J. M. Cano

Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis

Comparative studies of quantitative genetic and neutral marker differentiation have provided means for assessing the relative roles of natural selection and random genetic drift in explaining among‐population divergence. This information can be useful for our fundamental understanding of population differentiation, as well as for identifying management units in conservation biology. Here, we provide comprehensive review and meta‐analysis of the empirical studies that have compared quantitative genetic (QST) and neutral marker (FST) differentiation among natural populations. Our analyses confirm the conclusion from previous reviews – based on ca. 100% more data – that the QST values are on average higher than FST values [mean difference 0.12 (SD 0.27)] suggesting a predominant role for natural selection as a cause of differentiation in quantitative traits. However, although the influence of trait (life history, morphological and behavioural) and marker type (e.g. microsatellites and allozymes) on the variance of the difference between QST and FST is small, there is much heterogeneity in the data attributable to variation between specific studies and traits. The latter is understandable as there is no reason to expect that natural selection would be acting in similar fashion on all populations and traits (except for fitness itself). We also found evidence to suggest that QST and FST values across studies are positively correlated, but the significance of this finding remains unclear. We discuss these results in the context of utility of the QST–FST comparisons as a tool for inferring natural selection, as well as associated methodological and interpretational problems involved with individual and meta‐analytic studies.

Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks

Comparisons of neutral marker and quantitative trait divergence can provide important insights into the relative roles of natural selection and neutral genetic drift in population differentiation. We investigated phenotypic and genetic differentiation among Fennoscandian threespine stickleback (Gasterosteus aculeatus) populations, and found that the highest degree of differentiation occurred between sea and freshwater habitats. Within habitats, morphological divergence was highest among the different freshwater populations. Pairwise phenotypic and neutral genetic distances among populations were positively correlated, suggesting that genetic drift may have contributed to the morphological differentiation among habitats. On the other hand, the degree of phenotypic differentiation (PST) clearly surpassed the neutral expectation set by FST, suggesting a predominant role for natural selection over genetic drift as an explanation for the observed differentiation. However, separate PST/FST comparisons by habitats revealed that body shape divergence between lake and marine populations, and even among marine populations, can be strongly influenced by natural selection. On the other hand, genetic drift can play an important role in the differentiation among lake populations.

Dynamic Averaged and Simplified Models for MMC-Based HVDC Transmission Systems

Voltage-source converter (VSC) technologies are rapidly evolving and increasing the range of applications in a variety of fields within the power industry. Existing two- and three-level VSC technologies are being superseded by the new modular multilevel converter (MMC) technology for HVDC applications. The computational burden caused by detailed modeling of MMC-HVDC systems in electromagnetic transient-type (EMT-type) programs complicates the simulation of transients when such systems are integrated into large networks. This paper develops and compares different types of models for efficient and accurate representation of MMC-HVDC systems. The results show that the use of a specific type of model will depend on the conducted analysis and required accuracy.

Identifying footprints of directional and balancing selection in marine and freshwater three‐spined stickleback (Gasterosteus aculeatus) populations

Natural selection is expected to leave an imprint on the neutral polymorphisms at the adjacent genomic regions of a selected gene. While directional selection tends to reduce within‐population genetic diversity and increase among‐population differentiation, the reverse is expected under balancing selection. To identify targets of natural selection in the three‐spined stickleback (Gasterosteus aculeatus) genome, 103 microsatellite and two indel markers including expressed sequence tags (EST) and quantitative trait loci (QTL)‐associated loci, were genotyped in four freshwater and three marine populations. The results indicated that a high proportion of loci (14.7%) might be affected by balancing selection and a lower proportion (2.8%) by directional selection. The strongest signatures of directional selection were detected in a microsatellite locus and two indel markers located in the intronic regions of the Eda‐gene coding for the number of lateral plates. Yet, other microsatellite loci previously found to be informative in QTL‐mapping studies revealed no signatures of selection. Two novel microsatellite loci (Stn12 and Stn90) located in chromosomes I and VIII, respectively, showed signals of directional selection and might be linked to genomic regions containing gene(s) important for adaptive divergence. Although the coverage of the total genomic content was relatively low, the predominance of balancing selection signals is in agreement with the contention that balancing, rather than directional selection is the predominant mode of selection in the wild.

Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus) revealed by microsatellites

To assess the population genetic structure of the three‐spined stickleback, Gasterosteus aculeatus, variability at 18 microsatellite loci was examined in 1724 individuals from 74 locations covering most of the species distribution range in Europe. The results revealed high overall degree of differentiation (FST = 0.21) but contrasting level of divergence and genetic variability between habitat types. Marine populations were genetically relatively uniform even across great geographical distances as compared to substantial differentiation among freshwater populations. Analysis of molecular variance indicated low but significant (2.7%) variation in allele frequencies between geographical regions, but a negligible effect of habitat type (0.2%). The phylogenetic pattern was not explained by habitat type, but a weak signal of populations clustering according to geographical or water system origin was found. The results support the view that three‐spined stickleback marine ancestors colonized northern European fresh waters during the postglacial marine submergence c. 10 000 years ago, whereas in the Mediterranean region colonization probably dates back to the Pleistocene. The independent origins of river and lake populations indicate that they originate from multiple colonizations rather than sharing common ancestry. In the continuous marine environment, the low degree of differentiation among populations can be explained by gene flow among subpopulations and large effective population size buffering divergence in neutral markers. In contrast, among postglacially established freshwater populations differentiation appears to be driven by genetic drift and isolation. The stepwise mutations appear to have contributed to the population differentiation in the southern part of the three‐spined stickleback distribution range.

POPULATION DIFFERENTIATION IN G MATRIX STRUCTURE DUE TO NATURAL SELECTION IN RANA TEMPORARIA

The additive genetic variance-covariance matrix (G) is a concept central to discussions about evolutionary change over time in a suite of traits. However, at the moment we do not know how fast G itself changes as a consequence of selection or how sensitive it is to environmental influences. We investigated possible evolutionary divergence and environmental influences on G using data from a factorial common-garden experiment where common frog (Rana temporaria) tadpoles from two divergent populations were exposed to three different environmental treatments. G-matrices were estimated using an animal model approach applied to data from a NCII breeding design. Matrix comparisons using both Flury and multivariate analysis of variance methods revealed significant differences in G matrices both between populations and between treatments within populations, the former being generally larger than the latter. Comparison of levels of population differentiation in trait means using Q(ST) indices with that observed in microsatellite markers (F(ST)) revealed that the former values generally exceeded the neutral expectation set by F(ST). Hence, the results suggest that intraspecific divergence in G matrix structure has occurred mainly due to natural selection.

Female-Biased Expression on the X Chromosome as a Key Step in Sex Chromosome Evolution in Threespine Sticklebacks

Given that the genome of males and females are almost identical with the exception of genes on the Y (or W) chromosome or sex-determining alleles (in organisms without sex chromosomes), it is likely that many downstream processes resulting in sexual dimorphism are produced by changes in regulation. In early stages of sex chromosome evolution, as the Y-chromosome degenerates, gene expression should be significantly impacted for genes residing on the sex chromosome pair as regulatory mutations accumulate. However, this has rarely been examined because most model organisms have clearly diverged sex chromosomes. Fish provide a unique opportunity to examine the evolution of sex chromosomes because genetic sex determination has evolved quite recently in some groups of fish. We compared sex-specific transcription in threespine stickleback (Gasterosteus aculeatus) liver tissue using a long-oligo microarray. Of the 1,268 genes that were differentially expressed between sexes, a highly significant proportion (23%) was concentrated on chromosome 19, corresponding to the recently described nascent sex chromosomes. The sex-biased genes are enriched for different functional categories in males and females, although there is no specific functional enrichment on the sex chromosomes. Female-biased genes are concentrated at one end of the sex chromosome, corresponding to a deletion in the Y, suggesting a lack of global dosage compensation. Prior research on threespine sticklebacks has demonstrated various degrees of dissimilarity in upstream regions of genes on the Y providing a potential mechanism for the observed patterns of female-biased expression. We hypothesize that degeneration of the Y chromosome results in regulatory mutations that create a sex-specific expression pattern and that this physical concentration of sex-biased expression on the nascent sex chromosome may be a key feature characterizing intermediate phases of sex chromosome evolution.

A Bayesian framework for comparative quantitative genetics

Bayesian approaches have been extensively used in animal breeding sciences, but similar approaches in the context of evolutionary quantitative genetics have been rare. We compared the performance of Bayesian and frequentist approaches in estimation of quantitative genetic parameters (viz. matrices of additive and dominance variances) in datasets typical of evolutionary studies and traits differing in their genetic architecture. Our results illustrate that it is difficult to disentangle the relative roles of different genetic components from small datasets, and that ignoring, e.g. dominance is likely to lead to biased estimates of additive variance. We suggest that a natural summary statistic for G-matrix comparisons can be obtained by examining how different the underlying multinormal probability distributions are, and illustrate our approach with data on the common frog (Rana temporaria). Furthermore, we derive a simple Monte Carlo method for computation of fraternity coefficients needed for the estimation of dominance variance, and use the pedigree of a natural Siberian jay (Perisoreus infaustus) population to illustrate that the commonly used approximate values can be substantially biased.

Genetic evidence for male‐biased dispersal in the three‐spined stickleback (Gasterosteus aculeatus)

Sex‐biased dispersal is capable of generating population structure in nonisolated populations and may affect adaptation processes when selective conditions differ among populations. Intrasexual competition for local resources and/or mating opportunities predicts a male‐biased dispersal in polygynous species and a female bias in monogamous species. The patterns of sex‐biased dispersal in birds and mammals are well explained by their respective mating systems, but the picture emerging from fish studies is still mixed. Using neutral genetic markers, we investigated whether there is any evidence for sex‐biased dispersal among Baltic Sea populations of the three‐spined stickleback (Gasterosteus aculeatus). The null hypothesis of non sex‐biased dispersal was rejected in favour of male‐biased dispersal in this species. As the three‐spined stickleback has a polygynous mating system, the observed male bias in dispersal is consistent with the hypothesis that local mate competition might drive the observed pattern. Although more research both on the proximate and ultimate causes behind the observed pattern is needed, our results serve as a first step towards understanding patterns of sex‐biased dispersal in this species.

Bayesian approaches in evolutionary quantitative genetics

The study of evolutionary quantitative genetics has been advanced by the use of methods developed in animal and plant breeding. These methods have proved to be very useful, but they have some shortcomings when used in the study of wild populations and evolutionary questions. Problems arise from the small size of data sets typical of evolutionary studies, and the additional complexity of the questions asked by evolutionary biologists. Here, we advocate the use of Bayesian methods to overcome these and related problems. Bayesian methods naturally allow errors in parameter estimates to propagate through a model and can also be written as a graphical model, giving them an inherent flexibility. As packages for fitting Bayesian animal models are developed, we expect the application of Bayesian methods to evolutionary quantitative genetics to grow, particularly as genomic information becomes more and more associated with environmental data.