- Research article
- Open Access
Phylogeography and historical demography of the Lusitanian snail Elona quimperiana reveal survival in unexpected separate glacial refugia
© Vialatte et al; licensee BioMed Central Ltd. 2008
- Received: 09 June 2008
- Accepted: 19 December 2008
- Published: 19 December 2008
Present day distributions of Palearctic taxa in northern latitudes mainly result from populations having survived in local patches during the Late Pleistocene and/or from recolonizing populations from southern temperate refugia. If well-studied Mediterranean and eastern European refugia are widely accepted, some recent biogeographical assumptions still remain unclear, such as the occurrence of multiple glacial refugia in Iberia and cryptic refugia in northern Europe during the last glaciations. The Lusitanian snail Elona quimperiana has a remarkably disjunct distribution, limited to northwestern France (Brittany), northwestern Spain and the Basque Country. By describing the phylogeographical structure of this species across its entire range, the present study attempts to identify refugia and subsequent recolonization routes.
Results based on 16S and COI gene sequences showed that the low genetic diversity observed in the Brittany populations should be associated with a recent demographic expansion. By contrast, populations from Spain exhibit several differentiated lineages and are characterized by demographic equilibrium, while the Basque populations are the only ones harboring typical distinct haplotypes. The center of the star-like networks of both gene sequences is occupied by a common ancestral-like haplotype found in Brittany and Spain, which might have originated from the middle of Northern Spain (i.e. Asturias, eastern Lugo and western Cantabria). Estimates of the divergence time between the Spain-Brittany and Basque lineages strongly suggest that E. quimperiana survived the Pleistocene glaciations in distinct refugia on the Iberian Peninsula, one of which is situated in Picos de Europa, and the other in the Basque Country. The occurrence of a northern refugium in France cannot be rejected as of yet.
Present results confirm the Iberian origin of the land snail E. quimperiana and strongly support the emerging phylogeographic hypothesis of multiple refugia in Iberia during the last glaciations. The scenario of a spatial expansion of E. quimperiana from an Iberian refuge located in Asturias to northern areas provides the most probable explanation for the present distribution of this land snail. By harboring distinct haplotypes, the Basque Country populations appear to be of great importance in terms of potential adaptation, long term persistence and hence, the conservation of E. quimperiana.
- Last Glacial Maximum
- Basque Country
- Land Snail
- Glacial Refugium
- Disjunct Distribution
Geographically structured populations are the result of historical and/or contemporary demography. Some of them may experience either little or no genetic contact for long periods of time, due to physical, ecological or geographical barriers (e.g. [1–6]). More recent and rapid events, such as extinction, introduction or fragmentation, often linked to human activities, may also produce spatially partitioned populations (e.g. [7, 8]).
For European species, the Quaternary glaciations are a major historical factor shaping the patterns of spatial population structure [9–13]. During these periods, the ice sheet induced the preservation of many species, but only in isolated refugia, resulting in population divergence via genetic drift and local selection . The commonly recognized refugia in Western Europe during the Quaternary glaciations are on the Iberian and the Italian peninsulas [10, 14, 15]. It has been suggested that the northern regions of Europe were post-glacially colonized, generally from these refuges [10, 14]. Recent phylogeographic and biogeographic studies have uncovered multiple refugia in Iberia (see  for a review). However, the number, location and habitat composition of these 'refugia in refugia' still remain poorly known. Scenarios other than the northern expansion from southern refugia have also been proposed. On one hand, cold-tolerant species, such as Mustela erminea , could have naturally expanded their repartition range during the Quaternary glaciations. On the other hand, the presence of additional putative refugia has been advanced to explain the distribution of poor cold-hardy species [18, 19]. The hypothesis of local, but relatively recent and short-lived refugia much further north of the Mediterranean refugia is concordant with the discontinuity of the Pleistocene ice sheet in this region . These temperate refugia are particularly recognized to explain the survival of some communities, such as freshwater fish . The principal biome of unglaciated northern Europe during the late Pleistocene cold stages was the steppe tundra, i.e. a treeless vegetation type . The presence of small isolated populations of trees in buffered local microclimates is also suspected in northwestern Europe during the Pleistocene; but, except for one controversial site in Belgium , no temperate forest refugia for animal species have actually been precisely localized in this part of Europe. Therefore, contemporary demographic factors are more likely to explain well-separated populations of poor cold-hardy species in Western Europe, such as human introductions (e.g. ), or the recent extinction of intermediate populations .
The length of 16S rDNA sequences ranged from 479 to 481 bp, with a total of 19 substitutions, including two indels at positions 123 and 420, while the length of the COI sequences was 683 bp, with a total of 47 substitutions. Eleven haplotypes were identified among the 54 snails analyzed for the 16S gene: eight from Spain, three from Brittany, and one from the Basque Country. Brittany had only one haplotype (haplotype 1) in common with Spain; this haplotype was the most frequent one, since 30 individuals shared it. Twenty-three haplotypes were obtained for the COI gene among the 81 individuals analyzed: eleven from Spain, six from Brittany (including one in common with Spain) and seven from the Basque Country. The most frequent haplotype (haplotype A), shared by more the half of the specimens, was also the only one common to both Brittany and Spain.
The second haplogroup, Hg11, comprised only one haplotype (H11), which only occurred in Basque snails from Bqα (Sare) and Bqβ (Toloza Betulu).
Genetic polymorphism for different subsets of E. quimperiana populations according to their geographic origin.
Demographic analyses testing hypothesis of E. quimperiana population expansion.
Ramos-Onsins & ozas'R2
Raggedness index r
Bayesian estimation of time to the most recent common ancestor
Time to the most recent common ancestor (TMRCA; in million years, Myr) for all E. quimperiana sequences and for the two phylogenetic lineages defined.
Standard molecular clock estimates
Divergence time estimates
4% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
6.86% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
2% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
2.2% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
3% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
0.5% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
2% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
10% per Myr
mean (in Myr)
95% hpd upper
95% hpd lower
In spite of its name, an ancient Iberian origin of Elona quimperiana is obvious, as has been suggested earlier . This is strongly supported by the observation that most of the mtDNA diversity is found in Spain, and by the fact that Spanish haplotypes have a central position in both of the star-like sequence networks. Our genetic comparison of populations from the two disjunct distribution areas of E. quimperiana reveals that the genetic differentiation does not mirror the large geographical discontinuity of the species range.
Besides the strong genetic divergence of the Basque lineage, the present results also show that in the Spain-Brittany lineage, (i) the genetic diversity is higher in Spain, (ii) the Spanish and Brittany populations share one common haplotype for each gene, which is, moreover, the most frequent in the two areas, and (iii) the Spanish populations are at demographic equilibrium, while the Brittany ones would have experienced a recent expansion. Three scenarios might be considered in order to explain the origin of Brittany populations: 1 – a recent introduction by human activities, 2 – an ancient northward colonization preceding the last glacial period, as demonstrated for other Lusitanian species , 3 – a spatial expansion after the Last Glacial Maximum (LGM), also from native Spanish populations . In the first case, it is expected to have haplotypes in common with the source and introduced zones, as illustrated by 16S rDNA-H1 and COI-HA. All of the other haplotypes found in Brittany are specific to this area, suggesting that they probably appeared in Brittany after an introduction. However, such post-introduction genetic diversification is more typical for species with high colonization capabilities, which is not the case for E. quimperiana . Moreover, related life history features, inconsistent with human activities or production, render multiple introductions improbable. All of these points make the first assumption rather unlikely.
The second hypothesis conforms to predictions of the effects of the ice ages on genetic variability in populations: populations with historical distributions in northern latitudes present lower genetic diversity, with fewer differentiated lineages, than southern populations (Hewitt  and Avise ). This has been demonstrated in other ectotherm species . An ancient expansion of populations from Iberia through France during the Pleistocene interglacial periods may be plausible, since during these periods, the environmental conditions in Western Europe (e.g. high precipitation and cool temperatures) were particularly favorable to E. quimperiana, all the more so given that oak was a dominant tree species . Under this hypothesis, a subset of southern haplotypes (from the Picos de Europa refugium) would have expanded northward, while others (from the Pyrenees refugium) remained in the south. Glaciations would have subsequently eradicated most of the E. quimperiana populations, except in the Iberian refugia and in a northern refuge zone. Indeed, small microenvironmentally favorable zones might have been created by oak trees in Western Europe . According to paleoclimatic reconstructions, the local environmental conditions in close proximity to the arboreal vegetation were indeed warmer and more humid than regional simulations of the full-glacial climate . Within close proximity to the trees, poor cold-hardy flora and fauna were also able to survive the extremes of the LGM. It is also possible that the Pleistocene refuge in northwestern France may involve caves, as suspected in Belgium for other poor cold-hardy animals and deciduous trees . Elona quimperiana is indeed frequently observed in caves , where it survives by coprophagous and necrophagous feeding.
Unfortunately, our results cannot distinguish between the second and the third scenario. The latter implies a colonization of Brittany after the last glaciations. As illustrated by oak (Quercus sp.) dispersal in Great Britain some 10 000-9500 years ago , the oceanic climate of the west coast in France could have allowed a rapid spread of E. quimperiana from southern refugia to northern areas. Since this snail is strongly associated with oak forests, its dispersal may follow the tree expansion pattern. Human deforestation in intermediate areas between the Basque Country and Brittany, around 1000-500 years ago, may have created induced open habitats that are hostile for E. quimperiana , thus potentially explaining its present disjunct distribution.
There is no fossil record of E. Quimperiana due to the extreme fragility of its thin shell. Although the occurrence of a northern refugium should not be discarded a priori, an exhaustive sampling of the southern distribution range (based on a new imperative inventory, since many recorded sites appear to be presently disturbed by human activities) where Pleistocene refugia are obvious, appears necessary in order to clarify the colonization history of Brittany by E. quimperiana.
The present results confirm the Iberian origin of the land snail E. quimperiana and reveal a genetic differentiation separating a Basque lineage from monophyletic clade grouping sequences from Brittany and Spain. Divergence time estimates suggest the coexistence of these lineages in the Iberian refugia during the LGM, and strongly support the hypothesis of 'refugia in refugia' during glaciations. The identification of Iberian lineages allows the precision of the glacial refugia in the Basque Country and Asturias locations. Moreover, the species' ecology (inhabiting deciduous oak forests) allows researchers to sharpen their focus on the type of habitat present in these refugia during the glaciations. The scenario of a spatial expansion of E. quimperiana from the Iberian refugia located in Asturias to northern areas in France is the most probable for explaining the present distribution of the land snail. Inferences based on a spatial genetic structure analysis should be helpful to discriminate between a pre-glacial expansion implying the existence of glacial refugia in Brittany, or a post-glacial expansion followed by the human oak deforestation along the Atlantic coast in France.
Tissue samples were taken from a total of 81 individuals legally collected in 19 field populations across Brittany (France, sites BZH1 to BZH11), the Basque Country (France and Spain, sites BQα and BQβ) and Northern Spain (sites Sp1 to Sp6) between 2006 and 2007 (Fig 1). The other sites where this species was previously inventoried (see  for a review) were thoroughly searched, but no snails were found. The principal threat to this species is probably deforestation in those areas.
DNA Extraction, Amplification and Sequencing
Foot tissue was dissected from each individual and placed in a 10% chelex solution, with 15 μl of proteinase K (10 mg/ml). Samples were incubated overnight at 55°C, and then briefly vortexed, before being boiled for 2 × 15 min. After a centrifugation at 10,000 g for 5 s, the DNA in the supernatant was used in the subsequent amplifications.
DNA was amplified by the polymerase chain reaction (PCR) for the mitochondrial 16S rDNA on a set of 54 individuals, and mitochondrial cytochrome c oxydase-1 (COI) on 81 individuals. The 16S rDNA and COI gene fragments correspond, respectively, to a 480 base pair sequence using the primers 984 (5'-CGCCTGTTTAACAAAAACAT-3') and 16S2 (5'-CTGGCTTACGCCGGTCTG-3') , and to a 683 base pair sequence using the primers FCOI (5'-ACTCAACGAATCATAAAGATATTGG-3') and RCOI (5'-TATACTTCAGGATGACCAAAAAATCA-3') [50, 51]. PCRs were carried out in 25 μl volumes containing 0.5 μl (10 μM) of each forward and reverse primers, 12.5 μl of the Diamond DNA Polymerase – 500 (Bioline®), 10.25 μl of UP water and 1.25 μl of DNA template. The PCR conditions for the 16S rDNA gene were an initial denaturation step of 94°C (3 min), followed by 35 cycles of 94°C (30 s), 49°C (30 s), 72°C (40 s) and a final extension phase at 72°C for 4 min. Those for the COI gene were an initial denaturation step of 94°C (5 min), followed 35 cycles of 94°C (45 s), 52°C (45 s),72°C (1 min) and a final extension phase at 72°C for 7 min. The PCR products were sequenced in both directions on an automated sequencer using the PCR primers (PE Applied Biosystems 310 Genetic Analyser, UMR 6553; plate-forme de séquençage génotypage OUEST-genopole®).
Sequences were aligned using CLUSTAL W  and were manually checked in the BIOEDIT sequence editing program . The sequences have been submitted to GenBank (Accession N° FJ491809-FJ491943). Sequence polymorphism analyses (haplotype diversity h and nucleotide diversity π) were carried out with DNASP version 4.10.  and ARLEQUIN version 3.1 . The land snails Cantareus aspersus and Cepaea nemoralis were used as outgroups.
Phylogenetic relationships among haplotypes were estimated using maximum likelihood (ML) and Markov-Chain Monte-Carlo (MCMC) bayesian-based inference (BI) methods. ML and BI analyses were performed using PAUP* version 4.0b10  and MRBAYES v. 3.1.1-p1  softwares, respectively. The best fit model of nucleotide substitutions was selected prior to ML and BI using the Akaike Information Criterion . The software MrAIC v.1.4.2  was used to evaluate the fit of the data to 24 different models of nucleotide substitutions. The resulting best fit model was the F81 model  for the 16S rDNA region, with an unequal rate for base frequencies and equal rates for transitions and transversion. For the COI gene, the best fit model was the HKY model  with two different rates for transitions and transversion, unequal base frequencies, a parameter for invariable sites (I) and a gamma distribution parameter that describes the rate variation across variable sites (Γ). The model of nucleotide substitution was incorporated in PHYML and in MRBAYES for the ML and BI analyses respectively. For the ML analysis, the robustness of inferences was assessed by bootstrap resampling using 1,000 repetitions. For the Bayesian analysis, the posterior probabilities of trees and parameters were approximated with Markov-Chain Monte-Carlo and Metropolis coupling. We ran two independent MCMC analyses with four chains and a temperature set to 0.2. Each chain was run for 2,000,000 cycles with trees sampled every 100 generations. Posterior probabilities were obtained from the 50% majority rule consensus of trees sampled after discarding the trees saved before chains reached apparent stationarity (i.e. a 'burn-in period" of 50,000 generations for 16S rDNA).
We used network-based approaches for intraspecific phylogenetic analyses to deal with the low divergence among individuals and the possible persistence of ancestral nodes . The median joining algorithm implemented in the NETWORK v. 22.214.171.124 software  was used with the default settings for constructing networks (weight = 10 and e = 0), and we simplified the median networks that contained all of the possible equally shortest trees by running the MP (maximum parsimony) calculation option.
The demographic history of the populations was inferred using two of the most powerful tests of population expansion: (i) Fu's Fs , which represents the probability of observing a similar or a higher number of haplotypes in a random neutral population given the observed value of theta. In populations that have experienced recent expansion, large negative values of Fs are expected, due to an excess of rare alleles; (ii) Ramos-Onsins & Rozas' R 2 statistics, representing the difference between the number of singleton mutations and the average number of pairwise differences. Recent population expansions are expected to be associated with low values of this parameter. R2 and Fs statistics were estimated using DNASP v. 4.10.9  and ARLEQUIN v. 3.1  respectively, and their significance was assessed using 1,000 coalescent simulated resamplings. In order to evaluate the possible historical events of population growth or decline, mismatch distribution analyses were also performed ; in the first case, populations show unimodal distributions, while in the second case the populations at demographic equilibrium present multimodal distributions . Mismatch distributions were computed for each haplogroup and compared to the expected distributions obtained under a model of sudden expansion.
Molecular clock and divergence times
A molecular-clock likelihood ratio-test (LRT, [47, 50]) was first conducted on the 16S rDNA and COI sequences (considering the three bases and only the third base of codon) to ascertain whether or not the Elona sequences were evolving at a homogeneous rate along all of the branches in the phylogenies. This test compares the log-likelihood of the ML trees under alternative molecular clock assumptions (i.e. a relaxed vs. an enforced molecular clock). The statistic A = 2(lnL1–lnL2) could be compared with a distribution with (n-2) degrees of freedom (where n is the number of sequences). Divergence dates were computed using BEAST in order to provide estimates of time to the most common ancestor (TMCRA) for E. quimperiana populations, along with the TMCRAs of the Brittany-Spain (Hg1 and HgA) and the Basque lineages (see Results). An HKY model of nucleotide substitution was employed with a sequence divergence rate based on several different published rates for molluscs. While the divergence rates for 16S rDNA are estimated at around 2% per Myr for animals , the estimates for gastropods vary between 0.5 – 0.6% [71, 72] up to an accelerated rate of 10% per Myr, as seen in the land snail Mandarina sp . For COIGENE, we used rates from bivalve species inferred from geological events . These rates range from 0.03 to 6.84% per Myr, depending on the codon position considered. The number of mutations recorded for the COI first- and second-positions (7 of 456 nucleotides) and COI third-positions (39 of 227 nucleotides) may reflect a variation in rates of substitution among these types of sites, in favor of a higher rate for COI third-positions. Given that the clades of the BI tree, based on the two first codon positions of COI, appeared to not be statistically supported (result not shown), we applied COI third-positions rates only when estimating divergence times (4 to 6.86% per Myr). These time estimates were then used to infer the 16S rDNA mutation rates by testing several substitution rates (0.5%, 2% and 10% per Myr).
We thank M.A. Coutellec and Ana Puente for their help with the sample collection, Olivier Lemoine and anonymous referees for their comments on the results.
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