Ecological restoration of forests, meadows, reefs, or other foundational ecosystems during climate change depends on the discovery and use of individuals able to withstand future conditions. For coral reefs, climate-tolerant corals might not remain tolerant in different environments because of widespread environmental adjustment of coral physiology and symbionts. Here, we test if parent corals retain their heat tolerance in nursery settings, if simple proxies predict successful colonies, and if heat-tolerant corals suffer lower growth or survival in normal settings. Before the 2015 natural bleaching event in American Samoa, we set out 800 coral fragments from 80 colonies of four species selected by prior tests to have a range of intraspecific natural heat tolerance. After the event, nursery stock from heat-tolerant parents showed two to three times less bleaching across species than nursery stock from less tolerant parents. They also retained higher individual genetic diversity through the bleaching event than did less heat-tolerant corals. The three best proxies for thermal tolerance were response to experimental heat stress, location on the reef, and thermal microclimate. Molecular biomarkers were also predictive but were highly species specific. Colony genotype and symbiont genus played a similarly strong role in predicting bleaching. Combined, our results show that selecting for host and symbiont resilience produced a multispecies coral nursery that withstood multiple bleaching events, that proxies for thermal tolerance in restoration can work across species and be inexpensive, and that different coral clones within species reacted very differently to bleaching.

High-throughput sequencing technologies are currently revolutionizing the field of biology and medicine, yet bioinformatic challenges in analysing very large data sets have slowed the adoption of these technologies by the community of population biologists. We introduce the 'Simple Fool's Guide to Population Genomics via RNA-seq' (SFG), a document intended to serve as an easy-to-follow protocol, walking a user through one example of high-throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom-made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components and F(ST) outlier analyses. Although the technical aspects of population genomics are changing very quickly, our hope is that this document will help population biologists with little to no background in high-throughput sequencing and bioinformatics to more quickly adopt these new techniques.

Environmental heterogeneity gives rise to phenotypic variation through a combination of phenotypic plasticity and fixed genetic effects. For reef-building corals, understanding the relative roles of acclimatization and adaptation in generating thermal tolerance is fundamental to predicting the response of coral populations to future climate change. The temperature mosaic in the lagoon of Ofu, American Samoa, represents an ideal natural laboratory for studying thermal tolerance in corals. Two adjacent back-reef pools approximately 500 m apart have different temperature profiles: the highly variable (HV) pool experiences temperatures that range from 24.5 to 35 • C, whereas the moderately variable (MV) pool ranges from 25 to 32 • C. Standardized heat stress tests have shown that corals native to the HV pool have consistently higher levels of bleaching resistance than those in the MV pool. In this review, we summarize research into the mechanisms underlying this variation in bleaching resistance, focusing on the important reef-building genus Acropora. Both acclimatization and adaptation occur strongly and define thermal tolerance differences between pools. Most individual corals shift physiology to become more heat resistant when moved into the warmer pool. Lab based tests show that these shifts begin in as little as a week and are equally sparked by exposure to periodic high temperatures as constant high temperatures. Transcriptome-wide data on gene expression show that a wide variety of genes are co-regulated in expression modules that change expression after experimental heat stress, after acclimatization, and even after short term environmental fluctuations. Population genetic scans show associations between a corals' thermal environment and its alleles at 100s to 1000s of nuclear genes and no single gene confers strong environmental effects within or between species. Symbionts also tend to differ between pools and species, and the thermal tolerance of a coral is a reflection of individual host genotype and specific symbiont types. We conclude the review by placing this work in the context of parallel research going on in other species, reefs, and ecosystems around the world and into the broader framework of reef coral resilience in the face of climate change.