Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

Gilks, William P.; Pennell, Tanya M.; Flis, Ilona; Webster, Matthew T.; Morrow, Edward H.

doi:10.12688/f1000research.9912.1

Cited by 3 publications

(1 citation statement)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This method has been recently employed in D. melanogaster and allowed to combine cytological screens with whole genome sequencing to generate and analyze fully phased genomes with known inversion polymorphisms [33]. Additionally, this approach was used to sequence and characterize a panel of more than 200 wild-type chromosomes from a North American D. melanogaster population [34].…”

Section: Genomic Sequencing and Phasing Of Hemiclonesmentioning

confidence: 99%

Population Genomics on the Fly: Recent Advances in Drosophila

Haudry

Laurent

Kapun

2020

Methods in Molecular Biology

View full text Add to dashboard Cite

Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its world-wide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this bookchapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of non-coding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.

show abstract

Section: Genomic Sequencing and Phasing Of Hemiclonesmentioning

confidence: 99%

Population Genomics on the Fly: Recent Advances in Drosophila

Haudry

Laurent

Kapun

2020

Methods in Molecular Biology

View full text Add to dashboard Cite

show abstract

Sex differences in deleterious mutational effects in Drosophila melanogaster: combining quantitative and population genetic insights

2021

View full text Add to dashboard Cite

Fitness effects of deleterious mutations can differ between females and males due to: (i) sex differences in the strength of purifying selection; and (ii) sex differences in ploidy. Although sex differences in fitness effects have important broader implications (e.g., for the evolution of sex and lifespan), few studies have quantified their scope. Those that have belong to one of two distinct empirical traditions: (i) quantitative genetics, which focusses on multi-locus genetic variances in each sex, but is largely agnostic about their genetic basis; and (ii) molecular population genetics, which focusses on comparing autosomal and X-linked polymorphism, but is poorly suited for inferring contemporary sex differences. Here we combine both traditions to present a comprehensive analysis of female and male adult reproductive fitness among 202 outbred, laboratory-adapted, hemiclonal genomes of Drosophila melanogaster. While we find no clear evidence for sex differences in the strength of purifying selection, sex differences in ploidy generate multiple signals of enhanced purifying selection for X-linked loci. These signals are present in quantitative genetic metrics—i.e., a disproportionate contribution of the X to male (but not female) fitness variation—and population genetic metrics—i.e., steeper regressions of an allele’s average fitness effect on its frequency, and proportionally less nonsynonymous polymorphism on the X than autosomes. Fitting our data to models for both sets of metrics, we infer that deleterious alleles are partially recessive. Given the often-large gap between quantitative and population genetic estimates of evolutionary parameters, our study showcases the benefits of combining genomic and fitness data when estimating such parameters.

show abstract

Patterns of Genomic Differentiation in the Drosophila nasuta Species Complex

Mai

Nalley

Bachtrog

2019

Molecular Biology and Evolution

View full text Add to dashboard Cite

The Drosophila nasuta species complex contains over a dozen recently diverged species that are distributed widely across South-East Asia, and which shows varying degrees of pre- and postzygotic isolation. Here, we assemble a high-quality genome for D. albomicans using single-molecule sequencing and chromatin conformation capture, and draft genomes for 11 additional species and 67 individuals across the clade, to infer the species phylogeny and patterns of genetic diversity in this group. Our assembly recovers entire chromosomes, and we date the origin of this radiation ∼2 Ma. Despite low levels of overall differentiation, most species or subspecies show clear clustering into their designated taxonomic groups using population genetics and phylogenetic methods. Local evolutionary history is heterogeneous across the genome, and differs between the autosomes and the X chromosome for species in the sulfurigaster subgroup, likely due to autosomal introgression. Our study establishes the nasuta species complex as a promising model system to further characterize the evolution of pre- and postzygotic isolation in this clade.

show abstract

Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

Cited by 3 publications

References 19 publications

Population Genomics on the Fly: Recent Advances in Drosophila

Population Genomics on the Fly: Recent Advances in Drosophila

Sex differences in deleterious mutational effects in Drosophila melanogaster: combining quantitative and population genetic insights

Patterns of Genomic Differentiation in the Drosophila nasuta Species Complex

Contact Info

Product

Resources

About