Transcriptome analysis of a wild bird reveals physiological responses to the urban environment

Hannah Watson,Martin N Andersson,Caroline Isaksson,Elin Videvall

doi:10.1038/srep44180

Abstract

Identifying the molecular basis of environmentally induced phenotypic variation presents exciting opportunities for furthering our understanding of how ecological processes and the environment can shape the phenotype. Urban and rural environments present free-living organisms with different challenges and opportunities, which have marked consequences for the phenotype, yet little is known about responses at the molecular level. We characterised transcriptomes from an urban and a rural population of great tits Parus major, demonstrating striking differences in gene expression profiles in both blood and liver tissues. Differentially expressed genes had functions related to immune and inflammatory responses, detoxification, protection against oxidative stress, lipid metabolism, and regulation of gene expression. Many genes linked to stress responses were expressed at higher levels in the urban birds, in accordance with our prediction that urban animals are exposed to greater environmental stress. This is one of the first studies to reveal transcriptional differences between urban- and rural-dwelling animals and suggests an important role for epigenetics in mediating environmentally induced physiological variation. The study provides valuable resources for developing further in-depth studies of the mechanisms driving phenotypic variation in the urban context at larger spatial and temporal scales.

Highlights

To develop genomic resources and lacks sufficient controls to derive urban/rural comparisons[20]
Many genes linked to stress responses were expressed at higher levels in the urban, compared with the rural, dwelling birds; this suggests that differences in diet and stress exposure, e.g. pollution and pathogens, between the two environments may underlie the observed variation in gene expression
While only 9% (n = 53) of the differentially expressed genes were common to liver and blood (Supplementary Fig. S2A), 28% (n = 130) of the significantly overrepresented gene ontology (GO) terms were common to both tissues (Supplementary Fig. S2B)

Summary

Introduction

To develop genomic resources and lacks sufficient controls to derive urban/rural comparisons[20]. To gain insight into the key molecular mechanisms underlying physiological responses to urban environments, we performed high-throughput Illumina RNA sequencing (RNA-seq) to characterise replicated transcriptomes from liver and whole blood tissues from a pair of urban and rural great tit populations in Sweden. Both the avian liver and blood are sensitive to changes in diet[21,23] and pollutant exposure[24,25] and, are expected to contribute to differences in gene expression in relation to urbanisation[26,27]. Whether our results, derived from a single pair of populations, reflect a general difference between urban and rural populations across larger spatial scales should be verified, and this study provides valuable resources to inform the design of future studies

Methods

Results

Conclusion