Inheritance of litter size at birth in farmed arctic foxes (Alopex lagopus, Canidae, Carnivora)

Genetic polymorphism under cyclical selection in long-lived species: The complex effect of age structure and maternal selection

Maternal selection and overlapping generations can facilitate the stable coexistence of alleles under temporally fluctuating environment. Using mathematical models, we considered the complex effect of both factors on the maintenance of genetic polymorphism in cyclically changing environments. We concentrated on asymmetric cyclic selection, which allows describing fluctuations of environments by analogy of food resources cycles with rare peaks and prolonged decline of prey abundance. The complex effect of maternal selection and overlapping generations turned out to work as follows: although overlapping generations always tend to dilate the polymorphism region, odd and even external cycles produce different types of polymorphism regions. Maternal selection under external odd cycles extends the coexistence region comparing with classic selection. Even cycles produce a part of parameter region, where the picture changes radically, and classic selection becomes more effective in maintaining polymorphism. Our models have clear biological interpretation, because we tried to model a situation demonstrated by natural populations of arctic foxes. The litter size being a major life history trait is a sex-limited female trait. It is influenced by maternal selection with cyclical fluctuations because of oscillations in food abundance. Arctic fox is a long-lived species having an age structure. The obtained results showed that compared with the simple Mendelian inheritance in the classic model, this trait inheritance allows polymorphism to be maintained in a wider range of the parameter that characterizes the advantage of survival in a small litter. Besides, adding overlapping generations to the model further broadens the parameter space for the protected polymorphism. Thus, this study shows that maternal selection and overlapping generations increases the chances of maintaining polymorphism in populations of arctic foxes.

Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila

In many species, genomic data have revealed pervasive adaptive evolution indicated by the fixation of beneficial alleles. However, when selection pressures are highly variable along a species' range or through time adaptive alleles may persist at intermediate frequencies for long periods. So called “balanced polymorphisms” have long been understood to be an important component of standing genetic variation, yet direct evidence of the strength of balancing selection and the stability and prevalence of balanced polymorphisms has remained elusive. We hypothesized that environmental fluctuations among seasons in a North American orchard would impose temporally variable selection on Drosophila melanogaster that would drive repeatable adaptive oscillations at balanced polymorphisms. We identified hundreds of polymorphisms whose frequency oscillates among seasons and argue that these loci are subject to strong, temporally variable selection. We show that these polymorphisms respond to acute and persistent changes in climate and are associated in predictable ways with seasonally variable phenotypes. In addition, our results suggest that adaptively oscillating polymorphisms are likely millions of years old, with some possibly predating the divergence between D. melanogaster and D. simulans. Taken together, our results are consistent with a model of balancing selection wherein rapid temporal fluctuations in climate over generational time promotes adaptive genetic diversity at loci underlying polygenic variation in fitness related phenotypes.

Herein, we investigate the genomic basis of rapid adaptive evolution in response to seasonal fluctuations in the environment. We identify hundreds of polymorphisms (seasonal SNPs) that undergo dramatic shifts in allele frequency – on average between 40 and 60% – and oscillate between seasons repeatedly over multiple years, likely inducing high levels of genome-wide genetic differentiation. We provide evidence that seasonal SNPs are functional, being both sensitive to an acute frost event and associated with two stress tolerance traits. Finally, we show that some seasonal SNPs are possibly ancient balanced polymorphisms. Taken together, our results suggest that environmental heterogeneity can promote the long-term persistence of functional polymorphisms within populations that fuels fast directional adaptive response at any one time.

Unequal resource allocation among colonies produced by fission in the ant Cataglyphis cursor

How organisms allocate limited resources to reproduction is critical to their fitness. The size and number of offspring produced have been the focus of many studies. Offspring size affects survival and growth and determines offspring number in the many species where there is a trade-off between size and number. Many social insects reproduce by colony fission, whereby young queens and accompanying workers split off from a colony to form new colonies. The size of a new colony (number of workers) is set at the time of the split, and this may allow fine tuning size to local conditions. Despite the prevalence of colony fission and the ecological importance of social insects, little is known of colony fission except in honey bees. We studied colony fission in the ant Cataglyphis cursor. For clarity, "colony" and "nest" refer to colonies before and after colony fission, respectively (i.e., each colony fissions into several nests). The reproductive effort of colonies was highly variable: Colonies that fissioned varied markedly in size, and many colonies that did not fission were as large as some of the fissioning colonies. The mother queen was replaced in half of the fissioning colonies, which produced 4.0 +/- 1.3 (mean +/- SD) nests of markedly varied size. Larger fissioning colonies produced larger nests but did not produce more nests, and resource allocation among nests was highly biased. When a colony produced several nests and the mother queen was not replaced, the nest containing the mother queen was larger than nests with a young queen. These results show that the pattern of resource allocation differs between C. cursor and honey bees. They also suggest that C. cursor may follow a bet-hedging strategy with regard to both the colony size at which fission occurs and the partitioning of resources among nests. In addition, colony fission may be influenced by the age and/or condition of the mother queen, and the fact that workers allocating resources among nests have incomplete knowledge of the size and number of nests produced. These results show that the process of colony fission is more diverse than currently acknowledged and that studies of additional species are needed.

Breaking loops in large complex pedigrees

For pedigrees with multiple loops, exact likelihoods could not be computed in an acceptable time frame and thus, approximate methods are used. Some of these methods are based on breaking loops and approximations of complex pedigree likelihoods using the exact likelihood of the corresponding zero-loop pedigree. Due to ignoring loops, this method results in a loss of genetic information and a decrease in the power to detect linkage. To minimize this loss, an optimal set of loop breakers has to be selected. In this paper, we present a graph theory based algorithm for automatic selection of an optimal set of loop breakers. We propose using a total relationship between measured pedigree members as a proxy to power. To minimize the loss of genetic information, we suggest selection of such breakers whose duplication in a pedigree would be accompanied by a minimal loss of total relationship between measured pedigree members. We show that our algorithm compares favorably with other existing loop-breaker selection algorithms in terms of conservation of genetic information, statistical power and CPU time of subsequent linkage analysis. We implemented our method in a software package LOOP_EDGE, which is available at http://mga.bionet.nsc.ru/nlru/.

Two-locus epistasis with sexually antagonistic selection: a genetic Parrondo's paradox

An example is provided where, with antagonistic selection and epistatic interaction of alleles at two loci, an autosomal allele can rise in frequency, persist in the population, and even continue to fixation, despite having an apparently lower average fitness than the alternative allele, in a process similar to Parrondo's paradox.

Optimal peeling order for pedigrees with incomplete genotypic information

The likelihood approach is common in linkage analysis of large extended pedigrees. Various peeling procedures, based on the conditional independence of separate parts of a pedigree, are typically used for likelihood calculations. A peeling order may significantly affect the complexity of such calculations, particularly for pedigrees with loops or when many pedigrees members have unknown genotypes. Several algorithms have been proposed to address this problem for pedigrees with loops. However, the problem has not been solved for pedigrees without loops until now. In this paper, we suggest a new graph theoretic algorithm for optimal selection of peeling order in zero-loop pedigrees with incomplete genotypic information. It is especially useful when multiple likelihood calculation is needed, for example, when genetic parameters are estimated or linkage with multiple marker loci is tested. The algorithm can be easily introduced into the existing software packages for linkage analysis based on the Elston-Stewart algorithm for likelihood calculation. The algorithm was implemented in a software package PedPeel, which is freely available at http://mga.bionet.nsc.ru/nlru/.