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29 results for “Littorina”
An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis
<p>This Zenodo archive contains the dataset analysed in the paper "An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis" published in Evolutionary Application in 2022:</p> <ul> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/FAB_LG3_maf1_SNP_Hexcess_depth10.vcf">FAB_LG3_maf1_SNP_Hexcess_depth10.vcf </a>: vcf for LG3 unpruned for LD containing 295 individuals genotyped at 58,246 filtered SNPs</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/FAB_LG3_maf1_SNP_Hexcess_depth10_thin.vcf">FAB_LG3_maf1_SNP_Hexcess_depth10_thin.vcf </a>: vcf for LG3 pruned for LD containing 295 individuals genotyped at 9,905 filtered SNPs</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/FAB_AK_maf1_SNP_Hexcess_depth10.vcf">FAB_AK_maf1_SNP_Hexcess_depth10.vcf</a> : vcf for contig265 containing the arginine kinase gene: 295 individuals genotyped at 70 filtered SNPs</li> </ul> <p>The archive also include some of the R script used to performed the analyses of the manuscrit:</p> <ul> <li> </li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/Population_genetic_Ark_analyses.R">Population_genetic_Ark_analyses.R </a>: Script to perform PCA +phenotypic cline + FST + Hobs + FIS</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/Suspension_bridge_fit.R">Suspension_bridge_fit.R </a>: Script to perform the suspension bridge fit used to found evidence of gene flux inside the inversion.</li> <li><a href="https://zenodo.org/api/files/cd560cff-56d4-4f72-95be-e70939f2b85f/Cline_function.R">Cline_function.R </a>: function used to fit the allelic frequency variation (cline) along the transect</li> </ul> <p>The raw sequences are available in NCBI.</p> <p>Abstract of the study: Understanding the genetic targets of natural selection is one of the most challenging goalsof population genetics. Some of the earliest candidate genes were identified from associations between allozyme allele frequencies and environmental variation. One such example is the clinal polymorphism in the arginine kinase (<em>Ak</em>) gene in the marine snail <em>Littorina fabalis</em>. While other enzyme loci do not show differences in allozyme frequencies among populations, the <em>Ak</em> alleles are near differential fixation across repeated wave exposure gradients in Europe. Here, we use this case to illustrate how a new sequencing toolbox can be employed to characterize the genomic architecture associated with historical candidate genes. We found that the <em>Ak</em> alleles differ by 9 non-synonymous substitutions, which perfectly explain the different migration patterns of the allozymes during electrophoresis. Moreover, by exploring the genomic context of the <em>Ak</em> gene, we found that the three main <em>Ak</em> alleles are located on different arrangements of a putative chromosomal inversion that reaches near fixation at the opposing ends of two transects covering a wave exposure gradient. This shows <em>Ak</em> is part of a large (3/4 of the chromosome) genomic block of differentiation, in which <em>Ak</em> is unlikely to be the only target of divergent selection. Nevertheless, the non-synonymous substitutions among <em>Ak</em> alleles and the complete association of one allele with one inversion arrangement suggest that the <em>Ak</em> gene is a strong candidate to contribute to the adaptive significance of the inversion.</p> <p> </p> <p> </p>
Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina
When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, <i>Littorina saxatilis</i>, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in <i>L. saxatilis</i> with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.
AFLP and geometric morphometrics for Littorina fabalis
<p>Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared the patterns of habitat-related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model-based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.</p>
Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution
<p>Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence. </p>
Population density and size structure data for macroecology analysis on <em>Littorina littorea</em> from different locations along the Atlantic North American coast
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Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution
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Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina
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AFLP and geometric morphometrics for Littorina fabalis
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Data from: Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata
<p>Characterizing the patterns of hybridization between closely related species is crucial to understand the role of gene flow in speciation. In particular, systems comprising multiple contacts between sister species offer an outstanding opportunity to investigate how reproductive isolation varies with environmental conditions, demography and geographic contexts of divergence. The flat periwinkles, <i>Littorina obtusata</i> and <i>L. fabalis</i> (Gastropoda)<u>,</u><i> </i>are two intertidal sister species with marked ecological differences compatible with late stages of speciation. Although hybridization between the two was previously suggested, its extent across the Atlantic shores of Europe remained largely unknown. Here, we combined genetic (microsatellites and mtDNA) and morphological data (shell and male genital morphology) from multiple populations of flat periwinkles in north-western Iberia to assess the extent of current and past hybridization between <i>L. obtusata</i> and <i>L. fabalis</i> under two contrasting geographic settings of divergence (sympatry and allopatry). Hybridization signatures based on both mtDNA and microsatellites were stronger in sympatric sites, although evidence for recent extensive admixture was found in a single location. Misidentification of individuals into species based on shell morphology was higher in sympatric than in allopatric sites. However, despite hybridization, species distinctiveness based on this phenotypic trait together with male genital morphology remained relatively high. The observed variation in the extent of hybridization among locations provides a rare opportunity for future studies on the consequences of different levels of gene flow for reinforcement, thus informing about the mechanisms underlying the completion of speciation.</p>
Data from: Shared and non-shared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale
Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small 'wave' ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, 'crab' ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities among ecotype-pairs on three close islands (< 10 km distance) connected by weak gene flow (Nm~0.03) and with recent common ancestry (< 10,000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared among all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.
Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.
Negative frequency dependent selection maintains shell banding polymorphisms in two marine snails (Littorina fabalis and L. saxatilis)
<p>The presence of shell bands is common in gastropods. The marine snails, <i>Littorina fabalis</i> and <i>L. saxatilis</i>, are<i> </i>both polymorphic for this trait. Such polymorphism would be expected to be lost by the action of genetic drift or directional selection, but it appears to be widespread at relatively constant frequencies. This suggests it is maintained by balancing selection on the trait or on a genetically linked trait. Using long time-series of empirical data, we compared potential effects of genetic drift and negative frequency-dependent selection, in the two species. The contribution of genetic drift to changes in the frequency of bands in <i>L. fabalis</i> was estimated using the effective population size estimated from microsatellite data, while the effect of genetic drift in <i>L. saxatilis</i> were derived from previously published study. Frequency-dependent selection was assessed comparing the cross-product estimator of fitness with the frequency of the polymorphism across years using a regression analysis. Both studied species showed patterns of negative frequency-dependent selection. In addition, in <i>L. fabalis</i>, contributions from genetic drift could explain some of the changes in banding frequency. Overdominance and heterogeneous selection did not fit well to our data. The possible biological explanations resulting on the maintenance of the banding polymorphism are discussed.</p>
Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on FST values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.
FIGURE 10. Echinolittorina lineolata. A, Littorina lineolata d in The genus Echinolittorina Habe, 1956 (Gastropoda: Littorinidae) in the western Atlantic Ocean 2184
FIGURE 10. Echinolittorina lineolata. A, Littorina lineolata d'Orbigny, 1840, lectotype, Rio de Janeiro, Brazil (BMNH 1854.12.4.363/1). B, Bara Cunha, 60 km S Natal, Rio Grande do Norte, Brazil (BMNH 20080975). C, E, Curumirin, Rio de Janeiro state, Brazil (MZSP 31267). D, Araruama Point, Cabo Frio, Rio de Janeiro state, Brazil (BMNH 20080976). F, Pernambuco, Brazil (BMNH 1844.8.7.1). G, Pernambuco, Brazil (BMNH 1924.12.3.10). H, Natal, Brazil (BMNH 20080977). I, I. Queimada Grande, São Paulo state, Brazil (MZSP 24919). J, Cabo Polonia, Uruguay (USNM 359202). K, Barra, Rio Grande, Brazil (BMNH 1958.4.10.2). L, I. Sta Barbara, Abrolhos Arch., Brazil (USNM 770002).
Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
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Negative frequency dependent selection maintains shell banding polymorphisms in two marine snails (Littorina fabalis and L. saxatilis)
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Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
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Data from: Shared and non-shared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale
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Thermal performance curves dataset based on <em>Littorina littorea</em> from different locations along a latitudinal gradient: Physiological and life history traits
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Data from: Genome-wide association analyses reveal polygenic genomic architecture underlying divergent shell morphology in Spanish Littorina saxatilis ecotypes
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