From Nature to the Lab: Establishing Drosophila Resources for Evolutionary Genetics

Vítor G. Faria,Élio Sucena

doi:10.3389/fevo.2017.00061

Abstract

In recent years important tools have been developed in Drosophila to capture with the greatest possible accuracy the variation found in nature. Efforts such as the Drosophila melanogaster Genetic Reference Panel (DGRP) or the Drosophila Synthetic Population Resource Panel (DSRP) allied to the advances in whole-genome sequencing and analysis have propelled to unprecedented level our capacity to dissect the genotype-phenotype map. However, several practical problems arise upstream of these analyses starting with the collection and identification of wild specimens. These problems are dealt with in different ways by each researcher generating solutions not necessarily compatible across laboratories. Here, we provide a systematic coverage of every phase of this process based on our experience, and suggest procedures to maximize and share the generated resources potentiating future applications. We propose a detailed pipeline to guide researchers from collection in the wild to the development of a large array of molecular and genetic resources. We designed a multiplex-PCR that distinguishes sister species D. melanogaster and D. simulans and is diagnostic of the presence/absence of Wolbachia infection. These procedures may extend to other cryptic species pairs and endosymbionts. We developed a standardized protocol to create, replicate and maintain isofemale lines and outbred populations. Finally, we explore the potential of outbred populations across several applications from experimental evolution, to introgression of transgenic constructs or mutant alleles, and genomic analyses. We hope to contribute to the success in developing Drosophila resources for evolutionary genetics studies and facilitate exchanges across laboratories based on a common set of procedures.

Highlights

To study the evolution of species in a controlled and accurate way is undoubtedly a challenge
Experimental evolution can establish direct causation between selection in a given environment and the genetic and phenotypic changes observed in a population
We provide a highthroughput method by multiplex-PCR to identify the species and the individual status of Wolbachia infection that can be extended to other species

Summary

Introduction

To study the evolution of species in a controlled and accurate way is undoubtedly a challenge. The complexity of factors acting simultaneously on individuals inevitably blurs the conclusions that can be drawn To minimize this risk by facilitating the control of experimental conditions, we must bring populations from nature to the laboratory. Experimental evolution can establish direct causation between selection in a given environment and the genetic and phenotypic changes observed in a population. This powerful approach departs from the comparative method in three fundamental aspects: (i) knowledge of the ancestral state, (ii) knowledge of the adaptive trajectories in real-time, (iii) high degree of replication under controlled selection and control regimes (Gibbs et al, 1997; Magalhães and Matos, 2012; Kawecki et al, 2012)

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