Armando Caballero

Developments in the prediction of effective population size.

Effective population size is a key parameter in evolutionary and quantitative genetics because it measures the rate of genetic drift and inbreeding. Predictive equations of effective size under a range of circumstances and some of their implications are reviewed in this paper. Derivations are made for the simplest cases, and the inter-relations between different formulae and methods are discussed.

Interrelations between effective population size and other pedigree tools for the management of conserved populations

Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.

Analysis of genetic diversity for the management of conserved subdivided populations

Recent studies in the literature have appliedphylogenetic methods based on genetic distancesto set priorities for conservation of domesticanimal breeds. While these methods may beappropriate for between-species conservation,they are clearly inappropriate forwithin-species breed conservation, because theyignore within-breed variation. In this paper weshow the basic tools to analyse geneticdiversity in subdivided populations withinspecies, and illustrate the errors incurred byapplying methods based exclusively on geneticdistances. We also show that maximisation ofgenetic diversity (minimisation of coancestryor kinship) is equivalent to maximisation ofeffective population size, as in undividedpopulations, and derive a generalisation ofprevious equations for the prediction ofeffective size. Finally, we discuss thestrategies for conservation in the light of thetheory.

Developments in predicting the effective size of subdivided populations

The effective population size is the parameter that summarizes the magnitude of genetic drift and increase in inbreeding occurring in a population. In this paper, developments in the prediction equations for the effective size of populations subdivided under various models are reviewed, and extensions are made in several cases. Derivations are shown for some simple models, and the relationships among these equations and with those for a single unsubdivided population are discussed. The effect of population subdivision on neutral genetic variation and its implications are explained.

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

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.

Systems of mating to reduce inbreeding in selected populations

Stochastic simulation is used to compare different systems of mating to reduce rates of inbreeding in selection programmes with phenotypic or animal model best linear unbiased prediction (BLUP) evaluation. Compensatory mating (the mating between individuals from the largest selected families to individuals from the smallest) turns out to be proportionately about 0-30 more effective than minimum coancestry matings for situations with low rates of inbreeding, such as phenotypic selection or high population size, although the advantage is less apparent if common environmental effects are important. A modification of this system of mating is proposed which can be applied for overlapping generations, and this is shown to reduce rates of inbreeding proportionately by about 0-50 more than for discrete generations. Under high inbreeding, however, such as for BLUP selection and small population size, minimum coancestry matings, or even avoidance of sib matings are more effective. A procedure combining compensatory and minimum coancestry matings is also simulated and gives the largest reductions in the rate of inbreeding. The effects of these and other systems of mating on the rate of inbreeding are shown to occur through a reduction in the cumulative effect of selection and a deviation from Hardy-Weinberg proportions.

PHYLOGENETIC EVIDENCE FOR MULTIPLE SYMPATRIC ECOLOGICAL DIVERSIFICATION IN A MARINE SNAIL

Abstract 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.