Discrete or indiscrete? Redefining the colour polymorphism of the land snail Cepaea nemoralis

Evolutionary insights into Felidae iris color through ancestral state reconstruction

Few studies have explored eye (iris) color evolution beyond humans and domesticated animals. Felids exhibit significant eye color diversity, unlike their brown-eyed relatives, making them an ideal model to study the evolution of eye color in natural populations. Through machine learning analysis of public photographs, five felid eye colors were identified: brown, green, yellow, gray, and blue. The presence or absence of these colors was reconstructed on a phylogeny, as well as their specific quantitative shades. The ancestral felid population likely had brown-eyed and gray-eyed individuals, the latter color being pivotal for the diversification of eye color seen in modern felids. Additionally, yellow eyes are highly associated with and may be necessary for, the evolution of round pupils in felids. These findings enhance the understanding of eye color evolution, and the methods presented in this work are widely applicable and will facilitate future research into the phylogenetic reconstruction of color beyond irises.

Continuous variation in the shell colour of the snail Cepaea nemoralis is associated with the colour locus of the supergene

While the shell of the land snail Cepaea nemoralis is typically classed as yellow, pink, or brown, the reality is that colour variation is continuously distributed. To further understand the origin of the continuous variation, we used crosses of C. nemoralis to compare quantitative measures of the colour with the inferred genotype of the underlying supergene locus. We also used a recently developed linkage map to find quantitative trait loci that may influence colour. The results show that the colour locus of the supergene-at around 31.385 cM on linkage group 11-is involved in determining the quantitative chromatic differences that are perceptible to human vision. We also found some evidence that variation within colour classes may be due to allelic variation at or around the supergene. There are likely other unlinked loci involved in determining colour within classes, but confirmation will require greater statistical power. Although not investigated here, environmental factors, including diet, may also impact upon variation within colour types.

Temporal stability and directional change in a color cline of a marine snail from NW Spain

The evolution and maintenance of color clines is a classic topic of research in evolutionary ecology. However, studies analyzing the temporal dynamics of such clines are much less frequent, due to the difficulty of obtaining reliable data about past color distributions along environmental gradients. In this article, we describe a case of decades-long temporal stability and directional change in a color cline of the marine snail Littorina saxatilis along the coastal inlet of the Ría de Vigo (NW Spain). L. saxatilis from this area shows a clear color cline with 3 distinct areas from the innermost to the more wave-exposed localities of the Ría: the inner, protected localities show an abundance of fawn-like individuals; the intermediate localities show a high diversity of colors; and the outer, wave-exposed localities show populations with a high frequency of a black and lineated morph. We compare data from the 1970s and 2022 in the same localities, showing that the cline has kept relatively stable for at least over half a century, except for some directional change and local variability in the frequency of certain morphs. Multiple regression analyses and biodiversity measures are presented to provide clues into the selective pressures that might be involved in the maintenance of this color cline. Future research avenues to properly test the explanatory power of these selective agents as well as the possible origins of the cline are discussed.

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.

Piebaldism and chromatophore development in reptiles are linked to the tfec gene

Reptiles display great diversity in color and pattern, yet much of what we know about vertebrate coloration comes from classic model species such as the mouse and zebrafish.1,2,3,4 Captive-bred ball pythons (Python regius) exhibit a remarkable degree of color and pattern variation. Despite the wide range of Mendelian color phenotypes available in the pet trade, ball pythons remain an overlooked species in pigmentation research. Here, we investigate the genetic basis of the recessive piebald phenotype, a pattern defect characterized by patches of unpigmented skin (leucoderma). We performed whole-genome sequencing and used a case-control approach to discover a nonsense mutation in the gene encoding the transcription factor tfec, implicating this gene in the leucodermic patches in ball pythons. We functionally validated tfec in a lizard model (Anolis sagrei) using the gene editing CRISPR/Cas9 system and TEM imaging of skin. Our findings show that reading frame mutations in tfec affect coloration and lead to a loss of iridophores in Anolis, indicating that tfec is required for chromatophore development. This study highlights the value of captive-bred ball pythons as a model species for accelerating discoveries on the genetic basis of vertebrate coloration.

Arboreal snail genus Amphidromus Albers, 1850 of Southeast Asia: Shell polymorphism of Amphidromus cruentatus (Morelet, 1875) revealed by phylogenetic and morphometric analyses

Species of colourful arboreal snails of the genus Amphidromus from Southeast Asia commonly exhibit high intraspecific variation in shell morphology. Although highly polymorphic Amphidromus specimens with different colouration have been collected at the same locality and were revealed to possess similar genital organs, there is yet no morphometric or DNA analyses of these different shell morphs. This study is the first to reveal that both striped and stripeless morphs of A. cruentatus from Laos and Vietnam belong to the same mitochondrial (COI and 16S rRNA) lineage. Although the shell colouration between the striped and stripeless morphs is markedly different, morphometric and shell outline-based analyses indicated an overall similarity in shell shape. We also revised the systematics of A. cruentatus, in which we treated similar related species, namely A. eudeli, A. fuscolabris, A. thakhekensis, A. gerberi bolovenensis, A. goldbergi, A. pengzhuoani, A. eichhorsti and A. pankowskiae as junior synonyms of A. cruentatus. Amphidromus daoae, A. anhdaoorum, A. stungtrengensis, A. yangbayensis and A. yenlinhae, which were formerly regarded as junior synonyms, are considered as species different from A. cruentatus based on shell morphology and morphometric analyses. Preliminary phylogenetic analyses also retrieved some Amphidromus species groups as distinct mitochondrial lineages.

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.

Analysis of Egg Variation and Foreign Egg Rejection in Rüppell’s Weaver (Ploceus galbula)

Egg appearance is notable for its variation and as a source of recognition cues in bird species that are subject to egg-mimicking brood parasitism. Here I analyze the egg appearance of an East African weaverbird species that has variable eggs and is a host of brood parasitism by an egg-mimicking cuckoo, in order to (1) compare population variation to variation within a clutch as a measure of the distinctiveness of eggs; (2) assess modularity versus correlation among egg appearance traits as an indication of the complexity of egg signatures; and (3) address whether the eggs are discretely polymorphic or continuously variable in appearance. I also compare three methods of assessing egg coloration: reduction of spectral data to orthogonal components, targeted spectral shape variables, and avian visual modeling. Then I report the results of egg replacement experiments that assess the relationship between egg rejection behavior and the difference in appearance between own and foreign eggs. Rüppell’s weaver (Ploceus galbula) eggs are variable in appearance between individuals and consistent within a clutch, but vary widely in the distinctiveness of particular traits. Most aspects of color and spotting are decoupled from each other, including coloration likely to derive from different pigments. Egg ground color is bimodal, with a broad continuous class of off-white/UV eggs and another broad class of blue-green eggs. Variation in all other traits is unimodal and usually normal in distribution. Females reject foreign eggs on the basis of the difference in brightness of the ground color and spotting of foreign eggs relative to their own, and the difference in degree to which spots are aggregated at the broad end of the egg. This aggregation is among the most distinctive features of their eggs, but the brightness of the ground color and spotting brightness are not; the birds’ use of brightness rather than the more distinctive chromatic variation to recognize eggs might reflect the salience of achromatic contrast in a dim enclosed nest.

The multilevel organismal diversity approach deciphers difficult to distinguish nudibranch species complex

Species identification is a key procedure for broad-scoped ecological, phylogeographic and evolutionary studies. However, to perform a taxonomic study in the molecular era is a complicated task that has many pitfalls. In the present study we use particular examples of common but difficult to distinguish European species within the genus of Polycera (Nudibranchia, Mollusca) to discuss the general issues of the "cryptic species" problem that has broad biological and interdisciplinary importance and can significantly impede ecological, evolutionary, and other biodiversity-related research. The largest dataset of molecular and morphological information for European nudibranchs ever applied encompasses a wide geographical area and shapes a robust framework in this study. Four species are recognized in the species complex, including a new one. It is shown that a lack of appropriate taxonomic analysis led recently to considerable errors in species identity assessment of this complex. Chromatic polymorphism for each species is mapped in a periodic-like framework and combined with statistical analysis of the diagnostic features that considerably facilitates identification of particular species in the complex for biologists and practitioners. The present study evidently shows that "cryptic" and "non-cryptic" components are present within the same species. Therefore, this species complex is well suited for the exploring and testing of general biological problems. One of the main conclusions of this study is that division of biological diversity into "cryptic" and "non-cryptic" components is counterproductive. We propose that the central biological phenomenon of a species can instead be universally designated as multilevel organismal diversity thereby provide a practical set of methods for its investigation.

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.

Quantitative measures and 3D shell models reveal interactions between bands and their position on growing snail shells

The nature of shell growth in gastropods is useful because it preserves the ontogeny of shape, colour, and banding patterns, making them an ideal system for understanding how inherited variation develops, is established and maintained within a population. However, qualitative scoring of inherited shell characters means there is a lack of knowledge regarding the mechanisms that control fine variation. Here, we combine empirical measures of quantitative variation and 3D modeling of shells to understand how bands are placed and interact. By comparing five-banded Cepaea individuals to shells lacking individual bands, we show that individual band absence has minor but significant impacts upon the position of remaining bands, implying that the locus controlling band presence/absence mainly acts after position is established. Then, we show that the shell grows at a similar rate, except for the region below the lowermost band. This demonstrates that wider bands of Cepaea are not an artifact of greater shell growth on the lower shell; they begin wider and grow at the same rate as other bands. Finally, we show that 3D models of shell shape and banding pattern, inferred from 2D photos using ShellShaper software, are congruent with empirical measures. This work therefore establishes a method that may be used for comparative studies of quantitative banding variation in snail shells, extraction of growth parameters, and morphometrics. In the future, studies that link the banding phenotype to the network of shell matrix proteins involved in biomineralization and patterning may ultimately aid in understanding the diversity of shell forms found in molluscs.

Evo-devo of shell colour in gastropods and bivalves

Recent technical innovations are revealing surprising patterns in mollusc shell pigmentation, such as an unexpectedly modest role for melanins and rapid divergences in the mix of pigments used to achieve similar colour patterns. The elucidation of the molecular genetic basis of shell pigmentation has been slow, probably because of the high genome complexity of gastropods and bivalves. Recent work within the old field of evolutionary ecology of shell pigmentation allows a greater role for the analysis of large-geographic-scale patterns (sometimes employing citizen-science data), as well as experimental field studies. However, the field remains dominated by land snails as model organisms, while colour pattern evolution in marine gastropods and bivalves, particularly those not exposed to visual predators, remains mysterious.

Snails as Taxis for a Large Yeast Biodiversity

Yeasts are unicellular fungi that harbour a large biodiversity of thousands of species, of which particularly ascomycetous yeasts are instrumental to human food and beverage production. There is already a large body of evidence showing that insects play an important role for yeast ecology, for their dispersal to new habitats and for breeding and overwintering opportunities. Here, we sought to investigate a potential role of the terrestrial snails Cepaea hortensis and C. nemoralis, which in Europe are often found in association with human settlements and gardens, in yeast ecology. Surprisingly, even in a relatively limited culture-dependent sampling size of over 150 isolates, we found a variety of yeast genera, including species frequently isolated from grape must such as Hanseniaspora, Metschnikowia, Meyerozyma and Pichia in snail excrements. We typed the isolates using standard ITS-PCR-sequencing, sequenced the genomes of three non-conventional yeasts H. uvarum, Meyerozyma guilliermondii and P. kudriavzevii and characterized the fermentation performance of these three strains in grape must highlighting their potential to contribute to novel beverage fermentations. Aggravatingly, however, we also retrieved several human fungal pathogen isolates from snail excrements belonging to the Candida clade, namely Ca. glabrata and Ca. lusitaniae. Overall, our results indicate that diverse yeasts can utilise snails as taxis for dispersal. This courier service may be largely non-selective and thus depend on the diet available to the snails.

Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity

Using the nudibranch genus Amphorina as a model, ongoing speciation is demonstrated, as well as how periodic-like patterns in colouration can be included in an integrated method of fine-scale species delimitation. By combining several methods, including BPP analysis and the study of molecular, morphological, and ecological data from a large number of specimens within a broad geographic range from northern Europe to the Mediterranean, five species are recognised within the genus Amphorina, reviewed here for the first time. Two new species from the southwestern coast of Sweden are described, A. viriola sp. nov. and A. andra sp. nov. Evidence is provided of a recent speciation process between the two closely related, yet separate, species which inhabit the same geographic localities but demonstrate strict water depth differentiation, with one species inhabiting the shallow brackish top layer above the halocline and the other species inhabiting the underlying saltier water. The results presented here are of relevance for currently debated issues such as conservation in relation to speciation, fine species delimitation, and integration of molecular, morphological and ecological information in biodiversity studies. The periodic approach to biological taxonomy has considerable practical potential for various organismal groups.

Challenging the concept that eumelanin is the polymorphic brown banded pigment in Cepaea nemoralis

The common grove snail Cepaea nemoralis displays a stable pigmentation polymorphism in its shell that has held the attention of scientists for decades. While the details of the molecular mechanisms that generate and maintain this diversity remain elusive, it has long been employed as a model system to address questions related to ecology, population genetics and evolution. In order to contribute to the ongoing efforts to identify the genes that generate this polymorphism we have tested the long-standing assumption that melanin is the pigment that comprises the dark-brown bands. Surprisingly, using a newly established analytical chemical method, we find no evidence that eumelanin is differentially distributed within the shells of C. nemoralis. Furthermore, genes known to be responsible for melanin deposition in other metazoans are not differentially expressed within the shell-forming mantle tissue of C. nemoralis. These results have implications for the continuing search for the supergene that generates the various pigmentation morphotypes.

Eumelanin and pheomelanin pigmentation in mollusc shells may be less common than expected: insights from mass spectrometry

BACKGROUND

The geometric patterns that adorn the shells of many phylogenetically disparate molluscan species are comprised of pigments that span the visible spectrum. Although early chemical studies implicated melanin as a commonly employed pigment, surprisingly little evidence generated with more recent and sensitive techniques exists to support these observations.

RESULTS

Here we present the first mass spectrometric investigations for the presence of eumelanin and pheomelanin in 13 different molluscan species from three conchiferan classes: Bivalvia, Cephalopoda and Gastropoda. In the bivalve Mytilus edulis we demonstrate that eumelanin mainly occurs in the outermost, non-mineralised and highly pigmented layer of the shell (often referred to as the periostracum). We also identified eumelanin in the shells of the cephalopod Nautilus pompilius and the marine gastropods Clanculus pharaonius and Steromphala adriatica. In the terrestrial gastropod Cepaea nemoralis we verify the presence of pheomelanin in a mollusc shell for the first time. Surprisingly, in a large number of brown/black coloured shells we did not find any evidence for either type of melanin.

CONCLUSIONS

We recommend methods such as high-performance liquid chromatography with mass spectrometric detection for the analysis of complex biological samples to avoid potential false-positive identification of melanin. Our results imply that many molluscan species employ as yet unidentified pigments to pattern their shells. This has implications for our understanding of how molluscs evolved the ability to pigment and pattern their shells, and for the identification of the molecular mechanisms that regulate these processes.

Disruptive selection of shell colour in land snails: a mark–recapture study of Euhadra peliomphala simodae

Many theoretical studies have suggested that disruptive selection plays an important role in phenotypic divergence, but few studies have determined the action of disruptive selection on phenotypic divergence via field studies. This study investigated the effect of disruptive selection on shell colour polymorphism in the Japanese land snail Euhadra peliomphala simodae to determine whether extreme phenotypes of snail shell colour are favoured over intermediate phenotypes. We conducted field surveys on an oceanic island with black, yellow and intermediate-coloured E. p. simodae snails. We captured and marked ~1800 individual snails and monitored their survival over 18 months. We quantified shell colours against images and examined the frequency distribution of shell colour variation. The variation exhibited a bimodal distribution with a far lower frequency of intermediate-coloured snails than of black or yellow snails. The population sizes of the three snail groups fluctuated synchronously with the changing seasons. Bayesian estimates showed lower survival rates for juvenile intermediate-coloured snails than for juvenile black and yellow snails, implying there was disruptive selection associated with shell colour. We suggest this disruptive selection may have resulted in the evolutionary divergence of the snail’s shell colour within the lineage having high shell colour variation.

Recombination within the Cepaea nemoralis supergene is confounded by incomplete penetrance and epistasis

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.