SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies

Eric Pante,Pascale Garcia,Nicolas Bierne,Audrey Rohfritsch,Khalid Belkhir,Vanessa Becquet

doi:10.1371/journal.pone.0052302

Abstract

Hybrid zones are noteworthy systems for the study of environmental adaptation to fast-changing environments, as they constitute reservoirs of polymorphism and are key to the maintenance of biodiversity. They can move in relation to climate fluctuations, as temperature can affect both selection and migration, or remain trapped by environmental and physical barriers. There is therefore a very strong incentive to study the dynamics of hybrid zones subjected to climate variations. The infaunal bivalve Macoma balthica emerges as a noteworthy model species, as divergent lineages hybridize, and its native NE Atlantic range is currently contracting to the North. To investigate the dynamics and functioning of hybrid zones in M. balthica, we developed new molecular markers by sequencing the collective transcriptome of 30 individuals. Ten individuals were pooled for each of the three populations sampled at the margins of two hybrid zones. A single 454 run generated 277 Mb from which 17K SNPs were detected. SNP density averaged 1 polymorphic site every 14 to 19 bases, for mitochondrial and nuclear loci, respectively. An scan detected high genetic divergence among several hundred SNPs, some of them involved in energetic metabolism, cellular respiration and physiological stress. The high population differentiation, recorded for nuclear-encoded ATP synthase and NADH dehydrogenase as well as most mitochondrial loci, suggests cytonuclear genetic incompatibilities. Results from this study will help pave the way to a high-resolution study of hybrid zone dynamics in M. balthica, and the relative importance of endogenous and exogenous barriers to gene flow in this system.

Highlights

Understanding the adaptation of organisms to their environment is becoming a pressing matter, in the face of today’s anthropogenic pressures and rapid climate change (e.g. [1])
We present results of a transcriptomewide scan for single nucleotide polymorphisms (SNPs) with the 454 technology [26], performed in preparation for a large-scale study of the maintenance and dynamics of hybrid zones in the context of global climate change
The avalanche of data produced with the 454 platform allowed us to scan for nuclear and mitochondrial genes putatively under the influence of selection, detect about 17K SNPs, estimate their density across the genome, and pave the way to high-throughput population genetics for this species

Summary

Introduction

Understanding the adaptation of organisms to their environment is becoming a pressing matter, in the face of today’s anthropogenic pressures and rapid climate change (e.g. [1]). In response to elevated temperatures, the range of many terrestrial and marine species has shifted toward cooler zones (higher latitudes, altitudes, or deeper waters), leading to profound modifications in biogeographic, ecological, and evolutionary patterns [2,3,4]. In this context, hybrid zones are of particular interest, as they are an important component of both animal and plant systems, represent a key process in the maintenance of biodiversity, and sit at the very core of the process of speciation There is a very strong incentive to study the mechanisms involved in the dynamics of hybrid zones subjected to climate change

Objectives

Methods

Results

Discussion

Conclusion