Emilio Rolán-Alvarez

MORPHOLOGICAL DIFFERENTIATION AND GENETIC COHESIVENESS OVER A MICROENVIRONMENTAL GRADIENT IN THE MARINE SNAIL LITTORINA SAXATILIS

The marine gastropod Littorina saxatilis has different ecotypes in shores only a few meters apart. This has both taxonomic and evolutionary implications. Here we report on an extreme type of within‐shore dimorphism in shell characters. In the wave‐exposed rocky shores in northwestern Spain, we found one form of L. saxatilis in the upper‐level barnacle zone. It had a white, ridged shell, with black bands in the grooves. Another form confined to the lower‐shore mussel belt had a smooth shell that was either white and tessellated or darkly colored. These two forms cooccured in a narrow midshore zone together with individuals that had combined characters, but were present in low frequencies (11%–29%). We used principal‐component analysis of metric shell characters to study variation in shell size and shape. We found that the upper‐shore form was larger than the lower‐shore form. We also found small but significant differences in shell shape. Experiments in a common laboratory environment suggested the differences in shell ornamentation and color are inherited, but the individuals did not develop the morph‐specific characters until a shell height of about 3 mm. The occurrence of mainly two distinct forms may suggest the presence of two species that hybridize. An analysis of five polymorphic enzyme loci in populations of snails from three geographically separated sites indicated, however, that there was no positive correlation between morphological distances and genetic distances among populations on a geographic scale (tens of kilometers). Thus, we rejected the hypothesis of two species. However, on a microgeographic scale (meters), genetic differentiation between groups with the same form was less than differentiation between forms. This indicated a partial barrier to gene flow between the two forms, and preliminary mate choice data suggested this was caused by nonrandom mating in the midshore zone of overlap.

INCIPIENT REPRODUCTIVE ISOLATION BETWEEN TWO SYMPATRIC MORPHS OF THE INTERTIDAL SNAIL LITTORINA SAXATILIS

The study of speciation in recent populations is essentially a study of the evolution of reproductive isolation mechanisms between sub‐groups of a species. Prezygotic isolation can be of central importance to models of speciation, either being a consequence of reinforcement of assortative mating in hybrid zones, or a pleiotropic effect of morphological or behavioral adaptation to different environments. To suggest speciation by reinforcement between incipient species one must at least know that gene flow occurs, or have recently occurred, and that assortative mating has been established in the hybrid zone.

The maintenance of a cline in the marine snail Littorina saxatilis: The role of home site advantage and hybrid fitness

Steep clinal transitions in one or several inherited characters between genetically distinct populations are usually referred to as hybrid zones. Essentially two different mechanisms may maintain steep genetic clines. Either selection acts against hybrids that are unfit over the entire zone due to their mixed genetic origin (endogenous selection), or hybrids and parental types attain different fitness values in different parts of the cline (exogenous selection). Survival rate estimates of hybrids and parental forms in different regions of the cline may be used to distinguish between these models to assess how the cline is maintained. We used reciprocal transplants to test the relative survival rates of two parental ecotypes and their hybrids over microscale hybrid zones in the direct‐developing marine snail Littorina saxatilis (Olivi) on the rocky shores of Galicia, Spain. One of the parental forms occupies upper and the other lower shores, and the hybrids are found at various proportions (1–38%) along with both parental forms in a midshore zone a few meters wide. The survival rate over one month was 39‐52% of the native ecotype on upper shores, but only 2‐8% for the lower‐shore ecotype. In contrast, only 4‐8% of the upper‐shore ecotype but 53% of large (> 6 mm) and 8% of small (3‐6 mm) native lower‐shore ecotype survived in the lower shores. In the midshores, both the two parental ecotypes and the hybrids survived about equally well. Thus there is a considerable advantage for the native ecotypes in the upper and lower shores, while in the hybrid zone none of the morphs, hybrids included, are favored. This indicates that the dimorphism of L. saxatilis is maintained by steep cross‐shore selection gradients, thus supporting the selection‐gradient model of hybrid zones. We performed field and laboratory experiments that suggest physical factors and predation as important selective agents. Earlier studies indicate assortative mating between the two ecotypes in the midshore. This is unexpected in a hybrid zone maintained by selection gradients, and it seems as if the reproductive barrier compresses the hybrid zone considerably.

Comparing three different methods to detect selective loci using dominant markers

We carried out a simulation study to compare the efficiency of three alternative programs (dfdist, detseld and bayescan) to detect loci under directional selection from genome‐wide scans using dominant markers. We also evaluated the efficiency of correcting for multiple testing those methods that use a classical probability approach. Under a wide range of scenarios, we conclude that bayescan appears to be more efficient than the other methods, detecting a usually high percentage of true selective loci as well as less than 1% of outliers (false positives) under a fully neutral model. In addition, the percentage of outliers detected by this software is always correlated with the true percentage of selective loci in the genome. Our results show, nevertheless, that false positives are common even with a combination of methods and multitest correction, suggesting that conclusions obtained from this approach should be taken with extreme caution.

Impact of Amplified Fragment Length Polymorphism Size Homoplasy on the Estimation of Population Genetic Diversity and the Detection of Selective Loci

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.

ESTIMATING SEXUAL SELECTION AND SEXUAL ISOLATION EFFECTS FROM MATING FREQUENCIES

Abstract Sexual selection (defined as the change in genotypic or phenotypic frequencies of mated versus total population frequencies) and sexual isolation (defined as the deviation from random mating in mated individuals) show different evolutionary consequences and partially confounded causes. Traditionally, the cross-product estimator has been used to quantify sexual selection, whereas a variety of indexes, such as Yule V, Yule Q, YA, joint I, and others have been used to quantify sexual isolation. Because the two types of estimators use different scales, the effects of both processes cannot be monitored simultaneously. We describe three new related statistics that quantify both sexual selection (PSS) and sexual isolation (PSI) effects for every mating pair combination in polymorphic traits, as well as measure their combined effects (PTI = PSI × PSS). The new statistics have the advantage of providing information on every mating pair combination, quantifying the effects of sexual selection and isolation in the same units, and detecting asymmetry in sexual isolation. The ability of the new statistics to ascertain the biological causes of sexual selection and sexual isolation are investigated under different models involving distinct marginal frequencies, mate propensity, and mate choice coefficients. We also studied the use of classical isolation indexes applied on PSI coefficients, instead of on raw data. The use of the classical indexes applied to PSI coefficients considerably reduces the statistical bias of the estimates, revealing the good estimation properties of the new statistics. Corresponding Editor: E. Zouros

A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests

BackgroundThe detection of true significant cases under multiple testing is becoming a fundamental issue when analyzing high-dimensional biological data. Unfortunately, known multitest adjustments reduce their statistical power as the number of tests increase. We propose a new multitest adjustment, based on a sequential goodness of fit metatest (SGoF), which increases its statistical power with the number of tests. The method is compared with Bonferroni and FDR-based alternatives by simulating a multitest context via two different kinds of tests: 1) one-sample t-test, and 2) homogeneity G-test.ResultsIt is shown that SGoF behaves especially well with small sample sizes when 1) the alternative hypothesis is weakly to moderately deviated from the null model, 2) there are widespread effects through the family of tests, and 3) the number of tests is large.ConclusionTherefore, SGoF should become an important tool for multitest adjustment when working with high-dimensional biological data.

Proteomics in evolutionary ecology: linking the genotype with the phenotype

The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein–protein interactions, as well as the combined use of the different ‐omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.

Nonallopatric and parallel origin of local reproductive barriers between two snail ecotypes.

Theory suggests that speciation is possible without physical isolation of populations (hereafter, nonallopatric speciation), but recent nonallopatric models need the support of irrefutable empirical examples. We collected snails (Littorina saxatilis) from three areas on the NW coast of Spain to investigate the population genetic structure of two ecotypes. Earlier studies suggest that these ecotypes may represent incipient species: a large, thick‐shelled ‘RB’ ecotype living among the barnacles in the upper intertidal zone and a small, thin‐shelled ‘SU’ ecotype living among the mussels in the lower intertidal zone only 10–30 m away. The two ecotypes overlap and hybridize in a midshore zone only 1–3 m wide. Three different types of molecular markers [allozymes, mitochondrial DNA (mtDNA) and microsatellites] consistently indicated partial reproductive isolation between the RB and the SU ecotypes at a particular site. However, each ecotype was related more closely to the other ecotype from the same site than to the same ecotype from another site further along the Galician coast (25–77 km away). These findings supported earlier results based solely on allozyme variation and we could now reject the possibility that selection produced these patterns. The patterns of genetic variation supported a nonallopatric model in which the ecotypes are formed independently at each site by parallel evolution and where the reproductive barriers are a byproduct of divergent selection for body size. We argue that neither our laboratory hybridization experiments nor our molecular data are compatible with a model based on allopatric ecotype formation, secondary overlap and introgression.

Repeated evolution of reproductive isolation in a marine snail: unveiling mechanisms of speciation.

Distinct ecotypes of the snail Littorina saxatilis, each linked to a specific shore microhabitat, form a mosaic-like pattern with narrow hybrid zones in between, over which gene flow is 10–30% of within-ecotype gene flow. Multi-locus comparisons cluster populations by geographic affinity independent of ecotype, while loci under selection group populations by ecotype. The repeated occurrence of partially reproductively isolated ecotypes and the conflicting patterns in neutral and selected genes can either be explained by separation in allopatry followed by secondary overlap and extensive introgression that homogenizes neutral differences evolved under allopatry, or by repeated evolution in parapatry, or in sympatry, with the same ecotypes appearing in each local site. Data from Spain, the UK and Sweden give stronger support for a non-allopatric model of ecotype formation than for an allopatric model. Several different non-allopatric mechanisms can, however, explain the repeated evolution of the ecotypes: (i) parallel evolution by new mutations in different populations; (ii) evolution from standing genetic variation; and (iii) evolution in concert with rapid spread of new positive mutations among populations inhabiting similar environments. These models make different predictions that can be tested using comprehensive phylogenetic information combined with candidate loci sequencing.