Maximum Likelihood Estimation of Fitness Components in Experimental Evolution

Abstract

Estimating fitness differences between allelic variants is a central goal of experimental evolution. Current methods for inferring such differences from allele frequency time series typically assume that the effects of selection can be described by a fixed selection coefficient. However, fitness is an aggregate of several components including mating success, fecundity, and viability. Distinguishing between these components could be critical in many scenarios. Here, we develop a flexible maximum likelihood framework that can disentangle different components of fitness from genotype frequency data, and estimate them individually in males and females. As a proof-of-principle, we apply our method to experimentally evolved cage populations of Drosophila melanogaster, in which we tracked the relative frequencies of a loss-of-function and wild-type allele of yellow. This X-linked gene produces a recessive yellow phenotype when disrupted and is involved in male courtship ability. We find that the fitness costs of the yellow phenotype take the form of substantially reduced mating preference of wild-type females for yellow males, together with a modest reduction in the viability of yellow males and females. Our framework should be generally applicable to situations where it is important to quantify fitness components of specific genetic variants, including quantitative characterization of the population dynamics of CRISPR gene drives.

The yellow gene influences Drosophila male mating success through sex comb melanization

“…It remains unclear how D. willistoni males (and males of other species without sex combs) are able to efficiently grasp females prior to copulation (Video 16). However, differences in females might be part of the answer, as D. melanogaster y 1 mutant males are able to mate with y 1 mutant females at rates similar to wild-type males (Bastock, 1956; Dow, 1976; Heisler, 1984; Liu et al, 2019; Figure 4—figure supplement 3A, FET, p=1). That said, removing all melanin from D. melanogaster sex combs by knocking down Laccase-2 reduced mating efficiency with y 1 females (Figure 4—figure supplement 3B, FET, p=0.02 and 0.0001), suggesting that the brown melanin remaining in y 1 sex-combs (Figure 4B) played a role in the mating success of y 1 males with y 1 females.…”

Ecologically relevant arsenic exposure alters female mate preference and anxiety-like behavior in Betta splendens

“…Loss of female mate preference may have significant evolutionary consequences, as females across a variety of taxa have been shown to choose male traits that confer fitness benefits [43, 44, 45, 46]. The consequence of the loss in female preference for red color observed in this study is uncertain, however, there is evidence from other studies that the preference for red coloration may provide important benefits.…”

The complete chloroplast genome of Ilex ‘Emily Bruner’, Ilex cornuta ‘Burfordii’ × Ilex latifolia (Aquifoliaceae)

“…To reveal the phylogenetic position of 'Emily Bruner' with these members, a phylogenetic analysis was performed based on 10 complete cp genomes, and one taxa from Helwingia was served as outgroup. The neighbor-joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1000) were used for constructing phylogenetic trees using PhyML v3.0 (http://www.atgc-montpellier.fr/phyml/) (Liu et al 2019). The phylogenetic tree showed that 'Emily Bruner' closely related to its female parent I. cornuta species (Figure 1).…”

“…The neighbor-joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1000) were used for constructing phylogenetic trees using PhyML v3.0 ( http://www.atgc-montpellier.fr/phyml/ ) (Liu et al. 2019 ). The phylogenetic tree showed that ‘Emily Bruner’ closely related to its female parent I. cornuta species ( Figure 1 ).…”