• Data acquisition: starting from scratch, we collected 95% of the samples (>2,000 samples) for the whole project in the first two years via a network of international collaborators. A permanent staff engineer (Christelle Blassiau) in the lab has developed extraction and library preparation protocols for Illumina short-read DNA and RNA sequencing. Three species for Axis 1 and two species pairs for Axis 2 have been successfully sequenced to date at a sequencing service platform.
• Axis 1 “How ploidy affects the efficacy of adaptive and purifying selections within species”: one PhD student (Muskaan) was contracted from the 1st November 2023. She developed a bioinformatics pipeline to produce an annotated denovo transcriptome for each species and perform differential expression analyses between the sporophytic stage (diploid) and the gametophytic stage (haploid). She is currently applying her pipeline to a sequenced species (Polytrichum commune), which is used as a benchmark. She presented (talk and poster) her PhD project at the 29th European Meeting for PhD students in Evolutionary Biology (EMPSEB 2024 in Vienna).
• Axis 2 “How ploidy affects the efficacy of selection against hybridization between species?”: one PhD student (Fabien Rey-Giraud) was contracted from the 1st September 2023. He has developed a bioinformatics pipeline to produce an annotated denovo genome for each species pair, and perform demographic inferences from population genomic data. He is currently applying his pipeline to a sequenced species (Polytrichum commune), which is used as a benchmark. He presented (poster) his PhD project at the 57th Population Genetics Group (2024 at St. Andrews). One PostDoc (Arthur Zwaenepoel) was contracted from the 1st November 2022. He has completed theoretical work on the role of dominance, haploid selection and heterogeneous architectures on multilocus barriers to gene flow. We show that our theory for a general haplodiplontic life cycle bowls down to a strictly diploid model through a set of effective parameters. We also showed that more recessive local adaptation generates stronger barriers to gene flow and that increasing the relative strength of selection in the haploid phase, yields stronger effective selection at a selected locus. One might therefore expect that local adaptation would lead to stronger barriers to gene flow in predominantly haploid species and similar considerations apply within the genome of haplodiplontic species (i.e. genes with a haploid-biased expression acting as a stronger barrier to gene flow than diploid-bisaed genes). The University Assistant Himani Sachdeva (Maths department, Vienna) has been involved in Arthur’s supervision and development of these theoretical aspects. Arthur presented his modelling work at the 56th Population Genetics Group (poster, 2023 in London) and at the Probabilistic Modeling in Genomics conference (talk, 2024 in Vienna).
• Axis 3 “How efficient is selection on the sex chromosomes?”: one assistant engineer (Timothée Fichant) is producing sterile cultures in growing chambers for a few moss species. Mastering of these cultures is essential for obtaining uncontaminated high-molecular weight extractions from individual samples for long-read sequencing. To date, we have succeeded in growing four moss species.
