Molecular area effects in Cepaea

Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map

Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.

Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

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.

Qualitative and quantitative methods show stability in patterns of Cepaea nemoralis shell polymorphism in the Pyrenees over five decades

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. In this regard, 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 color by eye 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 color and evaluated it by comparing patterns of C. nemoralis shell color polymorphism in the Pyrenees, using both methods on present-day samples, and against historical data gathered in the 1960s using the traditional method. The main finding was that while quantitative measures of shell color reduced the possibility of error and standardized the procedure, the same altitudinal trends were recovered, irrespective of the method. The results also showed that there was a general stability in the local shell patterns over five decades, including altitudinal clines, with just some exceptions. Therefore, although subject to potential error human scoring of snail color data remains valuable, especially if persons have appropriate training. In comparison, while there are benefits in taking quantitative measures of color in the laboratory, there are also several practical disadvantages, mainly in terms of throughput and accessibility. In the future, we anticipate that genomic methods may be used to understand the potential role of selection in maintaining shell morph clines. In addition, photographs generated by citizen scientists conducting field surveys may be used with deep learning-based methods to survey color patterns.

Deep genetic structure at a small spatial scale in the endangered land snail Xerocrassa montserratensis

Species with small geographic ranges do not tend to have a high genetic structure, but some land snail species seem to be an exception. Xerocrassa montserratensis, an endangered land snail endemic to Catalonia (northeastern Iberian Peninsula), is an excellent model to study the processes affecting the phylogeography of specialized species of conservation concern. This species is restricted to xerophilous stony slopes and occurs within a small and fragmented area of ca. 500 km2. We sequenced the COI barcode region of 152 individuals from eight sites covering the entire range of the species. We found four genetic groups mostly coincident with their geographic distribution: a central ancestral group containing shared haplotypes among five localities and three groups restricted to a single locality each. Two of these derived groups were geographically and genetically isolated, while the third and most differentiated group was not geographically isolated. Geomorphologic and paleoclimatic processes during the Pleistocene can explain the divergence found between populations of this low dispersal species with historical fragmentation and secondary contacts. Nonetheless, recent passive large dispersal through streams was also detected in the central group. Overall, our study uncovered four evolutionary units, partially matching morphologically described subspecies, which should be considered in future conservation actions.

Unravelling the riddle of Radix: DNA barcoding for species identification of freshwater snail intermediate hosts of zoonotic digeneans and estimating their inter-population evolutionary relationships

Radix spp. are intermediate host snails for digenean parasites of medical and veterinary importance. Within this genus, species differentiation using shell and internal organ morphology can result in erroneous species identification, causing problems when trying to understand the population biology of Radix. In the present study, DNA barcoding, using cox1 and ITS2 sequences, identified populations of Radix auricularia and Radix balthica from specimens originally morphologically identified as Radix peregra from the UK. Assessment of cox1 and ITS2 as species identification markers showed that, although both markers differentiated species, cox1 possessed greater molecular diversity and higher phylogenetic resolution. Cox1 also proved useful for gaining insights into the evolutionary relationships of Radix species populations. Phylogenetic analysis and haplotype networks of cox1 indicated that R. auricularia appeared to have invaded the UK several times; some haplotypes forming a distinct UK specific clade, whilst others are more akin to those found on mainland Europe. This was in contrast to relationships between R. balthica populations, which had low molecular diversity and no distinct UK specific haplotypes, suggesting recent and multiple invasions from mainland Europe. Molecular techniques therefore appear to be crucial for distinguishing Radix spp., particularly using cox1. This barcoding marker also enables the population biology of Radix spp. to be explored, and is invaluable for monitoring the epidemiology of fluke diseases especially in the light of emerging diseases and food security.

RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene

Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a 'supergene' of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a lack of genetic markers. With a view to re-establish Cepaea as a prominent model of molecular ecology, we made six laboratory crosses of Cepaea nemoralis, five of which segregated for shell ground colour (C) and the presence or absence of bands (B). First, scoring of colour and banding in 323 individuals found no recombination between the C and B loci of the supergene. Second, using restriction site-associated DNA sequencing (RAD-Seq) of two parents and 22 offspring, we identified 44 anonymous markers putatively linked to the colour (C) and banding (B) loci. The genotype of eleven of the most promising RAD-Seq markers was independently validated in the same 22 offspring, then up to a further 146 offspring were genotyped. The closest RAD-Seq markers scored are within ~0.6 centimorgan (cM) of the C-B supergene linkage group, with the combined loci together forming a 35.8 cM linkage map of markers that flank both sides of the Cepaea C-B supergene.

An unusual phylogeography in the bushcricket Ephippiger ephippiger from Southern France

Pleistocene glaciations have played a major role in species divergence. The bushcricket Ephippiger ephippiger shows unusual patterns of intraspecific variation in multiple traits across Southern Europe. This is centred in Southern France, and evidence implies that it results from secondary contact after differentiation in Pleistocene refugia. However, the possible time scales involved, locations of the refugia and patterns of expansion remain obscure. This study sequenced the COII (507 BP) and cyt b (428 BP) mitochondrial genes to examine the intraspecific phylogeography of Western European samples of E. ephippiger. A minimum evolution tree revealed little resolution between described subspecies of E. ephippiger. Strikingly, populations from the Pyrenees and Mediterranean coastal region contained a complex genetic structure corresponding to major river valleys, independent of the traditional taxonomy. Samples of the subspecies E. e. vitium formed a distinct clade, perhaps supporting their taxonomic status. However, other forms (cruciger and cunii) were not genetically distinct, which is surprising given differences in their morphology and behaviour. The extent of the genetic divergence between Pyreneen valleys is unexpectedly deep, with average Tamura-Nei distances of around 14% (net distances of 11%) separating the main clades of coding COII sequences. Cyt b showed a similar pattern, but was confounded by some non-coding probable pseudogenes. If a conventional insect molecular clock is applied, these cryptic clades must pre-date the Pleistocene, and hypotheses for their history are discussed. However, mtDNA divergence in Ephippiger is not evolving in a clock-like manner, because a likelihood ratio test rejects clock assumptions for the COII sequences.

Genetic consequences of climatic oscillations in the Quaternary

An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.

History or current selection? A molecular analysis of 'area effects' in the land snail Cepaea nemoralis

We have used molecular variation in microsatellite and mitochondrial DNA to throw light on the origins of enigmatic geographical patterns, known as 'area effects', in the shell polymorphisms of the land snail Cepaea nemoralis. Our aim was to assess the relative importance of recent selection and historical events in the formation of these patterns. On the Marlborough Downs in Wiltshire, England, the 'type locality' for area effects, the frequencies of microsatellites are significantly associated with the frequencies of alleles for shell banding. A less clear association is found between microsatellites and shell colour. Mitochondrial haplotypes show no significant relationships. Although the correlated geographical patterns could be the results of random genetic drift from an initially uniform array of populations, the magnitudes of the patterns, and of the correlations between them, seem too strong to have arisen by drift since the last glaciation. Our results suggest that invasions from refugia have been the most important factors in forming area effects.

A two–stage model for Cepaea polymorphism

The history of the study of snails in the genusCepaeais briefly outlined.Cepaea nemoralisandC. hortensisare polymorphic for genetically controlled shell colour and banding, which has been the main interest of the work covered. Random drift, selective predation and climatic selection, both at a macro– and micro–scale, all affect gene frequency. The usual approach to understanding maintenance of the polymorphism, has been to look for centripetal effects on frequency. Possible processes include balance of mutation pressure and drift, heterozygote advantage, relational balance heterosis, frequency–dependent predation, multi–niche selective balance, or some combination of these. Mutational balance is overlaid by more substantial forces. There is some evidence for heterosis. Predation by birds may protect the polymorphism, and act apostatically to favour distinct morphs. Although not substantiated forCepaea, many studies show that predators behave in the appropriate manner, while shell colour polymorphisms in molluscs occur most commonly in species exposed to visually searching predators. It is not known whether different thermal properties of the shells help to generate equilibria. Migration between colonies is probably greater than originally thought. The present geographical range has been occupied for less than 5000 generations. Climatic and human modification alter snail habitats relatively rapidly, which in turn changes selection pressures. A simple simulation shows that migration coupled with selection which fluctuates but is not centripetal, may retain polymorphism for sufficiently long to account for the patterns we see today. There may therefore be a two–stage basis to the polymorphism, comprising long–term but weak balancing forces coupled with fluctuating selection which does not necessarily balance but results in very slow elimination. Persistence of genetic variants in this way may provide the conditions for evolution of a balanced genome.

Evolution and extinction of Partulidae, endemic Pacific island land snails

The broad outline of the systematics of the endemic Pacific island land snail family Partulidae has been understood for some time. The family is divided into three genera: Eua has four species, confined to Tonga and Samoa; Samoana has about 23 species, widely but sporadically distributed in Polynesia and the Mariana Islands; Partula has about 100 species, distributed from Belau to the Society Islands. This review integrates this systematic and biogeographic knowledge with work on ecology, population genetics and speciation that has concentrated especially on the recently speciated Partula spp. of Moorea in the Society Islands. Explanations of Moorean diversity (much of which seems unrelated to ecological factors) based on parapatric speciation and the evolution of morph ratio dines in the absence of isolation have predominated, although without incontrovertible support. Unitary explanations are probably not appropriate. Rather little is known of the basic biology of partulids. They are generally arboreal; feed on a wide range of partially decayed and living plant material; and are relatively long-lived, slow reproducing, ovoviviparous, cross- or self-fertilizing hermaphrodites. The phylogenetic and geographical origins of the three genera are unknown. Partula may have evolved, somewhere unknown, from Samoana, which evolved from Eua in the Tonga-Sam oa region, this being the region of origin of Eua; but the opposite sequence has also been postulated. The question is unresolved. Origins of the Moorean species are better understood as their inter-relationships are relatively clear. Rather few dispersal events probably took place and the Society Island fauna as a whole may be derived from but two colonization events - first by a Samoana sp. and later by a Partula sp., both of which then speciated in situ - with a few intra-archipelago colonization events taking place subsequently, predominantly in a southwesterly direction from the older to the younger islands. Many of the questions posed by the group may never be answered. Some species, notably those of Moorea, are already extinct in the wild; others are severely threatened. Artificial introductions of both plants and animals, combined with urban and agricultural development, have had significant impacts, but ill-conceived biological control programmes, targeted at the Giant African Snail, Achatina fulica , constitute currently the most serious threat. However, significant areas are still open to research. Analysis of DNA variation, combined with modern ideas of Pacific biogeography, should allow the whole range from the broad origins of the fauna to the detailed evolution within groups of species to be addressed. Some species may yet be relatively secure in the wild and allow field studies, but extraction of DNA from museum specimens provides an exciting opportunity to continue unravelling the evolutionary history of these endangered snails and to contribute further to our understanding of evolutionary processes and the biogeography of the Pacific.

Extreme divergence of mitochondrial DNA within species of pulmonate land snails

Mitochondrial DNA, inherited predominantly through the female line, has been exceptionally useful for reconstructing phylogenies (Avise, in Molecular markers, natural history and evolution. New York: Chapman and Hall (1994)). However, at the lowest taxonomic level, if there are polymorphisms within species the lineages of mitochondria need not correspond to the lineages of the species (Avise, in Phil. Trans. R. Soc. Lond. B 312, 325-342 (1986)). We find that a classic organism in ecological genetics, Cepaea nemoralis, has the most extreme intraspecific variation and polymorphism so far recorded, and that at least one other pulmonate land mollusc also has very high levels of mitochondrial diversity. Making the simplest assumptions, the data suggest times of divergence as long ago as 20 million years between haplotypes now coexisting within a single population. There are four overlapping explanations of the diversity: (i) that mitochondrial evolution in pulmonates is exceptionally fast; (ii) that the morphs have differentiated in isolated 'refuges' and then come together; (iii) that natural selection has acted to preserve the variation; and (iv) that the population structure of pulmonates favours the persistence of ancient haplotypes. We argue for the importance of the last explanation.

Large scale patterns of genetic differentiation at enzyme loci in the land snails Cepaea nemoralis and Cepaea hortensis

Samples of 231 populations of the land snails Cepaea nemoralis and C. hortensis from Britain, France, Switzerland and Spain were analysed for genetic polymorphism in six enzyme systems. These sibling species show similar levels of variation detected by electrophoresis, and have a generally similar degree of local divergence over homologous enzyme loci. As well as extensive local and regional differentiation, both species show large-scale changes in allele frequency across Europe. In C. hortensis there is a continuous gradient in allele frequency from northern Britain to northern Spain, while in C. nemoralis north-south clines on the continent of Europe are reversed in direction in Britain. There are few obvious correlations of allele frequency change at single loci with components of the environment. Patterns of allele frequency variation in 24 sympatric populations of the two species are generally independent of each other, although there is a positive association of the frequencies of alleles at a leucine aminopeptidase locus in the two species. The statistical significance of this association depends on a single locality, and there is little indication of shared patterns of allele frequency change which might reflect a common response to natural selection. In addition, there is no evidence that the extensive geographical change in C. nemoralis and C. hortensis is a precursor of speciation.