Although the land snail Cepaea nemoralis is one of the most thoroughly investigated colour polymorphic species, there have been few recent studies on the inheritance of the shell traits. Previously, it has been shown that the shell polymorphism is controlled by a series of nine or more loci, of which five make a single ‘supergene’ containing tightly linked colour and banding loci and more loosely linked pigmentation, spread band and punctate loci. However, one limitation of earlier work was that putative instances of recombination between loci within the supergene were not easily verified. We therefore generated a new set of C. nemoralis crosses that segregate for colour, banding and pigmentation, and several other unlinked shell phenotype loci. The snails were genotyped using a set of RAD-seq-derived loci that flank the supergene, and instances of recombination tested by comparing inferred supergene genotype against RAD-marker genotype. We found no evidence that suspected ‘recombinant’ individuals are recombinant between loci within the supergene. As point estimates of recombination between both colour/banding, and colour/pigmentation loci are zero, incomplete penetrance and epistasis are a better explanation for the apparent ‘recombinant’ phenotype of some snail shells. Overall, this work, therefore, shows that the architecture of the supergene may not be as previously supposed. It also provides a resource for fine mapping of the supergene and other major shell phenotype loci.

ACA and DRG = equal contributionsRunning head: Lack of recombination within the Cepaea nemoralis supergene AbstractAlthough the land snail Cepaea nemoralis is one of the most thoroughly investigated colour polymorphic species, there have been few recent studies on the inheritance of the shell traits. Previously, it has been shown that the shell polymorphism is controlled by a series of nine or more loci, of which five make a single 'supergene' containing tightly linked colour and banding loci and more loosely linked pigmentation, spread band and punctate loci. However, one limitation of earlier work was that putative instances of recombination between loci within the supergene were not easily verified. We therefore generated a new set of C. nemoralis crosses that segregate for colour, banding and pigmentation, and several other unlinked shell phenotype loci. The snails were genotyped using a set of RAD-seq loci that flank the supergene, and instances of recombination tested by comparing inferred supergene genotype against RAD-marker genotype. We found no evidence that suspected

Over the past century, the study of animal color has been critical in establishing some of the founding principles of biology, especially in genetics and evolution. More specifically, inherited variation in animal color has been used to understand the relative roles that natural selection and random genetic drift have to play in the establishment and maintenance of color polymorphism. In this respect, two of the

Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We, therefore, used phylogenomic methods to begin to investigate the post‐glacial history of Cepaea nemoralis, with a long‐term aim to understand the roles that selection and drift have in determining both European‐wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present‐day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mitochondrial DNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long‐distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work, therefore, provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.

One of the emerging strengths of working with the land snail genus Cepaea is that historical collections can be compared against modern day samples, for instance to understand the impact of changing climate and habitat upon shell morph frequencies. However, one potential limitation is that prior studies scored shell ground colour by eye, usually in the field, into three discrete colours yellow, pink or brown. This incurs both potential error and bias in comparative surveys. In this study, we therefore aimed to use a quantitative method to score shell colour, and evaluated it by comparing patterns of C. nemoralis shell colour polymorphism, using both methods on present day samples, and against historical data gathered in the 1960s using the traditional method. The Central Pyrenees were used as an exemplar, because previous intensive surveys sometimes showed sharp discontinuities of morph frequencies within and between valleys. Moreover, selective factors, such as climate or the human impact in the Pyrenees, have significantly changed since 1960s. The main finding was that while quantitative measures of shell colour reduced the possibility of error, and standardised the procedure, the same altitudinal trends were recovered, irrespective of the method. There was remarkable stability in the local shell patterns over five decades, with the exception of one valley that has been subject to increased human activity. Therefore, although subject to potential error, human-scoring of snail colour data remains valuable, especially if persons have appropriate training. In comparison, while there are benefits in taking quantitative measures of colour in the laboratory, there are also several practical disadvantages, mainly in terms of throughput and accessibility. In the future, we anticipate that both methods may be combined, for example, using automated measures of colour taken from photos generated by citizen scientists conducting field surveys.