Article
Evolutionary Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schlotterer
Summary: The study utilized two inbred Drosophila melanogaster strains exposed to extreme heat for 20 generations, detecting strong and highly parallel selection responses in 10 evolved replicates. The X chromosome showed a more pronounced selection response, and overall, the median selection coefficient for all chromosomes was higher in the two-genotype experiment compared to classic E&R studies. The study suggests that using two random genomes with sufficient variation is well-suited for analyzing polygenic adaptation.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Lucas P. Henry, Julien F. Ayroles
Summary: The microbial diversity in response to host selection differed significantly across studies associated with host traits, rather than selection duration. The study suggests that incorporating the microbiome into E&R experiments can provide critical insights into host-microbiome interactions and the genomic basis of adaptation.
Article
Biochemistry & Molecular Biology
Robert A. Linder, Behzad Zabanavar, Arundhati Majumder, Hannah Chiao-Shyan Hoang, Vanessa Genesaret Delgado, Ryan Tran, Vy Thoai La, Simon William Leemans, Anthony D. Long
Summary: In this study, we conducted a 200-generation Evolve and Resequence (E&R) experiment starting from a hybrid diploid recombined 18-way synthetic population. The replicate populations evolved at large effective population sizes and were exposed to different chemical challenges. We found that, in the sexual evolved populations, there were significant fitness gains and highly repeatable genome-wide haplotype changes within chemical treatments, but limited repeatability across chemical treatments. The adaptation seemed to be highly polygenic, with selected sites mainly dominated by rare variants or haplotype blocks harboring multiple mutations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Mark A. Phillips, Kenneth R. Arnold, Zer Vue, Heather K. Beasley, Edgar Garza-Lopez, Andrea G. Marshall, Derrick J. Morton, Melanie R. McReynolds, Thomas T. Barter, Antentor Hinton Jr
Summary: Experimental evolution with Drosophila melanogaster has been widely used to study aging and longevity, and the addition of DNA and RNA sequencing has allowed researchers to study the genetic basis of longevity. In this study, metabolomic data was incorporated to gain deeper insights into the physiological and genetic mechanisms underlying longevity differences in different populations of D. melanogaster. The metabolomic analysis revealed that aging affects mitochondrial metabolism and identified candidate genes associated with neurological development and function, as well as carbohydrate metabolism. These findings provide plausible genetic mechanisms for explaining longevity differences in this experimental system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Katrina B. Harris, Kenneth M. Flynn, Vaughn S. Cooper
Summary: Evolution and diversification of Pseudomonas aeruginosa populations in biofilm-promoting environments show that adaptation and genetic variation are maintained without the usual elimination of diversity by fixation events. Multiple mutations are preserved at intermediate frequencies, suggesting that some environments may expose a larger fraction of the genome and select for many adaptations at once. This challenges the conventional idea that strong selection would normally purge genetic and phenotypic diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Anna Maria Langmueller, Marlies Dolezal, Christian Schloetterer
Summary: Evolve and Resequence (E&R) studies explore the genomic selection response of populations in Experimental Evolution setups. Secondary E&R, as a promising experimental follow-up procedure, can enhance mapping resolution by allowing for additional recombination events. The crossing scheme and population size are crucial factors determining the power and resolution of secondary E&R, with a minimum population size of 4,800 individuals needed to achieve at least 75% power.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Michal Polak, Jorge L. Hurtado-Gonzales, Joshua B. Benoit, Kassie J. Hooker, Frances Tyler
Summary: This study demonstrated the existence of positive genetic covariance between a male secondary sexual trait, such as ornament size, and competitive fertilization success. The findings suggest that indirect postcopulatory sexual selection may magnify net selection on ornamental trait expression under certain conditions.
Article
Biology
Rupert Mazzucco, Christian Schloetterer
Summary: The influence of the microbiome on its host is well-documented, but the interplay among members of the microbiome is not yet well-understood. Longitudinal studies provide a promising approach to studying such interactions, and a recent study found that the composition of microbiome changes systematically across different temperature regimes, indicating functional interdependence among different microbiome components.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kathrin A. Otte, Christian Schloetterer
Summary: Shifting from SNP analysis to haplotype reconstruction improves the interpretation of E&R experiments, with haplovalidate allowing for detection of selected haplotypes in Pool-seq data.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Mark A. Phillips, Ian C. Kutch, Kaitlin M. McHugh, Savannah K. Taggard, Molly K. Burke
Summary: Synthetic recombinant populations are useful for dissecting the genetics of complex traits, with different construction methods affecting genetic variation and adaptive potential in the populations.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jeroen Dobbelaere, Tiffany Y. Su, Balazs Erdi, Alexander Schleiffer, Alexander Dammermann
Summary: Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. In this study, a set of 386 human genes associated with cilium assembly or motility were identified by analyzing the presence and absence pattern in the genomes of diverse eukaryotes. The novel genes were further characterized and found to be related to cilium defects in fruit flies and nematodes. This dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and provides a valuable resource for future studies.
Article
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
Summary: Utilizing a newly developed bioinformatics pipeline, Drosophila melanogaster's Pool-Seq data is mapped to a hologenome to create the largest genomic data repository to date, called DEST, including 271 population samples from over 100 locations worldwide. This dataset can be used to study spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Parvin Shahrestani, Elizabeth King, Reza Ramezan, Mark Phillips, Melissa Riddle, Marisa Thornburg, Zachary Greenspan, Yonathan Estrella, Kelly Garcia, Pratik Chowdhury, Glen Malarat, Ming Zhu, Susan M. Rottshaefer, Stephen Wraight, Michael Griggs, John Vandenberg, Anthony D. Long, Andrew G. Clark, Brian P. Lazzaro
Summary: The genetic architecture of antifungal immunity in natural populations is poorly understood. Population genetic approaches, including QTL mapping and evolve and resequence methods, were used to explore D. melanogaster immune defense against Beauveria bassiana. Results showed high variability in immune defense, with significant improvement in survivorship over generations and cross-resistance to a second B. bassiana strain after selection for increased defense. Both sexual dimorphism in defense and the specific pathogen exposure were found to influence immune defense.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Parvin Shahrestani, Elizabeth King, Reza Ramezan, Mark Phillips, Melissa Riddle, Marisa Thornburg, Zachary Greenspan, Yonathan Estrella, Kelly Garcia, Pratik Chowdhury, Glen Malarat, Ming Zhu, Susan M. Rottshaefer, Stephen Wraight, Michael Griggs, John Vandenberg, Anthony D. Long, Andrew G. Clark, Brian P. Lazzaro
Summary: The genetic architecture of antifungal immunity in natural populations is complex and influenced by factors such as host genotype and pathogen type in Drosophila melanogaster. The study reveals adaptive cross resistance in fruit flies by enhancing defense against fungi. Both QTL mapping and E&R experiments generated lists of potentially causal candidate genes, but the results were non-overlapping.
G3-GENES GENOMES GENETICS
(2021)
Article
Cell Biology
Uma P. Arora, Beth A. Sullivan, Beth L. Dumont
Summary: This study investigates the interplay between centromere variation and kinetochore protein sequence association in mice, and reveals strain-level differences in both CENP-A positioning and sequence preference along the core centromere satellite.
Article
Biology
Sheng-Kai Hsu, Ana Marija Jaksic, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schloetterer
Article
Evolutionary Biology
Francois Mallard, Viola Nolte, Christian Schloetterer
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Sheng-Kai Hsu, Chaimae Belmouaden, Viola Nolte, Christian Schloetterer
Summary: The study compared expression profiles of replicated Drosophila melanogaster populations exposed to two different temperature regimes in the laboratory for more than 80 generations. It identified genes and gene modules that evolved in the same direction in both temperature regimes, reflecting adaptation to common selection pressures. Additionally, temperature-specific expression changes were observed, with overlap between adaptive genes in experimental evolution and natural Drosophila populations along different temperature clines.
Article
Biochemistry & Molecular Biology
Kathrin A. Otte, Christian Schloetterer
Summary: Shifting from SNP analysis to haplotype reconstruction improves the interpretation of E&R experiments, with haplovalidate allowing for detection of selected haplotypes in Pool-seq data.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Evolutionary Biology
Anna Maria Langmueller, Marlies Dolezal, Christian Schloetterer
Summary: Evolve and Resequence (E&R) studies explore the genomic selection response of populations in Experimental Evolution setups. Secondary E&R, as a promising experimental follow-up procedure, can enhance mapping resolution by allowing for additional recombination events. The crossing scheme and population size are crucial factors determining the power and resolution of secondary E&R, with a minimum population size of 4,800 individuals needed to achieve at least 75% power.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Wei-Yun Lai, Christian Schloetterer
Summary: The study found that after 100 generations of adaptation to a new laboratory environment, the variance of gene expression in Drosophila simulans males was significantly reduced in 125 and 97 genes, suggesting that the drastic loss in environmental complexity may have triggered selection for reduced variance. This observation could have important implications for studies of adaptation processes in natural and experimental populations.
Article
Biology
Rupert Mazzucco, Christian Schloetterer
Summary: The influence of the microbiome on its host is well-documented, but the interplay among members of the microbiome is not yet well-understood. Longitudinal studies provide a promising approach to studying such interactions, and a recent study found that the composition of microbiome changes systematically across different temperature regimes, indicating functional interdependence among different microbiome components.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Manolis Lirakis, Viola Nolte, Christian Schloetterer
Summary: The genetic basis of adaptation to different environments has long been of interest to evolutionary biologists. This study performed a genome-wide scan on the sibling species of D. melanogaster, D. simulans, to characterize the genetic basis of dormancy. The results suggest that dormancy is a polygenic trait with many loci of small effect.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Robert Kofler, Viola Nolte, Christian Schlotterer
Summary: The dynamics of transposable element invasions are influenced by multiple factors, and the transposition rate is only one of them. By studying the temperature-dependent activity of the P-element, researchers found that despite differences in transposition rates, the copy numbers of the P-element were very similar at different temperatures. The decrease in insertion rate as the copy number approached a plateau was accompanied by the production of piRNAs. However, fewer P-element insertions were observed in piRNA clusters than expected, indicating that factors other than the trap model influenced the dynamics of TE invasions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: Experimental evolution combined with whole-genome sequencing is a powerful method to study the adaptive architecture of selected traits. This study shows that the presence of a second stressor affects the genomic selection response, and the combination of temperature and laboratory adaptation results in widespread synergistic effects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Biology
Christian Schloetterer
Summary: Experimental evolution is a useful tool for testing the predictability of evolution without the confounding effects of inaccurate forecasts. Parallel evolution has been studied in both asexual microorganisms and sexual species, but the predictability varies between different aspects. The predictability of genomic selection response for polygenic traits depends on the founder population and the adaptive architecture in the ancestral populations.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Eirini Christodoulaki, Viola Nolte, Wei-Yun Lai, Christian Schloetterer
Summary: This study proposes a new measurement of pleiotropy by integrating information from multiple phenotypes and generations. The results suggest that multiple loci of weak effect contribute to pleiotropy at the genome-wide level. The study also suggests that the modular architecture of gene expression can reduce the costs of pleiotropy.
Article
Biotechnology & Applied Microbiology
Kathrin A. Otte, Viola Nolte, Francois Mallard, Christian Schloetterer
Summary: Understanding the genetic architecture of temperature adaptation is crucial for predicting the impact of climate change on natural populations. Research showed that the adaptive architecture is more dependent on the ancestry of the founder population rather than the specific selection regime, as replicate populations from different environments demonstrated similar responses to cold temperature adaptation.
Article
Biology
Anna Maria Langmueller, Viola Nolte, Ruwansha Galagedara, Rodolphe Poupardin, Marlies Dolezal, Christian Schloetterer