Abstract

BackgroundThe oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks.ResultsWe show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus.ConclusionThis study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Highlights

  • The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations

  • To identify the relationship between the transcriptomes of the jaws and species in this study (Fig. 1), we extracted the expression of 16,669 genes from each sample and conducted hierarchical clustering analysis based on Euclidean distance

  • The species clustering of oral jaw apparatus (OJA) samples was different from lower pharyngeal jaw apparatus (PJA) (LPJA) samples and neither reflected the phylogenetic relationship of the species shown in (Fig. 1 phylogeny based on Irisarri*, Singh* et al 2018)

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Summary

Introduction

The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity We extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. The functional decoupling of these jaws is seen as a key innovation that permitted the oral jaw apparatus (OJA) to be solely dedicated to prey capture and the pharyngeal jaw apparatus (PJA) to prey processing, allowing for independent evolution. Their adaptive radiation in several East African lakes was hypothesised to be connected to their great efficiency to adapt to novel food sources [17]. Modularity at the transcriptional level in global gene expression has not been yet been investigated in detail

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