Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation.

AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within-and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15-25%) may occur with $50-100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a reduction of up to 15% in the power to detect selective loci. et al. 1995) is becoming one of the most popular methods in the fields of conservation and evolutionary genetics and ecology (Mueller and Wolfenbarger 1999;Bensch and Akesson 2005;Bonin et al. 2007;Meudt and Clarke 2007), as it combines a high reproducibility and information content with the possibility of making genomewide screenings. Because of the anonymous nature of the fragments generated by the AFLP technique, however, one major concern is the incidence of size homoplasy due to the lack of homology of comigrating fragments. This implies that fragments of a given size migrating in a band may involve more than one locus of the genome and, therefore, the inferences obtained from the band can produce misleading conclusions. T HE amplified fragment length polymorphism (AFLP) technique (VosSeveral empirical approaches have been used to estimate levels of homoplasy in AFLP data sets. A few studies have demonstrated the presence of homoplasy in AFLP data by sequencing comigrating fragments within t...

Parallel speciation can occur when traits determining reproductive isolation evolve independently in different populations that experience a similar range of environments. However, a common problem in studies of parallel evolution is to distinguish this hypothesis from an alternative one in which different ecotypes arose only once in allopatry and now share a sympatric scenario with substantial gene flow between them. Here we show that the combination of a phylogenetic approach with life-history data is able to disentangle both hypotheses in the case of the intertidal marine snail Littorina saxatilis on the rocky shores of Galicia in northwestern Spain. In this system, numerous phenotypic and genetic differences have evolved between two sympatric ecotypes spanning a sharp ecological gradient, and as aside effect of the former have produced partial reproductive isolation. A mitochondrial phylogeny of these populations strongly suggests that the two sympatric ecotypes have originated independently several times.Building upon earlier work demonstrating size-based assortative mating as the main contributor to reproductive isolation among ecotypes, our analysis provides strong evidence that divergent selection across a sharp ecological gradient promoted the parallel divergence of body size and shape between two sympatric ecotypes. Thus, divergent selection occurring independently in different populations has produced the marine equivalent of host races, which may represent the first step in speciation.

Electrophoretically detectable genetic variability of the Mediterranean mussel Mytilus galloprovincialis Lmk. was examined at 15 allozyme loci in 21 populations ranging from Santander (northern Spain) to Livorno (northwestern Italy). A major genetic break between Almeria and Alicante (southeastern Spain), as evidenced by 11 of 13 polymorphic loci examined, delimits 2 groups of populations with a high internal homogeneity. Roughly 75% of the total genetic differentiation was attributable to the divergence between these 2 groups of populations that displayed a genetic distance between them (D = 0.03) in the range of conspecific populations. This genetic break in M. galloprovincialis contrasts with earlier reports of genetic homogeneity among conspecific populations of the genus Mytilus over vast geographical distances, and represents an uncommon result in manne organisms with larval dispersal. The Zone of genetic divergence in M. galloprovincialis corresponds to a discontinuity in the distribution of this mussel, and to tbe position of the well-defined Almeria-Oran oceanographic front, with a distributional boundary between Atlantic and Mediterranean communities. In this region, other manne species exhibit similar patterns of intraspecific divergence, suggesting the action of common biogeographic processes. It is proposed that contemporary influences on gene flow related to an ecological barrier, perhaps in combination with selective pressures associated to water mass differences, maintain the abrupt change in southeastern Spain.

Mussels of the genus Mytilus have distinct and highly diverged male and female mitochondrial DNA (mtDNA) genomes with separate routes of inheritance. Previous studies of European populations of Mytilus trossulus demonstrated that 33% of males are heteroplasmic for a second mtDNA genome of increased length and that hybridization with Mytilus edulis does not block mtDNA introgression, in contrast to reports for American populations. Here, we demonstrate that the female mtDNA type of M. edulis has replaced the resident female mtDNA type of European M. trossulus. This is supported by COIII sequence data indicating that the female mtDNA of European M. trossulus is very similar to that of M. edulis and that in phylogenetic trees, the mtDNAs of these two species cluster together but separately from American M. trossulus sequences, the latter not being disturbed by introgressive hybridization. We also provide evidence that the mtDNA genome of increased length found in heteroplasmic males of European M. trossulus derives from a recent partition of an introgressed M. edulis female type into the male route of transmission. Neutrality tests reveal that European populations of M. trossulus display an excess of replacement polymorphism within the female mtDNA type with respect to conspecific American populations, as well as a significant excess of rare variants, of a similar magnitude to those previously reported for the invading European M. edulis mtDNA. Results are consistent with a nearly neutral model of molecular evolution and suggest that selection acting on European M. trossulus mtDNA is largely independent of the nuclear genetic background.

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The adaptive potential of a population depends on the amount of additive genetic variance for quantitative traits of evolutionary importance. This variance is a direct function of the expected frequency of heterozygotes for the loci which affect the trait (QTL). It has been argued, but not demonstrated experimentally, that long-term response to selection is more dependent on QTL allelic diversity than on QTL heterozygosity. Conservation programmes, aimed at preserving this variation, usually rely on neutral markers rather than on quantitative traits for making decisions on management. Here, we address, both through simulation analyses and experimental studies with Drosophila melanogaster, the question of whether allelic diversity for neutral markers is a better indicator of a high adaptive potential than expected heterozygosity. In both experimental and simulation studies, we established synthetic populations for which either heterozygosity or allelic diversity was maximized using information from QTL (simulations) or unlinked neutral markers (simulations and experiment). The synthetic populations were selected for the quantitative trait to evaluate the evolutionary potential provided by the two optimization methods. Our results show that maximizing the number of alleles of a low number of markers implies higher responses to selection than maximizing their heterozygosity.

We carried out an in silico analysis of the complete genome sequences of 14 species, including eukaryotes, prokaryotes, and archaea, to investigate the proportion of amplified fragment length polymorphism bands that are homoplasious for the different species, as well as the distribution of fragment lengths. We investigated several possible reasons for the disagreement, previously observed in Arabidopsis thaliana, between the observed fragment length distribution and the null random sequence distribution, which occurs in the direction of a deficit of fragments of small length and an excess of those of large length with respect to the null distribution. We made the following findings: 1) The positive relationship previously found between the percentage of homoplasy and genome size is a direct consequence of the number of observed bands and the GC content. For the same number of observed bands, the percentage of homoplasy is independent of the genome size of the species. 2) The disagreement between the observed fragment length distribution and the null random sequence distribution observed in A. thaliana is a phenomenon that also occurs in other species. 3) This disagreement is due neither to the structure of the genomes in isochores nor the possible impact of indels in reducing the number of restriction sites, two hypotheses discussed in the literature. 4) Nor is the disagreement eliminated by using restriction enzymes with balanced motifs. 5) The discrepancy seems to be caused, rather, by the nonrandom distribution of restriction enzyme motifs.