Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges.

Hanno Schmidt,Barbara Feldmeyer,Thomas Hankeln,Bastian Greshake,Markus Pfenninger

doi:10.1186/1471-2164-14-384

Abstract

BackgroundThere is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger).ResultsMore than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection.ConclusionsThree candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species’ ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.

Highlights

There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms
As we have used a minimum coverage of 10 reads per position in each species for Single nucleotide polymorphism (SNP) detection, we have discovered only segregating alleles with a frequency over 0.25 with a probability of > 90%
In accordance with recent meta-studies [5,57] on the genome-wide prevalence of positive selection in insects, the data presented here argue that such Darwinian processes are likely to have played an important role in the divergence of Chironomus piger and C. riparius

Summary

Introduction

There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. The recent progress in sequencing technology [12,13] and resultant ability to sequence whole transcriptomes or genomes even for non-model species opens up this opportunity [14] Such approaches allow at the same time pinpointing the genomic basis of ecologically relevant traits and their evolutionary history [15,16,17,18,19]. This may be accomplished in two different ways: Based on known ecological differences of the taxa under scrutiny it is possible to assess the processes driving the evolution of genes likely associated with the relevant traits. It remains challenging to functionally link the identified patterns with observed phenotypic differences

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Results

Discussion

Conclusion