Biology subjects

Allen, C.

Publications and source records attributed to Allen, C..

4 recordsLinked to original sources

bioRxiv2018

DGEN: A Test Statistic for Detection of General Introgression Scenarios

When two species hybridize, one outcome is the integration of genetic material from one species into the genome of the other, a process known as introgression. Detecting introgression in genomic data is a very important question in evolutionary biology. However, given that hybridization occurs between closely related species, a compli-cating factor for introgression detection is the presence of incomplete lineage sorting, or ILS. The D-statistic, famously referred to as the \"ABBA-BABA\" test, was pro-posed for introgression detection in the presence of ILS in data sets that consist of four genomes. More recently, DFOIL--a set of statistics--was introduced to extend the D-statistic to data sets of five genomes.\n\nThe major contribution of this paper is demonstrating that the invariants underly-ing both the D-statistic and DFOIL can be derived automatically from the probability mass functions of gene tree topologies under the null species tree model and alterna-tive phylogenetic network model. Computational requirements aside, this automatic derivation provides a way to generalize these statistics to data sets of any size and with any scenarios of introgression. We demonstrate the accuracy of the general statistic, which we call DGEN, on simulated data sets with varying rates of introgression, and apply it to an empirical data set of mosquito genomes.\n\nWe have implemented DGEN and made it available, both as a graphical user interface tool and as a command-line tool, as part of the freely available, open-source software package ALPHA (https://github.com/chilleo/ALPHA).

evolutionary biology↗

bioRxiv2018

Predicting and Analyzing the Response to Selection on Correlated Characters

The breeders equation generally provides robust predictions for the short-term evolution of single characters. When selection targets two or more characters simultaneously, there are often large discrepancies between predicted and observed responses. We assessed how well this standard model predicts responses to bivariate selection on wing color pattern characteristics in the tropical butterfly Bicyclus anynana. In separate laboratory selection experiments, two sets of serially repeated eyespots were subjected to ten generations of concerted and antagonistic selection for either size or color composition. We compared predicted and actual selection responses over successive generations, using the phenotypic data, selection differentials, and estimates of the genetic variance-covariance matrix G. We found differences in the precision of predictions between directions of selection but did not find any evidence of systematic biases in our predictions depending on the direction of selection. Our investigation revealed significant environmental effects on trait evolution across generations. When these were accounted for, predictions using the standard model improved considerably. In the experiment on eyespot size, secondary splitting of selection lines allowed the estimation of changes in G after nine generations of selection. Changes were not in general agreement with expectations from the breeders equation. A contour plot of prediction errors across trait space suggests that directional epistasis in the eyespot genotype-phenotype map might occur but estimates of changes in G are too model-dependent to verify whether they agree with that hypothesis. Altogether, our results underscore the need for quantitative genetics to investigate and estimate potential effects of multivariate non-linear genotype-phenotype maps and of environmental effects on G.

evolutionary biology↗

bioRxiv2017

Partial restoration of mutational robustness after addition of genetic polymorphism and in the presence of sexual selection

The interaction between mutational (i.e. genetic) robustness, cryptic genetic variation and epistasis is currently under much debate, as is the question whether mutational robustness evolved under direct selection or as a by-product of environmental robustness. Here we report that mutational robustness was restored in a mutant line of the butterfly Bicyclus anynana after the spontaneous mutation, comet, appeared in a genetically polymorphic wild type population. The comet mutation modified two phenotypic traits known to be under sexual selection in this butterfly: the dorsal forewing eyespot, which is normally round, but became comet-shaped, and the androconia, the structures producing the male sex pheromone, which were reduced in size. The comet mutant line remained phenotypically stable for [~]7 seven years, but when outcrossed to the genetically polymorphic wild type population, the outcrossed comet line surprisingly recovered the wild type phenotype within 8 generations. This suggests that mutational robustness against the comet mutation was recovered in the comet outcrossed line by epistatic interactions with the genetic polymorphism originating from wild types. The extent of wild type phenotype recovery in the comet outcrossed line was trait- and developmental temperature-dependent, such that mutational robustness was partially recovered at high, but not at low developmental temperatures. We hypothesized that sexual selection through mate choice, which is sex-reversed between developmental temperatures in this butterfly, could produce mutational robustness at a high (but not at a low) temperature. Females are the choosy sex and exert stabilizing or directional selection on male secondary sexual wing traits but only at higher temperatures. Male mating success experiments under semi-natural conditions then revealed that males with the typical comet mutant phenotype suffered from lower mating success compared to wild type males, while mating success of comet males resembling wild types was partially restored. Altogether, we document the roles of cryptic genetic variation and epistasis in restoration of mutational robustness against a spontaneous mutation with known fitness effects, and we provide experimental evidence, for the first time to our knowledge, that sexual selection can produce mutational robustness.

evolutionary biology↗

bioRxiv2017

The separation of auditory experience and the temporal structure of MEG recorded brain activity

Do brain oscillations limit the temporal dynamics of experience? This pre-registered study used the separation of auditory stimuli to track perceptual experience and related this to oscillatory activity using magnetoencephalography. The rates at which auditory stimuli could be individuated matched the rates of oscillatory brain activity. Stimuli also entrained brain activity at the frequencies at which they were presented and a progression of high frequency gamma band events appeared to predict successful separation. These findings support a generalised function for brain oscillations, across frequency bands, in the alignment of activity to delineate representations.

physiology↗