Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species

Stanton-Geddes et al. BMC Genomics (2016) 17:171 DOI 10.1186/s12864-016-2466-z RESEARCH ARTICLE Open Access Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species John Stanton-Geddes1,7* , Andrew Nguyen1, Lacy Chick2, James Vincent3, Mahesh Vangala3, Robert R. Dunn4, Aaron M. Ellison5, Nathan J. Sanders2,6, Nicholas J. Gotelli1 and Sara Helms Cahan1 Abstract Background: The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism’s transcriptome measured across an experimental gradient. We characterized thermal reactionomes of two common ant species in the eastern U.S, the northern cool-climate Aphaenogaster picea and the southern warm-climate Aphaenogaster carolinensis, across 12 temperatures that spanned their entire thermal breadth. Results: We found that at least 2 % of all genes changed expression with temperature. The majority of upregulation was specific to exposure to low temperatures. The cool-adapted A. picea induced expression of more genes in response to extreme temperatures than did A. carolinensis, consistent with the enhanced response hypothesis. In contrast, under high temperatures the warm-adapted A. carolinensis downregulated many of the genes upregulated in A. picea, and required more extreme temperatures to induce down-regulation in gene expression, consistent with the tolerance hypothesis. We found no evidence for a trade-off between constitutive and inducible gene expression as predicted by the genetic assimilation hypothesis. Conclusions: These results suggest that increases in upper thermal limits may require an evolutionary shift in response mechanism away from damage repair toward tolerance and prevention. Keywords: Aphaenogaster, Gene expression, Plasticity, Reactionome, Transcriptome Background Temperature regulates biological activity and shapes diversity from molecular to macroecological scales [1, 2]. Many species, especially small-bodied arthropods, live at temperatures close to their thermal limits and are at risk from current increases in temperature [3–5]. Thermal tolerance, the ability of individuals to maintain function and survive thermal extremes, depends on a complex interplay between the structural integrity of cellular * Correspondence: 1 Department of Biology, University of Vermont, Burlington, VT 05405, USA 7 Data Scientist, Dealer.com, 1 Howard St, Burlington, VT 05401, USA Full list of author information is available at the end of the article components and activation of physiological response mechanisms to prevent and/or repair damage [6, 7]. Thermal defense strategies are shaped by the environmental regime organisms experience [8] and thermal limits vary considerably among species and populations [3, 4, 9, 10]. These differences in thermal tolerance are largely genetic [11, 12] with a highly polygenic basis [13–16]. Outside of candidate genes [13], little is known about the evolution of thermal tolerance or the link between short-term physiological acclimation and longerterm adaptation to novel temperature regimes. This information is critical for understanding the adaptive potential of species to future climates [17]. © 2016 Stanton-Geddes et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Stanton-Geddes et al. BMC Genomics (2016) 17:171 To address this gap of knowledge, we need information on the extent to which selection has acted upon the diversity and plasticity of genes involved in thermal tolerance [17, 18]. In recent years, whole-organism gene expression approaches (e.g. transcriptomics) using highthroughput RNA sequencing (RNAseq) technology have been widely applied to identify genes involved in thermal tolerance [19–22] and other traits. Such studies typically use an ANOVA-type experimental or sampling design, with only a few environmental levels, and often find only a few dozen to hundred genes with differential expression in different thermal regimes. However, temperature and other environmental factors vary continuously in nature. As a result, such categorical comparisons (e.g. high vs. low temperatures) are likely to miss key differences that are due not just to whether it is hot, but rather how hot it is. Continuous variation is better characterized with a reaction norm approach, which describes variation in the phenotype of a single genotype across an environmental gradient [23]. Reaction norms differ not only in mean values, but also in their shapes [10, 24], and differences in the shape of reaction norms are often larger than differences in mean values at both the species and the population level [24]. In this study, we extend the reaction norm approach to RNAseq analysis and introduce the reactionome, which we define as a characterization of the reaction norm for all genes in an organism’s transcriptome across an environmental gradient. Although temporal patterns of transcriptional activity (e.g. fast- vs. slow- responding genes) are also important components of an organism’s transcriptional response to environmental conditions [25], we focus here on the response of transcripts across conditions at the same time point. We use the reactionome method to identify genes that are thermally responsive in two closely-related eastern North American ant species, Aphaenogaster carolinensis and A. picea [26, 27]. Aphaenogaster are some of the most common ants in eastern North America [28] where they are keystone seed dispersers [29–31]. Ants, and ecotherms in general, have little or no thermal safety margin [5] and thus are highly susceptible to climate change [4, 32], putting at risk important ecosystem services [33]. Growth chamber studies have demonstrated that reproduction of Aphaenogaster will be compromised by increased temperatures [34], while field studies [32] and simulations [35] indicate that ant species persistence will depend on combinations of physiology and species interactions. Aphaenogaster carolin (...truncated)