Genomic analysis of the four ecologically distinct cactus host populations of Drosophila mojavensis

Carson W Allan,Luciano M Matzkin

doi:10.1186/s12864-019-6097-z

Carson W Allan, Luciano M Matzkin

Open Access

https://doi.org/10.1186/s12864-019-6097-z

Copy DOI

Abstract

BackgroundRelationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilic Drosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues. Drosophila mojavensis is composed of four isolated populations across the deserts of western North America and each population has adapted to utilize different cacti that are chemically, nutritionally, and structurally distinct.ResultsHigh coverage Illumina sequencing was performed on three previously unsequenced populations of D. mojavensis. Genomes were assembled using the previously sequenced genome of D. mojavensis from Santa Catalina Island (USA) as a template. Protein coding genes were aligned across all four populations and rates of protein evolution were determined for all loci using a several approaches.ConclusionsLoci that exhibited elevated rates of molecular evolution tend to be shorter, have fewer exons, low expression, be transcriptionally responsive to cactus host use and have fixed expression differences across the four cactus host populations. Fast evolving genes were involved with metabolism, detoxification, chemosensory reception, reproduction and behavior. Results of this study give insight into the process and the genomic consequences of local ecological adaptation.

Highlights

Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise
In this study we explore the link between ecology and patterns of genomewide sequence variation in D. mojavensis, a fly endemic to the southwestern United States and northwestern Mexico that has become a model for the understanding of the genetics of adaptation [27]
In this first ever genome-wide analysis of the pattern of molecular evolution across the four ecologically distinct populations of D. mojavensis, we have begun to describe the genomic consequences of the adaptation of these cactophilic Drosophila to their respective environments

Summary

Introduction

Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilic Drosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues. By examining changes in the genetic code both at the level of individual genes and at the whole-genome level it is possible to gain a better understanding of how local ecological conditions can shape the pattern of variation within and between ecologically distinct populations [1, 2]. Host preferences and performance in this system facilitates the genetic and genomic isolation observed between the host populations, as each prefers a different microenvironment and likely does not interact and hybridize with members of the other population [11, 12]

Methods

Results

Discussion

Conclusion