Huang, Yun, Chain, Frederic J. J., Panchal, Mahesh, Eizaguirre, Christophe, Kalbe, Martin, Lenz, Tobias L., Samonte, Irene E., Stoll, Monika, Bornberg-Bauer, Erich, Reusch, Thorsten B.H. , Milinski, Manfred and Feulner, Philine G. D. (2016) Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Molecular Ecology, 25 (4). pp. 943-958. DOI 10.1111/mec.13520.

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Preview	Text (Fig. S1 Distribution of dispersion values in (a) head kidney samples and (b) spleen samples) mec13520-sup-0001-FigS1.pdf - Supplemental Material Available under License Creative Commons: Attribution 4.0. Download (99kB) | Preview
Preview	Text (Fig. S2 Counts of Diplostomum sp. across stickleback populations) mec13520-sup-0002-FigS2.pdf - Supplemental Material Available under License Creative Commons: Attribution 4.0. Download (92kB) | Preview
	Other (Table S1 Morphological data and parasite loads of sequenced fish) mec13520-sup-0003-TableS1.xlsx - Supplemental Material Available under License Creative Commons: Attribution 4.0. Download (58kB)
	Other (Table S2 Summary of library statistics in sequence quality filtering, sequence mapping and library scaling factor.) mec13520-sup-0004-TableS2.xlsx - Supplemental Material Available under License Creative Commons: Attribution 4.0. Download (59kB)
	Other (Table S3 Differentially expressed genes between lake and river across four population pairs) mec13520-sup-0005-TableS3.xlsx - Supplemental Material Available under License Creative Commons: Attribution 4.0. Download (54kB)
	Other (Table S4 Differentially expressed genes between lake and river in European populations.) mec13520-sup-0006-TableS4.xlsx - Supplemental Material Available under License Creative Commons: Attribution 4.0. Download (57kB)

Abstract

The observation of habitat-specific phenotypes suggests the action of natural selection. The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats across the northern hemisphere since the last glaciation, while giving rise to recurring phenotypes associated with specific habitats. Parapatric lake and river populations of sticklebacks harbour distinct parasite communities, a factor proposed to contribute to adaptive differentiation between these ecotypes. However, little is known about the transcriptional response to the distinct parasite pressure of those fish in a natural setting. Here, we sampled wild-caught sticklebacks across four geographical locations from lake and river habitats differing in their parasite load. We compared gene expression profiles between lake and river populations using 77 whole-transcriptome libraries from two immune-relevant tissues, the head kidney and the spleen. Differential expression analyses revealed 139 genes with habitat-specific expression patterns across the sampled population pairs. Among the 139 differentially expressed genes, eight are annotated with an immune function and 42 have been identified as differentially expressed in previous experimental studies in which fish have been immune challenged. Together, these findings reinforce the hypothesis that parasites contribute to adaptation of sticklebacks in lake and river habitats.

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