Periodic Reporting for period 1 - BryoFit (Selection efficacy at intraspecific and interspecific scales: insights from haplo-diplontic plants)
Okres sprawozdawczy: 2022-06-01 do 2024-11-30
Natural selection is a pillar of evolutionary biology: it tends to fix beneficial mutations and remove deleterious ones. But the factors that determine selection efficacy are yet poorly understood. A proposed factor is the interaction between mutations’ dominance and ploidy level: recessivity should reduce selection efficacy in diploids but not in haploids. Methodological limits make this challenging to test in species with a diploid-dominant life cycle. Yet, a whole phylogenetic clade under-explored in genomics gathers all the attributes to tackle this question: Bryophytes. Their life cycle is characterized by alternating a long haploid phase (gametophyte) with a short diploid phase (sporophyte), both phases being macroscopic. It is ideal for shedding light on what drives selection efficacy within and between species, thus, improving our understanding of adaptation and speciation.
1 How ploidy affects the efficacy of adaptive and purifying selections within species? Using comparative genomics, I will empirically test i) if selection is more efficient for haploid-biased genes (i.e. expressed primarily in the gametophyte) than diploid-biased genes, and ii) if that difference is reinforced in species with a more complex sporophyte.
2 How ploidy affects the efficacy of selection against hybridization between species? With theoretical developments, I will quantify the extent to which the length of gametophytic and sporophytic phases influences the accumulation rate of reproductive barriers against interspecies introgression. These predictions will be confronted with genomic estimates by developing a statistical inference method.
3 How efficient is selection in non-recombining genomes? I will take advantage of the Bryophytes’ U/V sexual system to assess the extent to which selection efficacy is reduced on their sex chromosomes. I will also tackle an overlooked issue: are U/V sex chromosomes efficient barriers to introgression?
1 How ploidy affects the efficacy of adaptive and purifying selections within species? Using comparative genomics, I will empirically test i) if selection is more efficient for haploid-biased genes (i.e. expressed primarily in the gametophyte) than diploid-biased genes, and ii) if that difference is reinforced in species with a more complex sporophyte.
2 How ploidy affects the efficacy of selection against hybridization between species? With theoretical developments, I will quantify the extent to which the length of gametophytic and sporophytic phases influences the accumulation rate of reproductive barriers against interspecies introgression. These predictions will be confronted with genomic estimates by developing a statistical inference method.
3 How efficient is selection in non-recombining genomes? I will take advantage of the Bryophytes’ U/V sexual system to assess the extent to which selection efficacy is reduced on their sex chromosomes. I will also tackle an overlooked issue: are U/V sex chromosomes efficient barriers to introgression?
• 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.
• 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.
Thus far, the most significant achievement of the ERC project is to have produced a theoretical framework to understand barriers to gene flow in the context of general life cycles and heterogeneous architectures of isolation, both in terms of selective and dominance effects. We consider this achievement to significantly advance the research in speciation because current models only consider simple life cycles and a homogeneous architecture of isolation. Extending this theory to general life cycles improves our understanding of the maintenance of barriers to gene flow in species with more complex life cycles, such as bryophytes, fungi and algae. Moreover, allowing for genome-wide variation in selective and dominance effects is a significant step forward in understanding more realistic scenarios of speciation. Our results showed that the maintenance of adaptive differentiation in the face of gene flow depends jointly on the extent of coupling between barrier loci, drift, dominance and variation in selective effects across loci. Finally, our theoretical framework also bears relevance to model-based inference of barriers to gene flow from genomic data, as none of the current approaches explicitly models the underlying genetic architecture of isolation.