Population genomics and environmental adaptation in Drosophila ananassae

• Applicant: Dr. Sonja Grath
• Subject Area: Evolution, Anthropology
• Term: from 2015 to 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 271330745

• Final Report Year: 2025

Final Report Abstract

Phase 1 of the project therefore used CCRT to explore the genetic basis of cold adaptation. First, we identified candidate genes involved in the physiological response to cold shock by comparing gene expression in cold-tolerant and cold-sensitive lines. Second, we could map three quantitative trait loci (QTL) that together explained a substantial 64% of the variation in CCRT in the ancestral population. Last, molecular genome editing tools based on CRISPR/Cas9 and PiggyBac systems, were established for the first time in D. ananassae to enable future functional studies of candidate genes, not only for cold stress tolerance. Phase 2 extended this work, motivated by debate about whether CCRT alone fully captures ecologically relevant cold tolerance. Further, experiments included cold acclimation and additional phenotypes. The key findings were that cold acclimation improves cold tolerance and dramatically alters gene expression, particularly in ionoregulatory tissues. Importantly, additional cold tolerance phenotypes, such as lethal time and cold shock mortality, were found not to correlate significantly with chill coma recovery time. This highlights that while CCRT is useful, studying multiple phenotypes provides a more complete understanding of cold tolerance. Further genomic analysis linked specific regions influencing CCRT to biological processes like muscle development and metabolism. Overall, this project advanced our knowledge of thermal adaptation in natural populations.

Publications

• Transcriptome Analysis Reveals Candidate Genes for Cold Tolerance in Drosophila ananassae. Genes, 9(12), 624.
  Königer, Annabella & Grath, Sonja
  
• The molecular basis of cold tolerance in Drosophila ananassae. [Doctoral dissertation, LMU Munich]
  Königer A.
  
• Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae. G3 Genes|Genomes|Genetics, 9(11), 3715-3725.
  Königer, Annabella; Arif, Saad & Grath, Sonja
  
• Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Molecular Biology and Evolution, 37(9), 2661-2678.
  Kapun, Martin; Barrón, Maite G.; Staubach, Fabian; Obbard, Darren J.; Wiberg, R. Axel W.; Vieira, Jorge; Goubert, Clément; Rota-Stabelli, Omar; Kankare, Maaria; Bogaerts-Márquez, María; Haudry, Annabelle; Waidele, Lena; Kozeretska, Iryna; Pasyukova, Elena G.; Loeschcke, Volker; Pascual, Marta; Vieira, Cristina P.; Serga, Svitlana; Montchamp-Moreau, Catherine ... & González, Josefa
  
• Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Molecular Biology and Evolution, 38(12), 5782-5805.
  Kapun, Martin; Nunez, Joaquin C. B.; Bogaerts-Márquez, María; Murga-Moreno, Jesús; Paris, Margot; Outten, Joseph; Coronado-Zamora, Marta; Tern, Courtney; Rota-Stabelli, Omar; Guerreiro, Maria P. García; Casillas, Sònia; Orengo, Dorcas J.; Puerma, Eva; Kankare, Maaria; Ometto, Lino; Loeschcke, Volker; Onder, Banu S.; Abbott, Jessica K.; Schaeffer, Stephen W. ... & Bergland, Alan O.
  
• Natural variation in the transcriptional response ofDrosophila melanogasterto oxidative stress. G3 Genes|Genomes|Genetics, 12(1).
  Ramnarine, Timothy J. S.; Grath, Sonja & Parsch, John
  
• Tropical super flies: Integrating Cas9 into Drosophila ananassae and its phenotypic effects. Journal of Insect Physiology, 147, 104516.
  Yılmaz, Vera M.; Ramnarine, Timothy J.S.; Königer, Annabella; Mussgnug, Selina & Grath, Sonja
  
• From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Molecular Ecology, 34(15).
  Hoedjes, Katja M.; Grath, Sonja; Posnien, Nico; Ritchie, Michael G.; Schlötterer, Christian; Abbott, Jessica K.; Almudi, Isabel; Coronado‐Zamora, Marta; Durmaz Mitchell, Esra; Flatt, Thomas; Fricke, Claudia; Glaser‐Schmitt, Amanda; González, Josefa; Holman, Luke; Kankare, Maaria; Lenhart, Benedict; Orengo, Dorcas J.; Snook, Rhonda R.; Yılmaz, Vera M. & Yusuf, Leeban
  
• Navigating the Cold: Integrative Transcriptome Sequencing Approach Reveals Ionoregulatory and Whole-Body Responses to Cold Acclimation in Drosophila ananassae. openRxiv.
  Yılmaz, Vera Miyase; Bao, Zhihui & Grath, Sonja
  
• Dissecting Cold Tolerance in Drosophila ananassae: A Multi-Phenotypic and Bulk Segregant Analysis.
  Yılmaz, Vera Miyase; Ohlhauser, Vincent; Kara, Fikri Tuğberk & Grath, Sonja