Identification of outliers in a genomic scan for selection along environmental gradients in the bamboo locust, Ceracris kiangsu.

Guo-Fang Jiang,Zhou Fan,Xiao-Jing Feng

doi:10.1038/srep13758

Abstract

Identification of loci under divergent selection is a key step in understanding the evolutionary process because those loci are responsible for the genetic variations that affect fitness in different environments. Understanding how environmental forces give rise to adaptive genetic variation is a challenge in pest control. Here, we performed an amplified fragment length polymorphism (AFLP) genome scan in populations of the bamboo locust, Ceracris kiangsu, to search for candidate loci that are influenced by selection along an environmental gradient in southern China. In outlier locus detection, loci that demonstrate significantly higher or lower among-population genetic differentiation than expected under neutrality are identified as outliers. We used several outlier detection methods to study the features of C. kiangsu, including method DFDIST, BayeScan, and logistic regression. A total of 97 outlier loci were detected in the C. kiangsu genome with very high statistical supports. Moreover, the results suggested that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, humidity and sunshine. These findings illustrate that divergent selection and potential local adaptation are prevalent in locusts despite seemingly high levels of gene flow. Thus, we propose that native environments in each population may induce divergent natural selection.

Highlights

For genotyping large populations for many markers, including single nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs), comparative anchor tagged sequences (CATs), and Expressed Sequence Tags (ESTs), have been developed
SNPs have been widely used to identify genome-wide loci by environment associations in model organisms[6], we concentrated on the utility of AFLP markers because they can be applied to non-model organisms and used to generate hundreds of potential loci widely distributed across the genome[7]
Our objectives were to (1) test whether C. kiangsu populations adapted to local environmental conditions due to adaptive divergence and display genomic signatures of divergent selection and (2) determine the environmental factors involved in local adaptation by explorative landscape genetic analysis

Summary

Introduction

For genotyping large populations for many markers, including single nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs), comparative anchor tagged sequences (CATs), and Expressed Sequence Tags (ESTs), have been developed. We applied the recently developed Samβ ada[14] method to detect signatures of natural selection in locusts genotyped with AFLP markers. The idea behind this individual-based method is to correlate marker occurrence with environmental data in an allele distribution model, which uses geo-referenced environmental data and geo-referenced individual molecular genetic data. Genome scans used in parallel with environmental data provide distinct clues for selective forces that act on molecular markers of adaptive relevance in the real landscape[17] and will complement and strengthen robustness of the final set of loci identified as potentially under selection[18]. Fan et al previously reported that this species has low levels of genetic structure and relatively high gene flow[17], suggesting shallow evolutionary trajectories and limited or absent adaptive divergence among local populations

Objectives

Methods

Results

Conclusion