• Major congratulations to PhD student Ioanna Kotari (Borges group), who earned a prestigious 2-year DOC fellowship from the ÖAW with her project "PoMo-cod: Integrating Demography and Selection in Codon evolution". During this fellowship she will aim to advance evolutionary biology through the development of "PoMo-cod" (Polymorphism-aware phylogenetic Model for CODon evolution). Traditional models often overlook genetic variation within species and other key factors such as demographic changes and selection on synonymous sites. PoMo-cod addresses these gaps by incorporating polymorphisms, population size variations, and GC-bias gene conversion, providing a more comprehensive understanding of evolutionary processes.

• We were sad to say goodbye this month to Rui Borges, who has been at the Institut since 2017, first as a postdoc and then as a group leader. But we are also excited for him about his new position as Lecturer in Statistics in the School of Mathematics and Statistics at University of St Andrews. Congratulations and good luck with the move!

• Student in the press: 

  Sarah Saadain, a first-year PhD student in the Kofler group, was interviewed in German for a radio show and podcast about insects by the ORF, a local radio and television broadcaster. She is not only studying Drosophila evolution, but also a passionate entomologist!

  Spotify links: 
  1. Wiener Nachtpfauenauge
  2. Kleiner und Großer Leuchtkäfer
  3. Große Eintagsfliege
  4. Mittlerer Weinschwärmer

  ORF links: this is the first episode and on the bottom you can see the other three:
  https://sound.orf.at/podcast/oe1/insekten/das-wiener-nachtpfauenauge

• Congratulations to Nina Flowers (Yamashita group) on her successful PhD defense: Feeding behavior of dry forest lemurs and monitoring of threats to their habitats

• New bioRxiv preprint: Pianezza R, Haider A and Kofler R. GenomeDelta: detecting recent transposable element invasions without repeat library.

• New publication in Genome Biol. by Hsu S-K, Lai W-Y, Novak J, Lehner F, Jakšić AM, Versace E and Schlötterer C: Reproductive isolation arises during laboratory adaptation to a novel hot environment.

• New paper out in Mol. Biol. Evol. by Kotari I, Kosiol C and Borges R: The patterns of codon usage between chordates and arthropods are different but co-evolving with mutational biases.

• New publication in Genome Biol. Evol. by Lai W-Y, Nolte V, Jakšić AM and Schlötterer C: Evolution of phenotypic variance provides insights into the genetic basis of adaptation.
   
• New bioRxiv preprint: Pianezza R, Scarpa A, Haider A, Signor S and Kofler R: Unveiling the complete invasion history of D. melanogaster: three horizontal transfers of transposable elements in the last 30 years.
   
• New paper in PNAS by Scarpa A, Pianezza R, Wierzbicki F and Kofler R: Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century.

• New paper in PLOS Genet. by Pianezza R, Scarpa A, Narayanan P, Signor S and Kofler R: Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s.
   
• Group leader Robert Kofler was invited to edit a special collection on "Transposable elements in genome evolution" for the journal Genome Biology: https://www.biomedcentral.com/collections/TEGE
   
• New paper in Genome Res. by Selvaraju D, Wierzbicki F and Kofler R: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA based host defense against invading P-elements.

• Also this year our students organised the international practical course "Experimental evolution: Exploring evolutionary forces in controlled environments” from Nov 27 to Dec 1, 2023 at the Vetmeduni. Our students planned the entire course, invited speakers for the morning sessions, screened applications from around the world and taught and tutored all practical sessions for the participants to train on real data. Link to course website
   
• We enjoyed our Xmas dinner to celebrate a successful year soon coming to an end, and, some days later, conquered the ice for a fun skating evening.

• New paper in Evol. Appl. by Buchner S, Hsu S-K, Nolte V, Otte KA and Schlötterer C: Effects of larval crowding on the transcriptome of Drosophila simulans.
   
• Ecol. Evol. accepted a paper by Xiao C, Duarri-Redondo S, Thorhölludottir DAV, Chen Y and Schlötterer C: Non-additive effects between genotypes: Implications for competitive fitness assays.
   
• Preprint by Pianezza R, Scarpa A, Narayanan P, Signor S and Kofler R: Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s

• Wierzbicki and Kofler: new paper our in BMC Biology: The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model.
   
• New Genetics paper out by Scarpa and Kofler: The impact of paramutations on the invasion dynamics of transposable elements.
   
• 31 PhD students and faculty joined this year's retreat at the beautiful surroundings of Altaussee. We had great weather at the foot of the Loser mountain and listened to exciting talks with plenty of discussion opportunities, had a free afternoon for hikes and relaxing and enjoyed traditional food, good company and a night walk.

• Our new cohort of students (Sara, Bilge, Sarah, Siraj, Sriparna, Shahab and Amin) was welcomed to the PopGen crowd by Christian Schlötterer, enjoying mild September weather with "Sturm" - partially fermented, new wine. Harvest season is a meaningful time for several projects run at the program as pomace at the vinyards is Drosophila Eldorado and perfect for collecting flies.

• Just out: collaborative paper of Kofler group with Sarah Signor (North Dakota State Univ., US) in PLoS Genet. - Signor, Vedanayagam, Kim, Wierzbicki, Kofler and Lai.
  Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species.
   
• New publication: Chen, Pelizzola and Futschik in BMC Bioinformatics:
  Haplotype based testing for a better understanding of the selective architecture.
   
• Paper our by Langmüller, Nolte, Dolezal and Schlötterer in Nucleic Acids Res.: The genomic distribution of transposable elements is driven by spatially variable purifying selection.

• New publication by Flowers, Fogaça, Razafindrabe, Razafimampiandra, Dolezal and Yamashita in Am. J. Biol. Anthropol.: Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species.
   
• Congratulations to Filip Wierzbicki (Kofler group) on his successful PhD defense: Transposable elements and piRNA clusters in Drosophila.

• New preprint: Scarpa, Pianezza, Wierzbicki and Kofler: Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster populations during the 19th century.
   
• New paper out in Genome Biology and Evolution by Lai, Otte and Schlötterer: Evolution of metabolome and transcriptome support a hierarchical organization of adaptive traits.
   
• Congratulations to Benjamin Wölfl (PopGen Vienna, Hermisson lab) on his successful PhD defense: "A theory of oligogenic adaptation of a quantitative trait"

• Call for Postdocs and PhD students open at the new special research program (SFB) "Polygenic Adaptation"
   
• Call for PhD students open at the Vienna Graduate School of Population Genetics
   
• Final Symposium of the Vienna Graduate School of Opulation Genetics is coming up May 15-17, 2023. Scientific program and details: link to website
   

• Congratulations to Wei-Yun Lai (Schlötterer group) on successfully defending her PhD thesis entitled "The role of polygenic adaptation and genetic redundancy in gene expression evolution".

• Paper by Barghi and Ramirez-Lanzas: A high throughput method for egg size measurement in Drosophila. (Sci. Rep.)

• Paper by Christian Schlötterer: 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. London. Ser. B, Biol.  Sci.)

• New preprint by Kotari, Kosiol and Borges in bioRxiv: The patterns of codon usage between chordates and arthropods are different but co-evolving with mutational biases.
   
• New preprint by Scarpa and Kofler in bioRxiv: The impact of paramutations on the invasion dynamics of transposable elements.

• New preprint by Wierzbicki and Kofler in bioRxiv: The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model.

• New preprint by Selvaraju, Wierzbicki and Kofler in bioRxiv: P-element invasions in Drosophila erecta shed light on the establishment of host control over a transposable element.

• Students of the Vienna Graduate School of Population Genetics organise the practical course "Experimental evolution: Bringing theory and practice together” from December 5 to 9, 2022 at the Vetmeduni Vienna. Our students coodinated the entire course, invited speakers, screened applications from around the world and planned, taught and tutored all practical sessions for the participants to train on real data.

  Link to course website

• We had a nice get-together for our Xmas party painting mugs and plates for colleagues, and enjoyed pizza. We celebrate a successful year, slowly emerging from the pandemic restrictions.
   
• Congratulations to Neda Barghi and colleagues! The Austrian Science Fund FWF approved the Special Research Programme (SFB) "Polygenic adaptation: from single selected loci to the infinitesimal model", lead by Neda Barghi. During a 4-year period, funds of 3,9 million Euro will enable the SFB members to conduct excellent research in the field of population genetics. The SFB is a joint collaboration of Neda Barghi (speaker), Robert Kofler and Christian Schlötterer (Institute of Population Genetics, Vetmeduni), vice speaker Joachim Hermisson and Himani Sachdeva (Univ. of Vienna), Magnus Nordborg and Kelly Swarts (GMI), and Nick Barton (ISTA).

• Congratulations to research associate Viola Nolte on her promotion to Vetmeduni's expert status in acknowledgement of her excellent and permanently high performance over the years.
   
• New preprint by Chen, Pelizzola and Futschik in bioRxiv: Haplotype based testing for a better understanding of the selective architecture.

• The Austrian Broadcasting Corporation (ORF) published an article about the unusually high number of fruit flies currently appearing in Vienna. While Drosophila populations indeed thrive every year during wine harvest season, this year's mild October temperatures caused by the climate crisis increase the fly's growth rates as explained by Christian Schlötterer: ORF News
   
• Paper out in Proceedings of the Royal Society B: Biological Sciences by Burny, Nolte, Dolezal and Schlötterer: Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster.

• Introductory course for PhD students is taught during September. More information: https://www.popgen-vienna.at/training/introductory-course/

• Prof. Stefan Kramer (see https://www.datamining.informatik.uni-mainz.de/stefan-kramer/) and PhD student Julia Siekiera, M.Sc. (see https://www.datamining.informatik.uni-mainz.de/julia-siekiera/) from the Institute of Computer Science of Johannes Gutenberg University Mainz will visit PopGen Vienna from August 3rd to August 5th to collaborate with the group of Christian Schlötterer. Julia Siekiera will give a talk on the joint work about deep learning in population genetics.

June 2022

• Paper out in MBE by Robert Kofler, Viola Nolte and Christian Schlötterer: The Transposition Rate Has Little Influence on the Plateauing Level of the P-element.

• Head of institute Christian Schlötterer, PopGen Vienna students Dagny Runarsdottir and Benjamin Wölfl (Univ. of Vienna), and former PopGen Vienna faculty member Angela Hancock are currently hosted by the Kavli Institute for Theoretical Physics (KITP). KITP as part of the University of California, Santa Barbara, is one of the most renowned institutes for theoretical physics and related fields. Christian Schlötterer was invited to co-coordinate the KITP workshop “Towards an Integrative View of Adaptation: Bridging Population and Quantitative Genetics” (June 13 - July 15, 2022).

May 2022

• Paper out in Genome Biol. by Christodoulaki, Nolte, Lai and Schlötterer: Natural variation in Drosophila shows weak pleiotropic effects. Press release German / English

April 2022

• Graduate alumna Ana Marija Jakšić, group leader at EPFL in Lausanne, was recently portayed in The Scientist: https://www.the-scientist.com/scientist-to-watch/ana-marija-jak-i-shapes-fruit-fly-brains-6986
   
• New collaborative paper out in G3 with participation of alumna Anna Maria Langmüller: A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles.
   
• Congratulations to Aglaia Szukala (PopGen Vienna / Paun group) on her successful PhD defense: "Parallel and adaptive processes during ecotype formation in Heliosperma pusillum"

March 2022

• Congratulations to PopGen Vienna alumna Polina Novikova, currently group leader at MPIZ in Cologne, on securing an ERC Starting Grant! Novikova lab: https://www.mpipz.mpg.de/novikova

February 2022

• Congratulations to Marta Pelizzola (Futschik group) on her successful PhD defense: "Developing and testing statistical methods for experimental evolution".

• New paper out in G3 by Emmanouil Lirakis, Viola Nolte and Christian Schlötterer:
  Pool-GWAS on reproductive dormancy in Drosophila simulans suggests a polygenic architecture.

January 2022

• Congratulations to Florian Schwarz (Kofler group) on his successful PhD defense: "Towards unraveling the dynamics of transposable elements."

December 2021

• Just out in Proc. R. Soc. B Biol. Sci. by Rupert Mazzucco and Christian Schlötterer: Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level.

• Accepted in Mol Ecol by Filip Wierzbicki, Robert Kofler and Sarah Signor: Evolutionary dynamics of piRNA clusters in Drosophila.

November 2021

• DK members Elif Bozlak and Lara Radovic and DK faculty member Barbara Wallner won the 1st prize at the VetIdeas Challenge. Congratulations!

• Congratulations to Robert Kofler on two FWF grants! ( P34965 “Unravelling the dynamics of transposable elements with long-read sequencing” and P35093 “Does the size of piRNA clusters predict the abundance of transposable element insertions?”)

• Congratulations to Sheng-Kai Hsu (Schlötterer group) on his successful PhD defense: "The role of sex evolution - Sexual conflict and Sexual selection."

• Paper by Wei-Yun Lai and Christian Schlötterer now accepted in Mol. Ecol.:  Evolution of phenotypic variance in response to a novel hot environment.

October 2021

• Early online in Genome Biol Evol by Claire Burny, Viola Nolte, Marlies Dolezal and Christian Schlötterer: Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation.

• Preprint in bioRxiv by Claire Burny, Viola Nolte, Marlies Dolezal and Christian Schlötterer: Genome-wide selection signatures reveal widespread synergistic effects of culture conditions and temperature stress in Drosophila melanogaster.

• Our winter term webinars resume. Details and registration here: https://www.popgen-vienna.at/news/seminars/

September 2021

• Congratulations to Anna Maria Langmüller (Schlötterer group) on her PhD zoom defense entitled "The detection of temperature-dependent fitness effects with Evolve and Resequence experiments". We wish Anna all the best for her new adventures as a postdoc at Cornell Univ. (US)

• Preprint by Kofler, Nolte and Schlötterer: The transposition rate has little influence on equilibrium copy numbers of the P-element.

August 2021

• Preprint by Wierzbicki, Kofler and Signor: Evolutionary dynamics of piRNA clusters in Drosophila.

July 2021

• PhD students Dagny Runarsdottir and Lara Radovic reach out to young researchers at Children's University to explain how populations evolve.

• Congratulations to alumna Ana Marija Jaksic for having been selected as a runner-up for the prestigious best student paper award for papers published in MBE during 2020 with the paper Neuronal Function and Dopamine Signaling Evolve at High Temperature in Drosophila.

• Early online in Genome Biol Evol by Langmüller, Dolezal and Schlötterer: Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments.

• Paper just out in Genome Biol by Otte, Nolte, Mallard and Schlötterer: The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime.

June 2021

• Paper recently accepted in Mol Ecol Res by Wierzbicki,* Schwarz*, Cannalonga and Kofler: Novel quality metrics allow identifying and generating high-quality assemblies of piRNA clusters. *shared authorship

• Preprint online, co-authored by AM Langmüller: A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles.

• Congratulations to Lara Radovic (Wallner group), winner of the student competition (genetics) at the Equine Science Society Virtual Symposium!

May 2021

• Scientific Advisory Board was organized online (May 17-20).

• Preprint just out: AM Langmüller et al.: Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations.

April 2021

• Congratulations to Emmanouil Lyrakis (Schlötterer group) on the highest exam grade for his PhD zoom defense "The physiological and genetic basis of reproductive dormancy in Drosophila fruit flies". We're happy to keep Manolis at the Bioinformatics and Biostatistics Platform.

• New preprint: Burny, Nolte, Dolezal and Schlötterer: Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation.

• New preprint: Wölfl, te Rietmole, Salvioli, Kaznatcheev, Thuijsman, Brown, Burgering and Staňková: The contribution of evolutionary game theory to understanding and treating cancer.

March 2021

• Congratulations to Martin Pontz (Bürger group) on successfully defending his PhD thesis "Effects of epistasis in population genetic two-locus models" online.

• Congratulations to Rui Borges on his FWF grant "PoMo-cod: a polymorphism-aware phylogenetic codon model".

• Collaborative paper in Sci Rep by Fischer, Koblmüller, Börger, Michelitsch, Trajanoski, Schlötterer, Guelly, Thallinger, Sturmbauer: Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika.

• Collaborative paper in Nat Protoc by Bayle, Fiche, Burny, Platre, Nollmann, Martinière and Jaillais: Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues.

February 2021

• Alumnus Thomas Taus was promoted to Teamleader - Reporting and Analysis at Porsche Informatik GmbH in Salzburg. Congratulations!

• Congratulations to our PhD candidate Anna Maria Langmüller, she received a Marie Skłodowska-Curie Individual Fellowship for 2 years of postdoctoral research at Cornell University and 1 year back at Univ. of Vienna!

January 2021

• New preprint: Langmüller, Dolezal and Schlötterer: Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments.

• New preprint: Lai, Nolte, Jakšić and Schlötterer: Evolution of phenotypic variance provides insights into the genetic basis of adaption.

• New preprint: Lai and Schlötterer: Evolution of gene expression variance during adaptation to high temperature in Drosophila.

• New preprint: Szukala et al.: Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae).

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