Experimental Evolution Across Different Thermal Regimes Yields Genetic Divergence in Recombination Fraction But No Divergence in Temperature-Associated Plastic Recombination

Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. Cyclical environmental conditions have also been shown to yield evolved increases in recombination frequency. Here were use a panel of replicated experimental evolution populations of D. melanogaster to test whether variable environments favor enhanced plasticity in recombination rate and/or increased recombination rate in response to temperature. In contrast to expectation, we find no evidence for either enhanced plasticity in recombination or increased rates of recombination in the variable environment lines. Our data confirm a role of temperature in mediating recombination fraction in D. melanogaster, and indicate that recombination is genetically and plastically depressed under lower temperatures. Our data further suggest that the genetic architectures underlying plastic recombination and population-level variation in recombination rate are likely to be distinct.

Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector

Motivation: The loci-ordering, based on two-point recombination fractions for a pair of loci, is the most important step in constructing a reliable and fine genetic map.Results: Using the concept from complex graph theory, here we propose a Laplacian ordering approach which uncovers the loci-ordering of multiloci simultaneously. The algebraic property for a Fiedler vector of a Laplacian matrix, constructed from the recombination fraction of the loci-ordering for 26 loci of barley chromosome IV, 846 loci of Arabidopsisthaliana and 1903 loci of Malus domestica, together with the variable threshold uncovers their loci-orders. It offers an alternative yet robust approach for ordering multiloci.Availability and implementation : Source code program with data set is available as supplementary data and also in a software category of the website (http://biophysics.dgist.ac.kr)Contact: [email protected] or [email protected] information: Supplementary data are available at Bioinformatics online.

On the bias of recombination fractions, Kosambi's and Haldane's distances based on frequencies of gametes

The estimation of recombination frequencies is a crucial step in genetic mapping. For the construction of linkage maps, nonadditive recombination fractions must be transformed into additive map distances. Two of the most commonly used transformations are Kosambi’s and Haldane’s mapping functions. This paper reports on the calculation of the bias associated with estimation of recombination fractions, Kosambi’s distances, and Haldane’s distances. I calculated absolute and relative biases numerically for a wide range of recombination fractions and sample sizes. I assumed that the ratio of recombinant gametes to the total number of gametes can be adequately represented by a binomial function. I found that the bias in recombination fraction estimates is negative, i.e., the estimator is an underestimate. However, significant values were only obtained when recombination fractions were large and sample sizes were small. The relevant estimates of recombination fractions were, therefore, nearly unbiased. Haldane’s and Kosambi’s distances were found to be strongly biased, with positive bias for the most interesting values of recombination fractions and sample sizes. The bias of Kosambi’s distance was considerably smaller than the bias of Haldane’s distance.