Island isolation and habitat heterogeneity correlate with DNA variation in a marine snail (Littorina saxatilis)

The null assumption of molecular variation is that most of it is neutral to natural selection. This is in contrast to variation in morphological traits that we generally assume is maintained by selection, and therefore often by selection coupled to environmental heterogeneity in time and space. Examples of molecular variation that vary over habitat-shifts, particularly in allozymes, show that the relative impact of non-neutral variation as compared to neutral variation might be substantial in some systems. To assess the importance of habitat-generated variation in relation to variation generated by random processes in nuclear DNA markers at small spatial scales, we compared the effects of island isolation and habitat heterogeneity on genetic substructuring in a rocky shore snail ( Littorina saxatilis ). This species has a restricted migration among islands owing to the lack of free-floating larvae. Earlier studies show that allozymes vary extensively as a consequence of isolation by water barriers among islands, but also as a consequence of divergent selection among different microhabitats within islands. In the DNA markers we observed genetic differentiation owing to island isolation at three of nine loci. In addition, variation at three loci correlated with habitat type, but the correlation for two of the loci was weak. Overall, isolation contributed slightly more to the genetic variation among populations than did habitat-related factors but the difference was small. It is concluded that both island isolation, which interrupts gene flow, and a heterogeneous habitat cause genetic substructuring at the DNA level in L. saxatilis in the studied area, and thus in this species we need to be somewhat concerned about habitat heterogeneity also at DNA loci.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 377–384.     

Genetic differentiation on multiple spatial scales in an ecotype-forming marine snail with limited dispersal: Littorina saxatilis

The population genetic structure of marine species lacking free-swimming larvae is expected to be strongly affected by random genetic drift among populations, resulting in genetic isolation by geographical distance. At the same time, ecological separation over microhabitats followed by direct selection on those parts of the genome that affect adaptation might also be strong. Here, we address the question of how the relative importance of stochastic vs. selective structuring forces varies at different geographical scales. We use microsatellite DNA and allozyme data from samples of the marine rocky shore snail Littorina saxatilis over distance scales ranging from metres to 1000 km, and we show that genetic drift is the most important structuring evolutionary force at distances > 1 km. On smaller geographical scales (< 1 km), divergent selection between contrasting habitats affects population genetic structure by impeding gene flow over microhabitat borders (microsatellite structure), or by directly favouring specific alleles of selected loci (allozyme structure). The results suggest that evolutionary drivers of population genetic structure cannot a priori be assumed to be equally important at different geographical scales. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 31–40.     

Enhanced colour polymorphisms in island populations of the land snail Euhadra peliomphala

Variations in visible genetic polymorphisms are assumed to decrease in populations on small islands because of intense founder effects, genetic drift and inbreeding. However, we have found evidence of a marked enhancement of colour polymorphisms within populations on small oceanic islands that were colonized from the mainland. The source populations on the mainland of the land snail Euhadra peliomphala in four oceanic islands were estimated by phylogenetic analysis of mitochondrial DNA sequences. Diversity of shell colour was higher in the island populations than in the source populations on the mainland. In addition, the shell colour morphs differed not only among populations from different islands but also between the island populations and the source populations on the mainland. By contrast, no mtDNA variations were found in any of the island populations, even though the source populations possessed high mtDNA diversity. Thus, components of colour morphs changed in the island populations after their colonization, and colour polymorphisms are enhanced in these islands despite the loss of genetic variation. The above findings suggest that ecological mechanisms such as morphological release owing to a release from competition may overcome the tendency toward reduced genetic variation in islands to enhance the colour polymorphism.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 417–425.     

Allozymic differentiation of Tunisian populations of Androctonus species and Buthus occitanus (Scorpiones: Buthidae)

We examined the population structure and phylogeny of Buthus occitanus (Amoreux, 1789), Androctonus amoreuxi (Audouin & Savigny 1812) and Androctonus australis (Linnaeus, 1758) in Tunisia, using horizontal starch gel and polyacrylamide gel electrophoresis to resolve allozymes at 18 loci. Populations of B. occitanus and A. amoreuxi showed little genetic variation, whereas A. australis populations showed moderate genetic variation. Moreover, despite the restricted dispersal abilities of these species, the allozyme analysis indicated very low levels of intraspecific population differentiation. The Island model of population differentiation best fitted the intraspecific variation, both for mainland populations and for the slightly more differentiated populations from two Mediterranean islands. No diagnostic, fixed alleles were observed between the species of Androctonus , which concurs with the results of nuclear ribosomal DNA analysis. Two subspecies of A. australis , A. a. garzonii Goyffon & Lamy, 1973 and A. a. hector Vachon, 1948, were not resolved by a phylogenetic analysis of the allozyme data. The most likely reasons for the slight population differentiation are either low mutation rates or recent range extensions promoted by human activities. The possibility of indirect gene flow between Androctonus species should also be explored.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 255–265.     

Extremely low levels of genetic diversity in the terrestrial orchid Epipactis thunbergii (Orchidaceae) in South Korea: implications for conservation

Levels of allozyme variation, population genetic structure, and fine-scale genetic structure (FSGS) of the rare, both sexually and clonally reproducing terrestrial orchid Epipactis thunbergii were examined for eight ( N  = 734) populations in a 20 × 20-km area in South Korea. Twenty-three putative allozyme loci resolved from 15 enzyme systems were used. Extremely low levels of allozyme variation were found within populations: the mean frequency of polymorphic loci was 3.8% [isocitrate dehydrogenase ( Idh-2 ) with two alleles was polymorphic across populations], the mean number of alleles per locus was 1.04, and the mean expected heterozygosity was 0.013. The overall fixation index was not significantly different from zero ( F _IS = 0.069), although the species is self-compatible. However, a significantly high degree of population differentiation was found between populations at Idh-2 ( F _ST = 0.388) in the studied area. Furthermore, spatial autocorrelation analyses revealed a significant FSGS (up to 3 m) within populations. These observations suggest that the main explanatory factors for the extremely low levels of genetic diversity and the shaping of the population genetic structure of E. thunbergii are genetic drift as a result of a small effective population size, a restricted gene flow, and the isolation of populations. Considering the current genetic structure of E. thunbergii , three guidelines are suggested for the development of conservation strategies for the species in South Korea: (1) protection of habitats of standing populations; (2) prohibition by law of any collection of E. thunbergii ; and (3) protection of nearby pollinator populations, given the fact that fruit set in natural habitats is very low.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 161–169.     

High variability of genetic pattern in giant clam (Tridacna maxima) populations within French Polynesia

Nine populations of giant clams, Tridacna maxima, from six islands of French Polynesia were screened for allozyme variation at ten polymorphic loci. The genetic structure of populations of T. maxima were studied at different spatial scales: within an island, between islands of the same archipelago and between archipelagos. Significant genetic differences were observed only between populations from different archipelagos, and genetic differentiation was correlated with geographical separation. However, these results were only supported by a single locus, PEP * and all other loci were homogeneous between studied populations. According to Lewontin & Krakauer's model, the genetic structure can be explained by selection. The selective factors most likely depend on the respective habitat of each archipelago. We also studied genotype–phenotype correlation using the colour of the clam mantle, and did not find any relationship between the mantle colour and the genetic structure of the individuals.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 221–231.     

Low population differentiation and high genetic diversity in the invasive species Carduus acanthoides L. (Asteraceae) within its native range in the Czech Republic

Colonizing species are predicted to suffer from reductions in genetic diversity during founding events. Although there is no unique mode of reproduction that is characteristic of successful plant colonizers, many of them are predominantly self-fertilizing or apomictic species, and almost all outcrossing colonizers are self-compatible. Carduus acanthoides comprises a species of disturbed habitats with wind-dispersed seeds that colonizes open spaces of various sizes. Population genetic diversity was expressed by assessing patterns of variation at nine putatively neutral allozyme loci within and among 20 natural populations in its native distribution range in the Czech Republic. Overall, C. acanthoides displayed high levels of genetic diversity compared to other herbaceous plants. The percentage of polymorphic loci was 84.5, with values of 2.37, 0.330, and 0.364 for the mean number of alleles per polymorphic locus ( A ), observed heterozygosity ( H _o), and expected heterozygosity ( H _e), respectively. There was only weak evidence of inbreeding within populations ( f  = 0.097) and very low genetic differentiation among populations ( θ  = 0.085). Analyses of the data provide strong evidence for isolation-by-distance for the whole study area. Even the colonizing species, C. acanthoides , currently supports a substantial amount of allozyme variation at both the species and population levels.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 596–607.     

Relationship between microspatial population genetic structure and habitat heterogeneity in Pomatias elegans (O.F. Müller 1774) (Caenogastropoda, Pomatiasidae)

In the present study the population genetic structure of the terrestrial snail Pomatias elegans was related to habitat structure on a microspatial scale. The genetic variability of 1607 individuals from 51 sampling sites in five different populations in Provence, France, was studied with an allozyme marker using population genetic methods, Mantel tests and spatial autocorrelation techniques were applied to different connectivity networks accounting for the structural features of the landscape. It is suggested that the population structure is, to a large extent, a function of the habitat quality, quantified as population density, and of the spatial arrangement of the habitat in the landscape and not of the geographical distance per se . In fragmented habitats, random genetic drift was the prevailing force for sampling sites separated by a few hundred meters.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 565–575.     

Inferences of selection and migration in the Danish house mouse hybrid zone

We analysed the patterns of allele frequency change for ten diagnostic autosomal allozyme loci in the hybrid zone between the house mouse subspecies Mus musculus domesticus and M. m. musculus in central Jutland. After determining the general orientation of the clines of allele frequencies, we analysed the cline shapes along the direction of maximum gradient. Eight of the ten clines are best described by steep central steps with coincident positions and an average width of 8.9 km (support limits 7.6–12.4) flanked by tails of introgression, indicating the existence of a barrier to gene flow and only weak selection on the loci studied. We derived estimates of migration from linkage disequilibrium in the centre of the zone, and by applying isolation by distance methods to microsatellite data from some of these populations. These give concordant estimates of σ =  0.5–0.8 km generation     . The barrier to gene flow is of the order of 20 km (support limits 14–28), and could be explained by selection of a few per cent at 43–120 underdominant loci that reduces the mean fitness in the central populations to 0.45. Some of the clines appear symmetrical, whereas others are strongly asymmetrical, and two loci appear to have escaped the central barrier to gene flow, reflecting the differential action of selection on different parts of the genome. Asymmetry is always in the direction of more introgression into musculus , indicating either a general progression of domesticus into the musculus territory, possibly mediated by differential behaviour, or past movement of the hybrid zone in the opposite direction, impeded by potential geographical barriers to migration in domesticus territory.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 593–616.     

The adaptive role of Phosphoglucomutase and other allozymes in a marine snail across the vertical rocky-shore gradient

Natural selection can play an important role in the maintenance of genetic polymorphisms, despite ongoing gene flow. In the present study, we use previously analysed allozymic loci and perform an F _ST outlier-based analysis to detect the signatures of divergent selection between sympatric ecotypes of the marine snail Littorina saxatilis at different localities. The results obtained show that different allozyme polymorphisms are affected (directly or indirectly) by selection at distinct geographical regions. The Phosmogluco mutase-2 locus was the best candidate for adaptation and further biochemical analyses were performed. The kinetic properties of the three more common genotypes of Pgm-2 were studied. The results obtained are concordant with two alternative hypotheses: (1) natural selection is acting directly on this locus or, more probably, (2) selection is affecting a genomic region tightly linked to the enzyme locus. In both cases, the known existence of a parallel and partially independent origin of these ecotypes would explain why different candidate loci were detected in different localities.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 225–233.     

Contrasting levels of genetic diversity between the common, self-compatible Liparis kumokiri and rare, self-incompatible Liparis makinoana (Orchidaceae) in South Korea

Levels of allozyme variation and intrapopulation spatial genetic structure of the two terrestrial clonal orchids Liparis kumokiri , a self-compatible relatively common species, and L. makinoana , a self-incompatible rare species, were examined for 17 ( N  = 1875) and four ( N  = 425) populations, respectively, in South Korea. Populations of L. makinoana harboured high levels of genetic variation ( H _e = 0.319) across 15 loci. In contrast, L. kumokiri exhibited a complete lack of allozyme variation ( H _e = 0.000). Considering the lack of genetic variability, it is suggested that current populations of L. kumokiri in South Korea originated from a genetically depauperate ancestral population. For L. makinoana , a significant deficit of heterozygosity (mean F _IS = 0.198) was found in population samples excluding clonal ramets, suggesting that pollen dispersal is localized, generating biparental inbreeding. The significant fine-scale genetic structuring (≤ 2 m) found in a previous study, in addition to the moderate levels of population differentiation ( F _ST = 0.107) and the significant relationship between genetic and geographical distances ( r  = 0.680) found here, suggests a leptokurtic distribution of seed dispersal for L. makinoana . Although populations of L. makinoana harbour high levels of genetic variation, they are affected by a recent genetic bottleneck. This information suggests that genetic drift and limited gene flow could be the main evolutionary forces for speciation of a species-rich genus such as Liparis .  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 41–48.     

Cryptic species within the freshwater isopod Mesamphisopus capensis (Phreatoicidea: Amphisopodidae) in the Western Cape, South Africa: allozyme and 12S rRNA sequence data and morphometric evidence

The freshwater phreatoicidean isopod Mesamphisopus capensis has been regarded as the most widespread of the four Mesamphisopus species occurring in the Western Cape, South Africa. To determine whether this species was monotypic across its distribution over two mountainous regions, separated by a low-lying coastal plain remnant, genetic differentiation among populations from 11 localities was studied through allozyme electrophoresis of 12 loci and sequencing of a 338-bp 12S rRNA mtDNA fragment from representative individuals. Populations of the two regions were separated by a mean identity value of 0.477. Fixed allele differences at two loci distinguished these regions. Estimates of θ indicated substantial differentiation among populations across the entire sample, as well as within each of the regions. Topologies derived through parsimony and neighbour joining supported the monophyly of the two regions. On the basis of these topologies, allele frequencies and an allozyme dendrogram, five groups were identified. Discriminant function analyses, performed on body and pereopod variables independently, revealed these groups to be well differentiated with a high rate of correct a posteriori reclassification. Using genetic distance criteria these five distinct forms may be considered to be putative species. From a conservation perspective, the two regions can be seen to represent two evolutionarily significant units, while the five groups should be regarded as management units.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 235–253.     

Phylogeography of the freshwater crayfish Cherax destructor Clark (Parastacidae) in inland Australia: historical fragmentation and recent range expansion

The yabby, Cherax destructor Clark, is the most widespread species in the most widespread genus of Australian freshwater crayfish. It has a distribution that spans several distinct drainage basins and biogeographical regions within semiarid and arid inland Australia. Here we report a study designed to investigate patterns of genetic variation within the species and hypotheses put forward to account for its extensive distribution using DNA sequences from the mitochondrial 16S rRNA gene region. Results of phylogenetic analyses contradicted previous allozyme data and revealed relatively deep phylogenetic structure in the form of three geographically correlated clades. The degree of genetic divergences between clades (8–15 bp) contrasted with the relatively limited haplotype diversity within clades (1–3 bp). Network-based analyses confirmed these results and revealed genetic structure on both larger and more restricted geographical scales. Nevertheless some haplotypes and 1-step clades had large distributions, some of which crossed boundaries between river basins and aquatic biogeographical regions. Thus both older and more recent historical processes, including fragmentation on a larger geographical scale and more recent range expansion on a local scale, appear to be responsible for the observed pattern of genetic variation within C. destructor . These results support elements of alternative hypotheses previously put forward to account for the evolutionary history of C. destructor and the origin of its large distribution.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 539–550.     

Linkage disequilibrium between a melanin-based colour polymorphism and tail length in the barn owl

A linkage disequilibrium between sexually selected and life history traits can be explained by three mutually non-exclusive mechanisms. Genes coding for two traits may be located close on the same chromosome, genes responsible for variation in one of the trait may pleiotropically alter the other, and non-random pairing with respect to two traits may generate a non-physical linkage disequilibrium between their genes. Knowledge of which of these three mechanisms is responsible for a covariation between two traits is of interest to understand why differently ornamented individuals differ in several phenotypic aspects. In Switzerland, barn owls Tyto alba mate randomly with respect to a colour polymorphism generating a large range of variants between reddish-brown and white, males being lighter coloured than females. Several studies have shown that plumage coloration is not neutral with respect to some life history components. To test whether coloration is genetically associated with body size, partial cross-fostering experiments were performed by exchanging some hatchlings between nests. These experiments showed that darker biological fathers produce longer-tailed offspring. This sex-specific pattern is consistent with the hypothesis of non-physical linkage disequilibrium. In line with this hypothesis, darker coloured males were mated with longer-tailed females, whereas female coloration was not associated with tail length of their mate. The finding that dark nestlings had a longer tail than their pale siblings also supports the physical linkage and pleiotropy hypotheses. Therefore, non-random pairing can generate or strengthen a genetic covariation between a secondary sexual character and a morphological trait.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 475–488.     

Morphological and genetic evidence supports the existence of two species in the genus Ophelia (Annelida, Polychaeta) from the Western Mediterranean

About 900 individuals of the intertidal polychaete Ophelia cf. bicornis were collected at four sandy beaches in Corsica, ten in Sardinia and one in Tuscany (Western Mediterranean). They were analysed morphologically and genetically to clarify the taxonomic status of the littoral species of Ophelia in the study area and to assess the population genetic structuring. Two morphotypes were distinguished on the basis of the number of nephridiopore pairs (five or six). Genetic distances, F -statistics and analysis of molecular variance based on eight allozyme genetic markers were consistent in showing the two morphotypes to separate at species level. Thus, the two morphotypes which most authors have included in O. bicornis s.l. are not one morphologically variable taxon, but instead constitute two valid species, namely O. bicornis Savigny, 1818, with six pairs of nephridiopores, and O. barquii Fauvel, 1927, with five pairs of nephridiopores. Mechanisms of ecological speciation in a background of gene flow can be taken into account to explain the origin of the two species. Moderate genetic differentiation was found among populations within each species, suggesting that dispersal may not be effective over large distances, or that local selection plays an important role in population differentiation.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 101–113.     

Molecular differentiation between coexisting species of Taraxacum sect. Erythrosperma (Asteraceae) from populations in south-east and west Germany

The present study focuses on the genetic differentiation between six coexisting species of Taraxacum sect. Erythrosperma . Twenty-six individuals of T. rubicundum , T. brachyglossum , T. tortilobum , T. lacistophyllum , T. parnassicum and T. scanicum were sampled at 14 locations in south-east (Bavaria) and west Germany (Eifel). Using random amplified polymorphic DNA (RAPD) analysis 139 fragments were amplified. Nineteen of these were found to be species specific. The level of polymorphic bands within the different Taraxacum species varied between 0% and 15.8%. An analysis of molecular variance (AMOVA) revealed strong differentiation between the investigated species: 14.3% of the molecular variance were found within the species, while 85.7% of the genetic variability was observed between the species. However, a geographical differentiation between the different regions could not be observed. All analysed species were clearly separated from each other in a cluster analysis using the neighbour joining technique. The observed strong genetic differentiation between the Taraxacum species clearly supports the agamospecies concept of Taraxacum sect. Erythrosperma , which is at present mainly based on morphological and cytological criteria  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 109–117.     

Limited mitochondrial DNA introgression in a Bombina hybrid zone

We analysed the variation at mitochondrial DNA (mtDNA) and six allozyme loci in two transects across a hybrid zone between the fire-bellied toads Bombina bombina and Bombina variegata in southern Poland. The mtDNA cline was narrower than allozyme clines in one transect (Przemyśl, β = 0.435, w  = 3.42 km) and shifted to the B .  bombina side in both (near Kraków by 1.32 km, α = 0.437, and near Przemyśl by 0.97 km, α = 0.319). Cytonuclear associations were weak. Narrowed mtDNA clines could be a by-product of female demography and lowered effective population size of mtDNA. Alternatively, restricted mtDNA introgression is a likely result of negative epistasis in recombinants augmented by environment-dependent selection because divergence of Bombina mitochondrial and nuclear genomes is large. The shift of the mtDNA cline, contrary to expectations from initial mating preferences and fecundity differences between the species, suggests that on the B .  bombina side of the zone hybrid females with B .  variegata mtDNA have a higher chance of leaving progeny.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 295–306.     

Stability of genetic structure and effective population size inferred from temporal changes of microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae)

Temporal evolution of genetic variability may have far-reaching consequences for a diverse array of evolutionary processes. Within the polders of the Bay of Mont-Saint-Michel (France), populations of the land snail Helix aspersa are characterized by a metapopulation structure with occasional extinction processes resulting from farming practices. A temporal survey of genetic structure in H . aspersa was carried out using variability at four microsatellite loci, in ten populations sampled two years apart. Levels of within-population genetic variation, as measured by allelic richness, H _e or F _is , did not change over time and similar levels of population differentiation were demonstrated for both sampling years. The extent of genetic differentiation between temporal samples of the same population established (i) a stable structure for six populations, and (ii) substantial genetic changes for four populations. Using classical F -statistics and a maximum likelihood method, estimates of the effective population size ( N _e) illustrated a mixture of stable populations with high N _e, and unstable populations characterized by very small N _e estimates (of 5–11 individuals). Owing to human disturbances, intermittent gene flow and genetic drift are likely to be the predominant evolutionary processes shaping the observed genetic structure. However, the practice of multiple matings and sperm storage is likely to provide a reservoir of variability, minimizing the eroding genetic effects of population size reduction and increasing the effective population size.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 89–102.     

Micro- and macrogeographic allozyme variation in Littorina fabalis; do sheltered and exposed forms hybridize?

Earlier studies of Swedish populations of the marine snail Littorina fabalis show that snails from different microhabitats (with a greater and lesser exposure to wave action) have almost diagnostic differences in one allozyme locus (arginine kinase, Ark ), and differ in adult size. Snails with 'sheltered' and 'exposed' Ark genotypes occur in sympatry in intermediary exposed sites and here adult sizes remain distinct. Approaching the microgeographic differentiation we studied the parts of two populations where the frequency of Ark changes dramatically over zones 50–120 m wide. The aim was to test if the transitional zones are best described as areas of mixing of two genetically separate populations, or if hybridization between the exposed and sheltered groups occurs. Heterozygotes were in deficiency along both clines but were still roughly twice as common as expected from a pure mixing of 'sheltered' and 'exposed' groups suggesting hybridization. Hybridization was also supported by the observation that snails homozygous for sheltered and exposed alleles mated at random with each other in both populations. On the macrogeographic scale, we found populations from exposed and sheltered sites in France and Wales being fixed for the same exposed and sheltered Ark alleles as found in Sweden. However, variation in three other highly polymorphic loci indicated geographic affinity rather than habitat similarity being the main factor of genetic coherence. These observations support a hypothesis of gene flow between exposed and sheltered populations of L. fabalis . Two Spanish populations were remarkably different with unique alleles at high frequencies in three of four strongly polymorphic loci.