DOI: 10.5061/dryad.8cz8w9gmn
title: Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish

description: 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.
description: For parasite screening and
 transcriptome sequencing (RNA-seq), we sampled between 16 and 22 adult
 <i>A. burtoni</i> 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 <i>A. burtoni</i> 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.
description: SL - standard length; TL - total length; W -weight; NA - missing
 data