Biology subjects

Lappo, E.

Publications and source records attributed to Lappo, E..

3 recordsLinked to original sources

bioRxiv2025

Coalescent theory of the {psi} directionality index

The{psi} directionality index was introduced by Peter & Slatkin (Evolution 67: 3274-3289, 2013) to infer the direction of range expansions from single-nucleotide polymorphism variation. Computed from the joint site frequency spectrum for two populations,{psi} uses shared genetic variants to measure the difference in the amount of genetic drift experienced by the populations, associating excess drift with greater distance from the origin of the range expansion. Although{psi} has been successfully applied in natural populations, its statistical properties have not been well understood. In this paper, we define {Psi} as a random variable originating from a coalescent process in a two-population demography. For samples consisting of a pair of diploid genomes, one from each of two populations, we derive expressions for moments [E] [{Psi}k] for standard parameterizations of bottlenecks during a founder event. For the expectation [E][{Psi}], we identify parameter combinations that represent distinct demographic scenarios yet yield the same value of [E][{Psi}]. We also show that the variance [V][{Psi}] increases with the time since the bottleneck and bottleneck severity, but does not depend on the size of the ancestral population; the ancestral population size affects{psi} computed from many biallelic loci only through its contribution to the total number of loci available for the computation. Finally, we analyze the values of [E][{Psi}] computed from existing demographic models of Drosophila melanogaster and compare them with empirically computed{psi} . Our work builds the foundation for theoretical treatments of the{psi} index and can help in evaluating its behavior in empirical applications. SummaryThe statistic known as the "directionality index" examines variants shared between two populations with a goal of identifying which population has experienced a greater amount of genetic drift. This study develops theoretical predictions for the directionality index in coalescent models of pairs of populations descended from a common ancestral population. It determines the influence of bottlenecks, population growth, and population sizes on the directionality index. In Drosophila melanogaster, patterns in genomic data accord with the direction of the model predictions, with{psi} suggesting a higher level of drift in European than in African populations.

genetics↗

bioRxiv2024

Dominance reversal protects large-effect resistance polymorphisms in temporally varying environments

Large-effect functional genetic variation is commonly found in natural populations, even though natural selection should erode such variants. Theory suggests that under fluctuating selective pressures, beneficial reversal of dominance - where alleles are dominant when beneficial and recessive when deleterious - can protect these loci from selection, allowing them to persist. However, empirical evidence for this mechanism remains elusive because testing requires direct measurements of selection and dominance in natural conditions. Here, we show that insecticide-resistant alleles at the Ace locus in Drosophila melanogaster persist worldwide at intermediate frequencies and exhibit beneficial reversal of dominance. By combining laboratory and large-scale field mesocosm experiments with insecticide manipulation, and mathematical modeling, we show that the benefits of the resistant Ace alleles are dominant while their fitness costs recessive. We further show that fluctuating insecticide selection generates chromosome-scale genomic perturbations at sites linked to the resistant Ace alleles, revealing broader genomic consequences of this mechanism. Overall, our results suggest that beneficial reversal of dominance contributes to the maintenance of functional genetic variation and impacts patterns of genomic diversity via linked fluctuating selection.

evolutionary biology↗

bioRxiv2022

Approximations to the expectations and variances of ratios of tree properties under the coalescent

Properties of gene genealogies such as tree height (H), total branch length (L), total lengths of external (E) and internal (I) branches, mean length of basal branches (B), and the underlying coalescence times (T) can be used to study population-genetic processes and to develop statistical tests of population-genetic models. Uses of tree features in statistical tests often rely on predictions that depend on pairwise relationships among such features. For genealogies under the coalescent, we provide exact expressions for Taylor approximations to expected values and variances of ratios Xn/Yn, for all 15 pairs among the variables {Hn, Ln, En, In, Bn, Tk}, considering n leaves and 2 [≤] k [≤] n. For expected values of the ratios, the approximations match closely with empirical simulation-based values. The approximations to the variances are not as accurate, but they generally match simulations in their trends as n increases. Although En has expectation 2 and Hn has expectation 2 in the limit as n [->] {infty}, the approximation to the limiting expectation for En/Hn is not 1, instead equaling{pi} 2/3 - 2 {approx} 1.28987. The new approximations augment fundamental results in coalescent theory on the shapes of genealogical trees.

genetics↗