Uthicke S et al. (2019), Little evidence of adaptation potential to ocea...

ECB-ART-47450

Ecol Evol 2019 Sep 01;917:10004-10016. doi: 10.1002/ece3.5563.

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Little evidence of adaptation potential to ocean acidification in sea urchins living in "Future Ocean" conditions at a CO2 vent.

Uthicke S , Deshpande NP , Liddy M , Patel F , Lamare M , Wilkins MR .

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Ocean acidification (OA) can be detrimental to calcifying marine organisms, with stunting of invertebrate larval development one of the most consistent responses. Effects are usually measured by short-term, within-generation exposure, an approach that does not consider the potential for adaptation. We examined the genetic response to OA of larvae of the tropical sea urchin Echinometra sp. C. raised on coral reefs that were either influenced by CO2 vents (pH ~ 7.9, future OA condition) or nonvent control reefs (pH 8.2). We assembled a high quality de novo transcriptome of Echinometra embryos (8 hr) and pluteus larvae (48 hr) and identified 68,056 SNPs. We tested for outlier SNPs and functional enrichment in embryos and larvae raised from adults from the control or vent sites. Generally, highest FST values in embryos were observed between sites (intrinsic adaptation, most representative of the gene pool in the spawned populations). This comparison also had the highest number of outlier loci (40). In the other comparisons, classical adaptation (comparing larvae with adults from the control transplanted to either the control or vent conditions) and reverse adaptation (larvae from the vent site returned to the vent or explanted at the control), we only observed modest numbers of outlier SNPs (6-19) and only enrichment in two functional pathways. Most of the outliers detected were silent substitutions without adaptive potential. We conclude that there is little evidence of realized adaptation potential during early development, while some potential (albeit relatively low) exists in the intrinsic gene pool after more than one generation of exposure.

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Species referenced: Echinodermata
Genes referenced: fst LOC100887844 LOC100893907

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	Figure 1. (a) Design of field experiments, with adult Echinometra sp. C collected from either Control (C) or Vent (V) sites, spawned, and their offspring explanted to both control locations (c) or vent locations (v). This gave rise to larvae with four histories (i.e., Cc = larvae from control adults explanted at control sites; Cv = larvae from control adults explanted at vent sites; Vc = larvae from vent adults explanted at control sites; Vv = larvae from vent adults explanted at vent sites). (b) Three potential Adaptive scenarios to changes in seawater pH for Echinometra sp. C larvae can be explored by detecting outlier SNPs between larvae of different histories. Classical adaptation (Cc vs. Cv) would indicate a potential for transgenerational adaptation at the genes carrying these outliers; Reverse adaptation (Vc vs. Vv) would indicate the potential for adaptation from ocean acidification to present‐day conditions, and Intrinsic adaptation (Cc vs. Vv, representative of standing genetic variation) represent long‐term (one full generation) intrinsic adaptation of the population at the vents. Classical adaptation and Reverse adaptation were tested after 8 and 48 hr of exposure. Intrinsic adaptation was only tested for 8 h larvae; SNPs in these larvae represent the closest approximation to allele frequencies in the parent populations from the control and the vent sites
	Figure 2. Cluster diagram of Echinometra sp. C larvae with parents from either control (C) or vent (V) location that have been transplanted to either the control (c) or vent (v) locations for 8 hr or 48 hr exposure before harvest. Clusters have been generated from 68,056 SNPs
	Figure 3. Distribution of F ST values for classical, reverse, and intrinsic adaptation. For classical and reverse adaptation, F ST distributions were calculated for 8 and 48 hr of exposure. Red vertical lines indicate the threshold for outliers based on the empirical outlier method. Due to the y‐axis scale, most outliers to the right of the vertical line are not visible. These are depicted in detail in Figure 4
	Figure 4. F ST versus log Q‐values for classical, reverse and intrinsic adaptation. Vertical lines indicate the threshold for outliers in the BayeScan analysis (FDR = 0.05). Red dots indicate overlap outliers between the BayeScan and the empirical method

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