Periodic Reporting for period 5 - GuppY (Recombination, sex-specific adaptation and evolution of the poeciliid sex chromosomes) Reporting period: 2021-07-01 to 2022-07-31 Summary of the context and overall objectives of the project Sex chromosomes have evolved independently countless times throughout the eukaryotes. As such, sex chromosomes represent one of the most pervasive examples of convergent evolution, as analogous yet unrelated sex chromosomes share many unique features that distinguish them from the rest of the genome. Although models for sex chromosome evolution have been proposed, they have been difficult to empirically test, largely because most model systems are at a terminal phase of sex chromosome divergence. Most work on sex chromosomes has therefore focused on the consequences of sex chromosome evolution, rather than the causes. In order to understand the forces catalyzing sex chromosome evolution, we focused on the guppies and related species, a unique study system at the earliest stages of sex chromosome divergence, which contain extensive polymorphism among populations and closely related species in the degree and region of recombination suppression, and with easily identified sexually antagonistic traits. GuppY leverages these characteristics along with cutting edge genomics, field collections, and lab experiments to identify the mechanisms, catalysts and consequences of recombination suppression between the sex chromosomes. We also quantified the role of sex-specific selection and sexual conflict in sex chromosome evolution and subsequent divergence. We used comparative, phenotypic and next-generation molecular genetic approaches in order to provide a cohesive and multi-faceted understanding of sex chromosome evolution across three evolutionary levels, integrating patterns of variation within populations, among populations, and across related species, encompassing short, medium and long time-spans and yielding unprecedented insight into multiple stages of evolutionary history. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far Sex chromosomes have evolved independently many times throughout the eukaryotes, and represent a remarkable case of genomic convergence, as unrelated sex chromosomes share many properties across distant taxa. Sex chromosomes evolve after recombination is halted between a homologous pair of chromosomes, but little is known about why this process occurs. The most commonly accepted theory of sex chromosome evolution predicts that recombination will be selected against in the region between a sex-determining gene and a nearby gene with sex-specific effects. This paper was the first direct test of this long-standing theory. We used replicate guppy (Poecilia reticulata) populations with varying level of sexual selection. In each replicate, increased sexual selection has led to an expansion of the non-recombining region. Remarkably, this has occurred independently in each population, suggesting that sex chromosomes can form very quickly and despite considerable gene flow. This study therefore offers the first direct empirical evidence of the forces underlying sexual chromosome formation, and indicates that sexual selection is a major force of genome evolution. This work was published as Wright et al. Nature Communications 2017. We followed this up with a detailed molecular analysis of the sex chromosomes in these populations (Almeia et al. Molecular Biology and Evolution 2020), and we showed that the male-specific region of the Y chromosome has collected substantial coding content through recent gene duplications (Lin et al. Molecular Ecology 2022).We then combined whole genome and transcriptome sequencing data to characterise the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged 20 mya. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata are largely homomorphic, with recombination persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely non-recombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of complete dosage compensation in this species, the first such documented case in teleost fish.This was published as Darolti et al. Proceedings of the National Academy of Sciences 2019; Darolti et al. Genome Biology and Evolution 2020; Darolti et al. Journal of Evolutionary Biology 2022.We also examined the role of the Y chromosome in guppy colouration using novel computational phenotyping approaches. Our results show that colour patterning itself is not Y-linked, contrary to long-standing paradigms, but that overall colouration does have significant Y effects. This was published as Morris et al. Proceedings of the Royal Society B, 2020. In contrast to guppies, we showed that the Y chromosome encodes the complex phenotypes of male para guppies, published as Sandkam et al. Nature Ecology and Evolution 2021.A major focus of the project has been understanding the genetic basis of sex-specific phenotypes, and this has been a very productive avenue, including van der Bijl et al. Evolution Letters 2021; Cooney et al. Evolution 2021;Wright et al. Molecular Ecology 2019; Bloch et al. Nature Ecology and Evolution 2018; Wright et al. Evolution Letters 2018; Mank Nature Reviews Genetics 2017; Corral Lopez Science Advances 2017. Overall, this project has provided a detailed, holistic and integrated understanding of sex chromosomes and the genetic architecture of sex-specific phenotypes. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) In this project, we developed new bioinformatic tools to deal with both sequence and phenotypic data. These included bioformatic pipelines designed to detect the earliest stages of sex chromosome evolution and artificial intelligence and neural nets designed to analyze high resolution phenotype data. We combined these novel approaches with field-caught specimens and lab selection experiments to provide unique insight into the evolution of male and female phenotypes, and the mechanisms by which the Y chromosome evolves. Our work has led to the establishment of guppies and related species as a key model system for the study of the earliest stages of sex chromosome evolution. Guppies, credit Clara Lacy
