Abstract Book Table of Contents Talks ................................................................................................................ 1 Posters .......................................................................................................... 69 Student presentations are indicated with (S) PopGroup52 Oxford 2019 Talks TALKS The mystery of the U-shaped spectra F. Freund, S. Matuszewski, E. Kerdoncuff, J. Jensen, M. Lapierre, A. Lambert and G. Achaz Collège de France, France Since the advent of the neutral theory of molecular evolution the standard neutral model (mutation-drift equilibrium) has been elevated as a reference model in light of which we routinely interpret population genetics data. Using either forward diffusion or backward coalescent approaches, it can be shown that the expected distribution of mutation frequencies (the so-called sites frequency spectrum, SFS) is proportional to 1/f, where f is the frequency of the mutations. We have collected a large collection of genome-wide SFS (averages of thousands of loci) from a diverse set of organisms, both eukaryotic (plants, fungi, animals) and prokaryotic (bacteria and archea). All the observed SFS were compared to the standard neutral SFS and, with only few exceptions, none fits the expectations of the reference model. The observed SFSs typically show an excess of low and high frequency variants, leading to what is known as U-shaped spectra. Including simple demographies (e.g. monotonic growth/decline) does not result in a perfect fit, neither can the inclusion of mis-orientation errors (erroneous swaps of derived and ancestral frequencies). We have therefore derived theoretical expectations from multiple mergers coalescent (MMC) models (i.e. Beta-coalescents and Xi-coalescents, that both can tuned by a single parameter) together with exponential growth and mis-orientation. MMC models emerge from modes of evolution where few individual can concentrate the parenthood of a large fraction of the population. This include some selective regimes (e.g. the genetic draft) or extremely skewed offspring distribution (e.g. sweep-take reproduction mode). Using both a likely-based approaches and least-square regressions, we show that this three parameter models (mis-orientation, growth rate plus concentrated parenthood) show an excellent fit to many of the observed SFS. We thus discuss the possible replacement of the old reference model by a new one that do fit most of the data (what is expected from a null model !). We further discuss the potential causes of the excellent fit of this new model together the challenging observation that the standard neutral model typically fails to fit the data. 1 PopGroup52 Oxford 2019 Talks A case of mitochondrial DNA recombination? Einar Árnason and Katrín Halldórsdóttir Department of Life and Environmental Sciences, University of Iceland, Iceland It is generally accepted that mitochondrial DNA does not recombine although several recent examples challenge this dogma. In a study of codfish genomics we have come across a case of potential recombination of widely separated mitochondrial DNAs. Is it real or an artifact of the method? We discuss the evidence for mitochondrial differences among the taxa in light of the whole genome nuclear differences. Tracing the source of Gastroenteritis with Machine Learning (S) Nicolas Arning, Daniel J. Wilson Big Data Institute, University of Oxford, UK Gastroenteritis is a food-borne disease commonly caused by the bacterium Campylobacter jejuni. Human infection sources can be under-cooked meat, contact with animal faeces or environmental sources like contaminated drinking water. Attributing the source of a gastroenteritis outbreak is important for applying public health regulations. Previous efforts depend on statistical inference through the comparison of genetic sequence between human and source samples. Our aim is to develop a new Machine Learning based application for source attribution to outperform the existing methods and broaden the spectrum of viable input. The choice of Machine Learning as a solution is due to its underuse, albeit reported success, in genomic contexts. This aim was implemented through unbiased choice of tools and use of a k-mer based approach applicable to any form of genetic sequence. This is especially useful with the ever growing amount of whole genome data available. We report a slight increase in accuracy and present a protocol which can be used for input forms unavailable for use with previous methods. Our results confirms the applicability of Machine learning in genomic contexts and can be used as a stepping stone for similar future endeavours. 2 PopGroup52 Oxford 2019 Talks Investigating Hybrid Male Sterility in the House Mouse (S) Paigan Aspinall, Shauni Doms, John Baines, Leslie Turner University of Bath, UK Mechanisms of the early stages of speciation can be understood by identifying barriers to gene flow between naturally hybridising species. A common barrier between recently diverged species is reduced fertility in hybrids, particularly males. The house mouse subspecies - Mus musculus musculus and Mus musculus domesticus - meet and interbreed in a natural hybrid zone running through central Europe. Hybrid male sterility has been observed as a barrier to gene flow in these house mouse subspecies. Previous studies of hybrid male infertility have focussed on gross phenotyping, which is likely to be a result of multiple genetic incompatibilities. Here we use crosses of strains derived from wild-caught M. m musculus-M. m. domesticus hybrids to investigate reproductive phenotypes in order to determine the number, type, severity and prevalence of fertility defects present. Unlike much of the previous hybrid male sterility work, we perform detailed histological analysis to identify the finer defects that are causing gross phenotypes. Complete sterility appears to be absent in hybrid crosses, but a large proportion of males exhibit fertility phenotypes below the range found in pure subspecies, and as a result likely suffer reduced fertility. The comparison of phenotypes indicates reduced hybrid fertility is highly variable among individuals, suggesting that multiple underlying genetic incompatibilities are responsible for segregation in the hybrid zone. These results are being used in quantitative trait locus (QTL) mapping to identify loci contributing to sterility phenotypes. 3 PopGroup52 Oxford 2019 Talks Epistatic interactions and the evolution of self-fertilisation Diala Abu Awad, Denis Roze Technical University of Munich, Germany Self-fertilization is a wide-spread reproductive strategy that is found in both hermaphroditic animals and plants. Natural populations exhibit a large range of self-fertilizing frequencies, from complete outcrossing (no self-fertilization) to almost exclusive self-fertilization. For self-fertilization to evolve, the levels of inbreeding depression (due to segregating deleterious mutations) maintained in populations must be sufficiently low and the purging of deleterious mutations must be possible. If these conditions are met, existing models predict that populations will evolve towards strict self-fertilization, implying that intermediate self-fertilization rates are not a stable state. This, however, does not concur with the existence of apparently stable mixed-mating strategies. This discrepancy between empirical observations and theoretical expectations could be due to the simplistic assumptions made concerning the underlying genetic architecture of traits affecting self- fertilization and fitness, often relying on single locus approximations. Recent works have shown that the consequences of self-fertilization on inbreeding depression in the presence of epistatic fitness interactions can differ greatly from single-locus approximations. It is therefore primordial that more complex genetic architectures are considered when studying the evolution of self-fertilization. Here we present a model based on Fisher's geometric model in which epistatic fitness interactions between loci arise naturally. Self- fertilization is allowed to evolve through mutations at a number of several interacting loci and fitness depends on n quantitative traits under selection. We determine the conditions necessary for the evolution of self-fertilization and whether or not mixed-mating strategies are stable in this context. Holobiont Suture Zones Joëlle Goüy de Bellocq, Wasimuddin, Alexis Ribas, Josef Bryja, Jaroslav Piálek, Stuart J.E. Baird Czech Academy of Sciences, Prague Parasite hybrid zones resulting from host secondary contact have never been described in nature although parasite hybridization is well known and secondary contact should affect them similarly to free-living organisms. When host populations are isolated, diverge, and re-contact, intimate parasites (host specific, direct life cycle) carried during isolation will also meet and so may form parasite hybrid zones. If so, we hypothesize these should be narrower than the host’s hybrid zone as shorter parasite generation time allows potentially higher divergence. We investigate multi-locus genetics of two parasites across the European house mouse hybrid zone. We find each host taxon harbours its own parasite taxa. These also hybridize: parasite hybrid zones are significantly narrower than the host’s. Here we show a host hybrid zone is a suture zone for a subset of its parasite community and highlight the potential of such systems as windows on the evolutionary processes of host-parasite