
|
Jakšić AM, Karner J, Nolte V, Hsu SK, Barghi N, Mallard F, Otte KA, Svečnjak L, Senti KA, Schlötterer C. Neuronal Function and Dopamine Signaling Evolve at High Temperature in Drosophila. Mol Biol Evol 2020; 37:2630-2640. [DOI: 10.1093/molbev/msaa116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Abstract
Neuronal activity is temperature sensitive and affects behavioral traits important for individual fitness, such as locomotion and courtship. Yet, we do not know enough about the evolutionary response of neuronal phenotypes in new temperature environments. Here, we use long-term experimental evolution of Drosophila simulans populations exposed to novel temperature regimes. Here, we demonstrate a direct relationship between thermal selective pressure and the evolution of neuronally expressed molecular and behavioral phenotypes. Several essential neuronal genes evolve lower expression at high temperatures and higher expression at low temperatures, with dopaminergic neurons standing out by displaying the most consistent expression change across independent replicates. We functionally validate the link between evolved gene expression and behavioral changes by pharmacological intervention in the experimentally evolved D. simulans populations as well as by genetically triggered expression changes of key genes in D. melanogaster. As natural temperature clines confirm our results for Drosophila and Anopheles populations, we conclude that neuronal dopamine evolution is a key factor for temperature adaptation.
Collapse
Affiliation(s)
- Ana Marija Jakšić
- Department of Molecular Biology and Genetics, Cornell University, NY
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Julia Karner
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Sheng-Kai Hsu
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Neda Barghi
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - François Mallard
- Institut de Biologie de l’École Normale Supérieure, Paris, France
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Lidija Svečnjak
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | | | | |
Collapse
|
29
|
Hsu SK, Jakšić AM, Nolte V, Lirakis M, Kofler R, Barghi N, Versace E, Schlötterer C. Rapid sex-specific adaptation to high temperature in Drosophila. eLife 2020; 9:e53237. [PMID: 32083552 PMCID: PMC7034977 DOI: 10.7554/elife.53237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 12/28/2022] Open
Abstract
The pervasive occurrence of sexual dimorphism demonstrates different adaptive strategies of males and females. While different reproductive strategies of the two sexes are well-characterized, very little is known about differential functional requirements of males and females in their natural habitats. Here, we study the impact environmental change on the selection response in both sexes. Exposing replicated Drosophila populations to a novel temperature regime, we demonstrate sex-specific changes in gene expression, metabolic and behavioral phenotypes in less than 100 generations. This indicates not only different functional requirements of both sexes in the new environment but also rapid sex-specific adaptation. Supported by computer simulations we propose that altered sex-biased gene regulation from standing genetic variation, rather than new mutations, is the driver of rapid sex-specific adaptation. Our discovery of environmentally driven divergent functional requirements of males and females has important implications-possibly even for gender aware medical treatments.
Collapse
Affiliation(s)
- Sheng-Kai Hsu
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
- Vienna Graduate School of Population Genetics, Vetmeduni ViennaViennaAustria
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
- Vienna Graduate School of Population Genetics, Vetmeduni ViennaViennaAustria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
| | - Manolis Lirakis
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
- Vienna Graduate School of Population Genetics, Vetmeduni ViennaViennaAustria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
| | - Neda Barghi
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
| | - Elisabetta Versace
- Department of Biological and Experimental Psychology, Queen Mary University of LondonLondonUnited Kingdom
| | | |
Collapse
|
30
|
Barghi N, Schlötterer C. Shifting the paradigm in Evolve and Resequence studies: From analysis of single nucleotide polymorphisms to selected haplotype blocks. Mol Ecol 2020; 28:521-524. [PMID: 30793868 PMCID: PMC6850332 DOI: 10.1111/mec.14992] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022]
Abstract
For almost a decade the combination of whole genome sequencing with experimental evolution (Evolve and Resequence, E&R; Turner, Stewart, Fields, Rice, & Tarone, 2011) has been used to study adaptation in outcrossing organisms. However, complications caused by inversions and hitchhiking variants have prevented this powerful approach from living up to its potential. In this issue of Molecular Ecology, Michalak, Kang, Schou, Garner, and Loeschke (2018), provide an important step ahead by using a population of Drosophila melanogaster devoid of segregating inversions to identify the genetic basis of resistance to five environmental stressors. They further address the challenge of hitchhiking variants by reconstructing selected haplotype blocks. While it is apparent that the haplotype block reconstruction needs further refinements, their work underpins the potential of E&R studies in Drosophila to address fundamental questions in evolutionary biology.
Collapse
Affiliation(s)
- Neda Barghi
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
31
|
Vlachos C, Burny C, Pelizzola M, Borges R, Futschik A, Kofler R, Schlötterer C. Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies. Genome Biol 2019; 20:169. [PMID: 31416462 PMCID: PMC6694636 DOI: 10.1186/s13059-019-1770-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The combination of experimental evolution with whole-genome resequencing of pooled individuals, also called evolve and resequence (E&R) is a powerful approach to study the selection processes and to infer the architecture of adaptive variation. Given the large potential of this method, a range of software tools were developed to identify selected SNPs and to measure their selection coefficients. RESULTS In this benchmarking study, we compare 15 test statistics implemented in 10 software tools using three different scenarios. We demonstrate that the power of the methods differs among the scenarios, but some consistently outperform others. LRT-1, CLEAR, and the CMH test perform best despite LRT-1 and the CMH test not requiring time series data. CLEAR provides the most accurate estimates of selection coefficients. CONCLUSION This benchmark study will not only facilitate the analysis of already existing data, but also affect the design of future data collections.
Collapse
Affiliation(s)
- Christos Vlachos
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Claire Burny
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marta Pelizzola
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Rui Borges
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria
| | - Andreas Futschik
- Institute of Applied Statistics, Johannes Kepler University, Linz, 4040, Austria
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria.
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, 1210, Austria.
| |
Collapse
|
32
|
Howie JM, Mazzucco R, Taus T, Nolte V, Schlötterer C. DNA Motifs Are Not General Predictors of Recombination in Two Drosophila Sister Species. Genome Biol Evol 2019; 11:1345-1357. [PMID: 30980655 PMCID: PMC6490297 DOI: 10.1093/gbe/evz082] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
Meiotic recombination is crucial for chromosomal segregation and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease toward centromeres and telomeres, with a dramatic impact on levels of variation in natural populations. Two close sister species, Drosophila simulans and Drosophila mauritiana do not only have higher recombination rates but also exhibit a much more homogeneous recombination rate that only drops sharply very close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation in D. melanogaster, we tested whether the difference in recombination landscape between D. melanogaster and D. simulans can be explained by the genomic distribution of recombination rate–associated sequence motifs. We constructed the first high-resolution recombination map for D. simulans based on 189 haplotypes from a natural D. simulans population and searched for short sequence motifs linked with higher than average recombination in both sister species. We identified five consensus motifs significantly associated with higher than average chromosome-wide recombination rates in at least one species and present in both. Testing fine resolution associations between motif density and recombination, we found strong and positive associations genome-wide over a range of scales in D. melanogaster, while the results were equivocal in D. simulans. Despite the strong association in D. melanogaster, we did not find a decreasing density of these short-repeat motifs toward centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape in D. melanogaster, nor the differences to D. simulans. The strong association seen for the sequence motifs in D. melanogaster likely reflects their impact influencing local differences in recombination rates along the genome.
Collapse
Affiliation(s)
- James M Howie
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | | | - Thomas Taus
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | | |
Collapse
|
33
|
Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep 2019; 9:6095. [PMID: 30988347 PMCID: PMC6465346 DOI: 10.1038/s41598-019-42640-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.
Collapse
Affiliation(s)
- Sabine Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Viktoria Dobretsberger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | | | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Jan E Janečka
- Department of Biological Sciences, Duquesne University, Pittsburgh, 15282, USA
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | | | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, 75123, Sweden
| | - Robert Schaefer
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Christian Schlötterer
- Institut fuer Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
- Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany
| | - Brandon Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
| |
Collapse
|
34
|
Barghi N, Tobler R, Nolte V, Jakšić AM, Mallard F, Otte KA, Dolezal M, Taus T, Kofler R, Schlötterer C. Genetic redundancy fuels polygenic adaptation in Drosophila. PLoS Biol 2019; 17:e3000128. [PMID: 30716062 PMCID: PMC6375663 DOI: 10.1371/journal.pbio.3000128] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/14/2019] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic-i.e., result from selection on a large number of genetic loci-but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes (AFCs) across many contributing loci. To resolve this, we use laboratory natural selection to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among beneficial alleles. We observed convergent responses for several phenotypes-e.g., fitness, metabolic rate, and fat content-and a strong polygenic response (99 selected alleles; mean s = 0.059). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. We discerned different evolutionary paradigms based on the heterogeneous genomic patterns among replicates. Redundancy and quantitative trait (QT) paradigms fitted the experimental data better than simulations assuming independent selective sweeps. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses using multiple alternative genetic pathways converging at a new phenotypic optimum. This key property of beneficial alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.
Collapse
Affiliation(s)
- Neda Barghi
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Raymond Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Marlies Dolezal
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Plattform Bioinformatik und Biostatistik, Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Thomas Taus
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
35
|
Hsu SK, Jakšić AM, Nolte V, Barghi N, Mallard F, Otte KA, Schlötterer C. A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment. Genes (Basel) 2019; 10:E89. [PMID: 30696109 PMCID: PMC6410183 DOI: 10.3390/genes10020089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/19/2019] [Accepted: 01/23/2019] [Indexed: 02/08/2023] Open
Abstract
Gene expression profiling is one of the most reliable high-throughput phenotyping methods, allowing researchers to quantify the transcript abundance of expressed genes. Because many biotic and abiotic factors influence gene expression, it is recommended to control them as tightly as possible. Here, we show that a 24 h age difference of Drosophilasimulans females that were subjected to RNA sequencing (RNA-Seq) five and six days after eclosure resulted in more than 2000 differentially expressed genes. This is twice the number of genes that changed expression during 100 generations of evolution in a novel hot laboratory environment. Importantly, most of the genes differing in expression due to age introduce false positives or negatives if an adaptive gene expression analysis is not controlled for age. Our results indicate that tightly controlled experimental conditions, including precise developmental staging, are needed for reliable gene expression analyses, in particular in an evolutionary framework.
Collapse
Affiliation(s)
- Sheng-Kai Hsu
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Neda Barghi
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Kathrin A Otte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | | |
Collapse
|
36
|
Fabian DK, Garschall K, Klepsatel P, Santos‐Matos G, Sucena É, Kapun M, Lemaitre B, Schlötterer C, Arking R, Flatt T. Evolution of longevity improves immunity in Drosophila. Evol Lett 2018; 2:567-579. [PMID: 30564440 PMCID: PMC6292704 DOI: 10.1002/evl3.89] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/24/2018] [Indexed: 12/20/2022] Open
Abstract
Much has been learned about the genetics of aging from studies in model organisms, but still little is known about naturally occurring alleles that contribute to variation in longevity. For example, analysis of mutants and transgenes has identified insulin signaling as a major regulator of longevity, yet whether standing variation in this pathway underlies microevolutionary changes in lifespan and correlated fitness traits remains largely unclear. Here, we have analyzed the genomes of a set of Drosophila melanogaster lines that have been maintained under direct selection for postponed reproduction and indirect selection for longevity, relative to unselected control lines, for over 35 years. We identified many candidate loci shaped by selection for longevity and late-life fertility, but - contrary to expectation - we did not find overrepresentation of canonical longevity genes. Instead, we found an enrichment of immunity genes, particularly in the Toll pathway, suggesting that evolutionary changes in immune function might underpin - in part - the evolution of late-life fertility and longevity. To test whether this genomic signature is causative, we performed functional experiments. In contrast to control flies, long-lived flies tended to downregulate the expression of antimicrobial peptides upon infection with age yet survived fungal, bacterial, and viral infections significantly better, consistent with alleviated immunosenescence. To examine whether genes of the Toll pathway directly affect longevity, we employed conditional knockdown using in vivo RNAi. In adults, RNAi against the Toll receptor extended lifespan, whereas silencing the pathway antagonist cactus--causing immune hyperactivation - dramatically shortened lifespan. Together, our results suggest that genetic changes in the age-dependent regulation of immune homeostasis might contribute to the evolution of longer life.
Collapse
Affiliation(s)
- Daniel K. Fabian
- Centre for Pathogen Evolution, Department of ZoologyUniversity of CambridgeCambridgeUnited Kingdom
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Kathrin Garschall
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Peter Klepsatel
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Institute of ZoologySlovak Academy of Sciences845 06 BratislavaSlovakia
| | | | - Élio Sucena
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Departamento de Biologia AnimalFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Martin Kapun
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Bruno Lemaitre
- Global Health InstituteSchool of Life Sciences, EPFLLausanneSwitzerland
| | | | - Robert Arking
- Department of Biological SciencesWayne State UniversityDetroitMichigan
| | - Thomas Flatt
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| |
Collapse
|
37
|
Faria VG, Martins NE, Schlötterer C, Sucena É. Readapting to DCV Infection without Wolbachia: Frequency Changes of Drosophila Antiviral Alleles Can Replace Endosymbiont Protection. Genome Biol Evol 2018; 10:1783-1791. [PMID: 29947761 PMCID: PMC6054199 DOI: 10.1093/gbe/evy137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
There is now ample evidence that endosymbionts can contribute to host adaptation to environmental challenges. However, how endosymbiont presence affects the adaptive trajectory and outcome of the host is yet largely unexplored. In Drosophila, Wolbachia confers protection to RNA virus infection, an effect that differs between Wolbachia strains and can be targeted by selection. Adaptation to RNA virus infections is mediated by both Wolbachia and the host, raising the question of whether adaptive genetic changes in the host vary with the presence/absence of the endosymbiont. Here, we address this question using a polymorphic D. melanogaster population previously adapted to DCV infection for 35 generations in the presence of Wolbachia, from which we removed the endosymbiont and followed survival over the subsequent 20 generations of infection. After an initial severe drop, survival frequencies upon DCV selection increased significantly, as seen before in the presence of Wolbachia. Whole-genome sequencing, revealed that the major genes involved in the first selection experiment, pastrel and Ubc-E2H, continued to be selected in Wolbachia-free D. melanogaster, with the frequencies of protective alleles being closer to fixation in the absence of Wolbachia. Our results suggest that heterogeneity in Wolbachia infection status may be sufficient to maintain polymorphisms even in the absence of costs.
Collapse
Affiliation(s)
- Vitor G Faria
- Instituto Gulbenkian de Ciência, Rua da quinta grande 6, 2780-156 Oeiras, Portugal.,Zoological Institute, Basel University, Basel, Switzerland
| | - Nelson E Martins
- Instituto Gulbenkian de Ciência, Rua da quinta grande 6, 2780-156 Oeiras, Portugal.,CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Élio Sucena
- Instituto Gulbenkian de Ciência, Rua da quinta grande 6, 2780-156 Oeiras, Portugal.,Departamento de Biologia Animal, edifício C2, Faculdade de Ciências, Universidade de Lisboa, Portugal
| |
Collapse
|
38
|
Mallard F, Nolte V, Tobler R, Kapun M, Schlötterer C. A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Genome Biol 2018; 19:119. [PMID: 30122150 PMCID: PMC6100727 DOI: 10.1186/s13059-018-1503-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/03/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS To investigate the genetic architecture of thermal adaptation - a highly complex trait - we performed experimental evolution on a natural Drosophila simulans population. Transcriptome and respiration measurements reveal extensive metabolic rewiring after only approximately 60 generations in a hot environment. Analysis of genome-wide polymorphisms identifies two interacting selection targets, Sestrin and SNF4Aγ, pointing to AMPK, a central metabolic switch, as a key factor for thermal adaptation. CONCLUSIONS Our results demonstrate that large-effect loci segregating at intermediate allele frequencies can allow natural populations to rapidly respond to selection. Because SNF4Aγ also exhibits clinal variation in various Drosophila species, we suggest that this large-effect polymorphism is maintained by temporal and spatial temperature variation in natural environments.
Collapse
Affiliation(s)
- François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Ray Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
- Present address: Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Martin Kapun
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
- Present address: Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
39
|
Endler L, Gibert J, Nolte V, Schlötterer C. Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits in Drosophila melanogaster. Mol Ecol 2018; 27:3207-3218. [PMID: 29957826 PMCID: PMC6120501 DOI: 10.1111/mec.14781] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/24/2018] [Accepted: 06/25/2018] [Indexed: 01/10/2023]
Abstract
Traits with a common genetic basis frequently display correlated phenotypic responses to selection or environmental conditions. In Drosophila melanogaster, pigmentation of the abdomen and a trident-shaped region on the thorax are genetically correlated. Here, we used a pooled replicated genomewide association approach (Pool-GWAS) to identify the genetic basis of variation in thoracic trident pigmentation in two Drosophila melanogaster populations. We confirmed the previously reported large effect of ebony and the association of the cosmopolitan inversion In(3R)Payne. For the first time, we identified tan as another major locus contributing to variation in trident pigmentation. Intriguingly, the regulatory variants of tan that were most strongly associated with female abdominal pigmentation also showed a strong association with trident pigmentation. We validated this common genetic basis in transgenic assays and found qualitatively similar effects on trident and abdominal pigmentation. Further work is required to determine whether this genetic correlation is favoured by natural selection or reflects a neutral by-product of a shared regulatory architecture.
Collapse
Affiliation(s)
- Lukas Endler
- Institute of PopulationsgenetikVetmeduni WienWienAustria
| | - Jean‐Michel Gibert
- CNRSBiologie du Développement Paris Seine‐Institut de Biologie Paris Seine (LBD‐IBPS)Sorbonne UniversitéParisFrance
| | - Viola Nolte
- Institute of PopulationsgenetikVetmeduni WienWienAustria
| | | |
Collapse
|
40
|
Kofler R, Senti KA, Nolte V, Tobler R, Schlötterer C. Molecular dissection of a natural transposable element invasion. Genome Res 2018; 28:824-835. [PMID: 29712752 PMCID: PMC5991514 DOI: 10.1101/gr.228627.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 04/10/2018] [Indexed: 02/07/2023]
Abstract
The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured a D. simulans population at an early stage of a P-element invasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, the P-element spread rapidly for 20 generations, but no further spread was noted later on. This plateauing of the invasion was mediated by the rapid emergence of P-element-specific piRNAs. Under cold conditions, we observed a lower expression of the P-element and a slower emergence of the piRNA defense, resulting in a three times slower invasion that continued beyond 40 generations. We conclude that the environment is a major factor determining the evolution of TEs in their host.
Collapse
Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria
| | | | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria
| | - Ray Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria
| | | |
Collapse
|
41
|
Lirakis M, Dolezal M, Schlötterer C. Redefining reproductive dormancy in Drosophila as a general stress response to cold temperatures. J Insect Physiol 2018; 107:175-185. [PMID: 29649483 DOI: 10.1016/j.jinsphys.2018.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 04/07/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Organisms regularly encounter unfavorable conditions and the genetic adaptations facilitating survival have been of long-standing interest to evolutionary biologists. Winter is one particularly stressful condition for insects, during which they encounter low temperatures and scarcity of food. Despite dormancy being a well-studied adaptation to facilitate overwintering, there is still considerable controversy about the distribution of dormancy among natural populations and between species in Drosophila. The current definition of dormancy as developmental arrest of oogenesis at the previtellogenic stage (stage 7) distinguishes dormancy from general stress related block of oogenesis at early vitellogenic stages (stages 8 - 9). In an attempt to resolve this, we scrutinized reproductive dormancy in D. melanogaster and D. simulans. We show that dormancy shows the same hallmarks of arrest of oogenesis at stage 9, as described for other stressors and propose a new classification for dormancy. Applying this modified classification, we show that both species express dormancy in cosmopolitan and African populations, further supporting that dormancy uses an ancestral pathway induced by environmental stress. While we found significant differences between individuals and the two Drosophila species in their sensitivity to cold temperature stress, we also noted that extreme temperature stress (8 °C) resulted in very strong dormancy incidence, which strongly reduced the differences seen at less extreme temperatures. We conclude that dormancy in Drosophila should not be considered a special trait, but is better understood as a generic stress response occurring at low temperatures.
Collapse
Affiliation(s)
- Manolis Lirakis
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria; Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
| | - Marlies Dolezal
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| |
Collapse
|
42
|
Abstract
Allele frequency time series data constitute a powerful resource for unraveling mechanisms of adaptation, because the temporal dimension captures important information about evolutionary forces. In particular, Evolve and Resequence (E&R), the whole-genome sequencing of replicated experimentally evolving populations, is becoming increasingly popular. Based on computer simulations several studies proposed experimental parameters to optimize the identification of the selection targets. No such recommendations are available for the underlying parameters selection strength and dominance. Here, we introduce a highly accurate method to estimate selection parameters from replicated time series data, which is fast enough to be applied on a genome scale. Using this new method, we evaluate how experimental parameters can be optimized to obtain the most reliable estimates for selection parameters. We show that the effective population size (Ne) and the number of replicates have the largest impact. Because the number of time points and sequencing coverage had only a minor effect, we suggest that time series analysis is feasible without major increase in sequencing costs. We anticipate that time series analysis will become routine in E&R studies.
Collapse
Affiliation(s)
- Thomas Taus
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Andreas Futschik
- Department of Applied Statistics, Johannes Kepler Universität Linz, Linz, Austria
| | | |
Collapse
|
43
|
Abstract
Fecundity is probably the most frequently studied fitness component in Drosophila. Nevertheless, currently used methods to measure fecundity are not well-suited for large-scale experiments, with many populations being assayed in parallel. Here we present a standardized pipeline to measure fecundity in many Drosophila population samples with substantially reduced hand on times. Using a high-contrast medium for egg laying, we developed a Java plug-in for ImageJ to quantify the number of eggs by image processing. We show that our method is fast and provides reliable egg counts.
Collapse
Affiliation(s)
- Pierre Nouhaud
- Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni, Vienna, Austria.,UMR 8197 IBENS, Paris, France
| | | | - Neda Barghi
- Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | | |
Collapse
|
44
|
Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin CJ, Schlötterer C, Rattei T, Brem G, Wallner B. Asian horses deepen the MSY phylogeny. Anim Genet 2018; 49:90-93. [PMID: 29333704 DOI: 10.1111/age.12635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2017] [Indexed: 01/09/2023]
Abstract
Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.
Collapse
Affiliation(s)
- S Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - C Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - D Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - R Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - M Neuditschko
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - S Rieder
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - B Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - G Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C-J Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - C Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, Austria
| | - T Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - G Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - B Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| |
Collapse
|
45
|
Gómez-Sánchez D, Schlötterer C. ReadTools: A universal toolkit for handling sequence data from different sequencing platforms. Mol Ecol Resour 2017; 18:676-680. [PMID: 29171165 DOI: 10.1111/1755-0998.12741] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/07/2017] [Accepted: 11/12/2017] [Indexed: 11/28/2022]
Abstract
Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms have resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented preprocessing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open-source Java toolkit designed to standardize and preprocess read data from different platforms. It manages FASTQ- and SAM-formatted inputs while dealing with platform-specific peculiarities and provides a standard SAM compliant output. The code and executable are available at https://github.com/magicDGS/ReadTools.
Collapse
Affiliation(s)
- Daniel Gómez-Sánchez
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.,Vienna Graduate School of Population Genetics, Wien, Vienna
| | | |
Collapse
|
46
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
47
|
Jakšić AM, Kofler R, Schlötterer C. Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster. Mol Ecol 2017; 26:5149-5159. [PMID: 28742942 DOI: 10.1111/mec.14259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) are mobile genetic elements that can move around the genome, and their expression is one precondition for this mobility. Because the insertion of TEs in new genomic positions is largely deleterious, the molecular mechanisms for transcriptional suppression have been extensively studied. In contrast, very little is known about their primary transcriptional regulation. Here, we characterize the expression dynamics of TE families in Drosophila melanogaster across a broad temperature range (13-29°C). In 71% of the expressed TE families, the expression is modulated by temperature. We show that this temperature-dependent regulation is specific for TE families and strongly affected by the genetic background. We deduce that TEs carry family-specific regulatory sequences, which are targeted by host-specific trans-acting factors, such as transcription factors. Consistent with the widespread dominant inheritance of gene expression, we also find the prevailing dominance of TE family expression. We conclude that TE family expression across a range of temperatures is regulated by an interaction between TE family-specific regulatory elements and trans-acting factors of the host.
Collapse
Affiliation(s)
- Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
48
|
Gibert JM, Blanco J, Dolezal M, Nolte V, Peronnet F, Schlötterer C. Strong epistatic and additive effects of linked candidate SNPs for Drosophila pigmentation have implications for analysis of genome-wide association studies results. Genome Biol 2017; 18:126. [PMID: 28673357 PMCID: PMC5496195 DOI: 10.1186/s13059-017-1262-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/19/2017] [Indexed: 01/01/2023] Open
Abstract
Background The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how many of the SNPs in the block, and which ones, are causative. Drosophila pigmentation is a powerful model to dissect the genetic basis of intra-specific and inter-specific phenotypic variation. Three tightly linked SNPs in the t-MSE enhancer have been identified in three D. melanogaster populations as major contributors to female abdominal pigmentation. This enhancer controls the expression of the pigmentation gene tan (t) in the abdominal epidermis. Two of the three SNPs were confirmed in an independent study using the D. melanogaster Genetic Reference Panel established from a North American population. Results We determined the functional impact of SNP1, SNP2, and SNP3 using transgenic lines to test all possible haplotypes in vivo. We show that all three candidate SNPs contribute to female Drosophila abdominal pigmentation. Interestingly, only two SNPs agree with the effect predicted by GWAS; the third one goes in the opposite direction because of linkage disequilibrium between multiple functional SNPs. Our experimental design uncovered strong additive effects for the three SNPs, but we also found significant epistatic effects explaining up to 11% of the total variation. Conclusions Our results suggest that linked causal variants are important for the interpretation of GWAS and functional validation is needed to understand the genetic architecture of traits. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1262-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie du Développement Paris Seine-Institut de Biologie Paris Seine (LBD-IBPS), case 24, 9 quai St-Bernard, 75005, Paris, France
| | - Jorge Blanco
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Wien, Austria
| | - Marlies Dolezal
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Wien, Austria
| | - Frédérique Peronnet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie du Développement Paris Seine-Institut de Biologie Paris Seine (LBD-IBPS), case 24, 9 quai St-Bernard, 75005, Paris, France
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Wien, Austria.
| |
Collapse
|
49
|
Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol 2017; 27:2029-2035.e5. [PMID: 28669755 DOI: 10.1016/j.cub.2017.05.086] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/19/2017] [Accepted: 05/26/2017] [Indexed: 11/25/2022]
Abstract
The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.
Collapse
Affiliation(s)
- Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
| | - Nicola Palmieri
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Thomas Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising 85354, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany; Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Leif Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4461, USA
| | - Robert Schaefer
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland
| | - Christian Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| |
Collapse
|
50
|
Otte KA, Schlötterer C. Polymorphism-aware protein databases - a prerequisite for an unbiased proteomic analysis of natural populations. Mol Ecol Resour 2017; 17:1148-1155. [DOI: 10.1111/1755-0998.12656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 01/12/2017] [Accepted: 01/20/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Kathrin A. Otte
- Institut für Populationsgenetik; Vetmeduni Vienna; Veterinärplatz 1 1210 Vienna Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik; Vetmeduni Vienna; Veterinärplatz 1 1210 Vienna Austria
| |
Collapse
|