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Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish

Citation

Rajkov, Jelena et al. (2020), Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish, Dryad, Dataset, https://doi.org/10.5061/dryad.8cz8w9gmn

Abstract

Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish Astatotilapia burtoni. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.

Methods

For parasite screening and transcriptome sequencing (RNA-seq), we sampled between 16 and 22 adult A. burtoni specimens per locality at a ~1:1 sex ratio from lake and river populations at the Kalambo River (Kalambo lake - KaL, Kalambo river - KaR1 and Kalambo river upstream - KaR2) and the Lunzua River (Lunzua lake - LzL, Lunzua river - LzR) in August 2017. Additionally, 10 adults per locality at a [~]1:1 sex ratio were sampled for parasite screening from the Chitili River (Chitili lake - ChL, Chitili river - ChR) in September 2018. Fish were caught by hook and line fishing and transported to the field station at Kalambo Lodge in buckets filled with water from sampling locations. Specimens were either processed within a few hours upon capture or kept alive for one night in concrete ponds filled with water from the respective sampling location. To evaluate plasticity in parasite and microbiota communities as well as in gene expression, we included 26 specimens from a previous experiment involving wild-caught adults (November 2015) from Kalambo lake (KaL) and river (KaR2) populations. These fish were kept in two separate concrete ponds (dimensions: 2m x 1m x 1m; length x width x depth) supplied with lake water mimicking lake-like conditions with respect to water temperature, chemistry and flow, at high density (~100 individuals per pond) from July 2016 until August 2017 and fed daily with commercial flake food. Fish were euthanized by pithing and immediately photographed, measured (±0.5 mm), weighed (±5 mg), sexed by visual inspection of external colouration and the genital papilla, and fin-clipped. Immediately after measuring each fish (see above), we dissected gills, skin, fins, eyes, intestinal tract, heart and liver, and exhaustively screened these organs for metazoan ecto- and endoparasites using a field stereomicroscope (Nikon, SMZ445). We first screened the outer surface of each A. burtoni specimen for monogeneans and crustaceans. Next, fins and gills were dissected and screened separately for ectoparasites. The gastrointestinal tract was excised from oesophagus to anus and placed in saline solution (0.9% NaCl). Livers and hearts were dissected and inspected in a Petri dish filled with lake water. Finally, the intestinal content and teased internal organs were pressed between two glasses of a Petri dish for examination. Endo-parasite specimens were separated according to higher helminth taxa (Acanthocephala, Cestoda, Digenea and Nematoda) following Paperna (1996). Immediately after parasite screening of the gills, one gill from each side as well as the spleen were dissected and preserved in RNAlater (Sigma-Aldrich) and later transferred to Individual TRIzol tubes which were weighed (±0.05 mg) before and after the spleen was added to calculate the spleen weight.

Usage Notes

SL - standard length; TL - total length; W -weight; NA - missing data

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 31003A_156405