Spatial analysis of allozyme and microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae)

The effect of landscape on functional connectivity and shell shape in the land snail Humboldtiana durangoensis

The populations of Humboldtiana durangoensis have experienced a drastic reduction in the effective population size; in addition, the species is threatened by anthropogenic activities. For the aforementioned, landscape genetics will serve as a tool to define the potential evolutionarily significant units (ESU) for this species. To complete our objective, we evaluated the effect of cover vegetation and climate on the functional connectivity of the species from the last glacial maximum (LGM) to the present as well as the effect of climate on shell shape. Partial Mantel tests, distance-based redundance analysis and a Bayesian framework were used to evaluate connectivity. On the other hand, geometric morphometrics, phylogenetic principal component analysis and redundancy analysis were used for the analysis of shell shape. Our results suggest that the suitable areas have been decreasing since the LGM; also, vegetation cover rather than climate has influenced the genetic connectivity among land snail populations, although temperature had a high influence on shell shape in this species. In conclusion, vegetation cover was the main factor that determined the functional connectivity for the land snail; however, local selective pressures led to different phenotypes in shell shape that allowed us to postulate that each one of the previously defined genetic groups must be considered as a different ESU.

The transcriptome of a "sleeping" invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum

Background

Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insight into the ecology, evolution, nutritional and medical properties of this highly adaptable organism, are missing. In this work, using next-generation sequencing (NGS) techniques we assessed a significant portion of the transcriptome of this non-model organism.

Results

Out of the 9445 de novo assembled contigs, 2886 (30.6%) returned significant hits and for 2261 (24%) of them Gene Ontology (GO) terms associated to the hits were retrieved. A high percentage of the contigs (69.4%) produced no BLASTx hits. The GO terms were grouped to reflect biological processes, molecular functions and cellular components. Certain GO terms were dominant in all groups. After scanning the assembled transcriptome for microsatellites (simple sequence repeats, SSRs), a total of 563 SSRs were recovered. Among the identified SSRs, trinucleotide repeats were the predominant followed by tetranucleotide and dinucleotide repeats.

Conclusion

The annotation success of the transcriptome of C. aspersum was relatively low. This is probably due to the very limited number of annotated reference genomes existing for mollusc species, especially terrestrial ones. Several biological processes being active in the aestivating species were revealed through the association of the transcripts to enzymes relating to the pathways. The genomic tools provided herein will eventually aid in the study of the global genomic diversity of the species and the investigation of aspects of the ecology, evolution, behavior, nutritional and medical properties of this highly adaptable organism.

Investigations of responses to metal pollution in land snail populations (Cantareus aspersus and Cepaea nemoralis) from a smelter-impacted area

A cross-transplantation field experiment was performed to investigate about possible adaptation/acclimatization to metal pollution in common garden snail Cantareus aspersus (ex-Helix aspersa) and brown-lipped grove snail Cepaea nemoralis populations. Adults were collected from an area surrounding a former smelter (ME), highly polluted by trace metals (TMs) for decades, and from an unpolluted site (BE). Subadults of first generation (F1) were exposed in microcosms in a 28-day kinetic study. Four exposure sites were chosen around the smelter along a soil pollution gradient (vegetation and soil otherwise comparable). Bioaccumulation in snail soft tissues globally increased with soil contamination, with Cd, Pb and Zn concentrations reaching 271, 187, 5527 μg g(-1), respectively. Accumulation kinetic patterns were similar between snail species but C. nemoralis showed greater TM levels than C. aspersus. Some inter-population differences were revealed in TM accumulation (bioaccumulation factors, accumulation kinetics) but did not suggest consistent adaptive responses. We did not detect negative effects of TM exposure on snail condition (body weight, shell size, shell weight). ME C. aspersus snails produced heavier shells than BE snails under exposure to TMs at the highest level, suggesting an adaptive response. The protocol used in this study, however, did not allow unambiguously distinguishing whether this response was due to genetic adaptation or to maternal effects. Abnormal but reversible shell development of adult ME C. nemoralis suggested physiological acclimatization. Differences in responses to TMs between populations are observed for conchological parameters, not for bioaccumulation, with different strategies according to the species (acclimatization or adaptation/maternal effects).

A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone

Background

Mitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that rely on multiple lines of evidence in areas of co-occurrence are particularly powerful to infer their specific status. We investigated the species boundaries of two cryptic lineages of the land snail genus Trochulus in a contact zone, using mitochondrial and nuclear DNA marker as well as shell morphometrics.

Results

Both mitochondrial lineages have a distinct geographical distribution with a small zone of co-occurrence. In the same area, we detected two nuclear genotype clusters, each being highly significantly associated to one mitochondrial lineage. This association however had exceptions: a small number of individuals in the contact zone showed intermediate genotypes (4%) or cytonuclear disequilibrium (12%). Both mitochondrial lineage and nuclear cluster were statistically significant predictors for the shell shape indicating morphological divergence. Nevertheless, the lineage morphospaces largely overlapped (low posterior classification success rate of 69% and 78%, respectively): the two lineages are truly cryptic.

Conclusion

The integrative approach using multiple lines of evidence supported the hypothesis that the investigated Trochulus lineages are reproductively isolated species. In the small contact area, however, the lineages hybridise to a limited extent. This detection of a hybrid zone adds an instance to the rare reported cases of hybridisation in land snails.

Extreme mtDNA divergences in a terrestrial slug (Gastropoda, Pulmonata, Arionidae): accelerated evolution, allopatric divergence and secondary contact

Extremely high levels of intraspecific mtDNA differences in pulmonate gastropods have been reported repeatedly and several hypotheses to explain them have been postulated. We studied the phylogeny and phylogeography of 51 populations (n = 843) of the highly polymorphic terrestrial slug Arion subfuscus (Draparnaud, 1805) across its native distribution range in Western Europe. By combining the analysis of single stranded conformation polymorphisms (SSCP) and nucleotide sequencing, we obtained individual sequence data for a fragment of the mitochondrial 16S rDNA and a fragment of the nuclear ITS1. Additionally, five polymorphic allozyme loci were scored. Based on the 16S rDNA phylogeny, five monophyletic haplotype groups with sequence divergences of 9-21% were found. Despite this deep mitochondrial divergence, the haplotype groups were not monophyletic for the nuclear ITS1 fragment and haplotype group-specific allozyme alleles were not found. Although there is evidence for an accelerated mtDNA clock, the divergence among the haplotype groups is older than the Pleistocene and their current allopatric ranges probably reflect allopatric divergence and glacial survival in separate refugia from which different post-glacial colonization routes were established. A range-overlap of two mtDNA groups (S1 and S2, 21% sequence divergence) stretched from Central France and Belgium up to the North of the British Isles. The nuclear data suggest that this secondary contact resulted in hybridization between the allopatrically diverged groups. Therefore, it seems that, at least for two of the groups, the deep mtDNA divergence was only partially accompanied by the formation of reproductive isolation.

Rangewide phylogeography of a terrestrial slug in Europe: evidence for Alpine refugia and rapid colonization after the Pleistocene glaciations

Intraspecific phylogeographical patterns largely depend on the life history traits of a species. Especially species with a high degree of cold tolerance, limited requirements towards habitat preferences, and relatively low active dispersal capacities may have responded in a different way to the Pleistocene climatological fluctuations than the majority of taxa studied so far. To evaluate this possibility, we studied Arion fuscus (Muller, 1774), a common and widespread European terrestrial slug, from 88 locations (N = 964). Sequence variation was assessed for fragments of the mitochondrial 16S rDNA and COI genes by means of single-strand conformation polymorphisms (SSCP) and subsequent DNA sequencing. Additionally, eight allozyme loci were scored in 843 individuals. Phylogenetic analysis revealed the presence of two major evolutionary lineages, one in the Balkan region and another in the Alps and the rest of Europe. The sequence divergence between the two lineages was limited (3.3%), but gene flow between the regions was absent, suggesting that the two regions have been isolated since the late Pliocene or early Pleistocene. Allozyme differentiation among geographical regions and mitochondrial DNA (mtDNA) lineages was low. The geographical patterns observed in our data showed that (i) haplotype and nucleotide diversities are very low in northern Europe, suggesting that single haplotypes rapidly colonized large areas; (ii) recently expanded haplotype clades have restricted distribution ranges, suggesting that current gene flow is low; and (iii) genetic diversity in the Alps is much higher than in other regions and estimated past gene flow from the Eastern Alps to other regions was high, suggesting that this was a refugial zone during the Pleistocene. This full-range phylogeography suggests the existence of an alternative refugial zone, situated north of the refugial areas currently recognized in most other taxa.

Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Aland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran's I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100-150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.

Streams over mountains: influence of riparian connectivity on gene flow in the Pacific jumping mouse (Zapus trinotatus)

In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.

Multiple paternity and postcopulatory sexual selection in a hermaphrodite: what influences sperm precedence in the garden snail Helix aspersa?

Sperm competition has been studied in many gonochoric animals but little is known about its occurrence in simultaneous hermaphrodites, especially in land snails. The reproductive behaviour of the land snail Helix aspersa involves several features, like multiple mating, long-term sperm storage and dart-shooting behaviour, which may promote sperm competition. Cryptic female choice may also occur through a spermatheca subdivided into tubules, which potentially allows compartmentalized sperm storage of successive mates. In order to determine the outcome of postcopulatory sexual selection in this species, we designed a cross-breeding experiment where a recipient ('female') mated with two sperm donors ('males'). Mates came from either the same population as the recipient or from a distinct one. To test for the influence a recipient can have on the paternity of its offspring, we excluded the effects of dart shooting by using only virgin snails as sperm donors because they do not shoot any dart before their first copulation. We measured the effects of size of mates as well as time to first and second mating on second mate sperm precedence (P2; established using microsatellite markers). Multiple paternity was detected in 62.5% of clutches and overall there was first-mate sperm precedence with a mean P2 of 0.24. Generalized linear modelling revealed that the best predictors of paternity were the time between matings and the time before first mating. Overall, both first and second mates that copulated quickly got greater parentage, which may suggest that postcopulatory events influence patterns of sperm precedence in the garden snail.

Molecular and ecological evidence for small-scale isolation by distance in an endangered damselfly, Coenagrion mercuriale

Coenagrion mercuriale (Charpentier) (Odonata: Zygoptera) is one of Europe's most threatened damselflies and is listed in the European Habitats directive. We combined an intensive mark-release-recapture (MRR) study with a microsatellite-based genetic analysis for C. mercuriale from the Itchen Valley, UK, as part of an effort to understand the dispersal characteristics of this protected species. MRR data indicate that adult damselflies are highly sedentary, with only a low frequency of interpatch movement that is predominantly to neighbouring sites. This restricted dispersal leads to significant genetic differentiation throughout most of the Itchen Valley, except between areas of continuous habitat, and isolation by distance (IBD), even though the core populations are separated by less than 10 km. An urban area separating some sites had a strong effect on the spatial genetic structure. Average pairwise relatedness between individual damselflies is positive at short distances, reflecting fine-scale genetic clustering and IBD both within- and between-habitat patches. Damselflies from a fragmented habitat have higher average kinship than those from a large continuous population, probably because of poorer dispersal and localized breeding in the former. Although indirect estimates of gene flow must be interpreted with caution, it is encouraging that our results indicate that the spatial pattern of genetic variation matches closely with that expected from direct observations of movement. These data are further discussed with respect to possible barriers to dispersal within the study site and the ecology and conservation of C. mercuriale. To our knowledge, this is the first report of fine-scale genetic structuring in any zygopteran species.

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.

Population genetic structure in a human-disturbed environment: a case study in the land snail Helix aspersa (Gastropoda: Pulmonata)

Local patterns of genetic variation were analysed in the land snail Helix aspersa for 32 populations sampled within a patchy agricultural landscape: the polders of the Bay of Mont-Saint-Michel (France). This investigation examined the allele frequencies at four enzymatic markers and five microsatellite loci through the genotyping of 580 individuals. A strongly significant population genetic substructuring (mean F(ST)=0.088, P<0.001) was found at the scale of the whole polders area (3050 ha) and both categories of markers displayed a similar magnitude of spatial genetic differentiation. We did not find any obvious effects of habitat fragmentation on the distribution of genetic variability. Despite the reality of habitat patchiness and environmental instability (related to farming practices), an isolation by distance process was clearly depicted, although selective pressures cannot be ruled out for one enzymatic locus. Overall, genetic drift, along with occasional long-distance episodes of gene flow, was presumably the most likely evolutionary force that shaped the observed pattern of genetic variation.

Extinction-colonization dynamics structure genetic variation of spotted sunfish (Lepomis punctatus) in the Florida Everglades

The population genetics of aquatic animals in the Florida Everglades may be strongly influenced by extinction and colonization dynamics. We combined analyses of allozyme and microsatellite loci to test the hypothesis that two levels of population structure are present for spotted sunfish (Pisces: Centrarchidae: Lepomis punctatus) inhabiting the Everglades. We hypothesized that annual cycles of marsh dry-down increase local-scale genetic variation through a process of local extinction and colonization; we hypothesized that barriers to gene flow by levee/canal systems create a second, regional level of genetic variation. In 1996 and 1997, we sampled spotted sunfish from 11 Everglades sites that were distributed in three regions separated by levees. We documented patterns of genetic variation at 7 polymorphic allozyme loci and 5 polymorphic microsatellite loci. Most genetic variation was present among local populations, according to both types of genetic markers. Furthermore, samples from marsh sites were heterogeneous, while those from canals were not. These data supported our hypothesis that dry-down events and local population dynamics in the marsh have a significant effect on population genetic structure of spotted sunfish. We found no support for our hypothesis that water-management structures superimpose a second level of genetic structure on this species, possibly because canals obscure historical structure by facilitating gene flow or because the complete canal system has been in place for fewer than 20 generations of this species. Our data suggests a continent-island (canal-marsh) structure of populations with high gene flow among regions and recurrent mixing in marshes from canal and creek habitats.