Holobiont traits shape climate change responses in cryptic coral lineages

As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e., cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), obscuring the main drivers of thermal tolerance. Here, we leverage a holobiont (massive Porites) with high fidelity for C15 photobionts to investigate adaptive variation across classic (“typical” conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). L1 and L2 were more closely related to populations ~4300 km away, suggesting that some lineages..., Materials and Methods
Site selection and sample collection
Three extreme and three paired classic sites were selected in Chelbacheb, Palau. Extreme sites were shallow semi-enclosed lagoons with high water retention, increased light attenuation, and distinct assemblages of massive Porites lineages compared to classic sites (Rivera et al., 2022; van Woesik et al., 2012). Between 2010 and 2018, these sites had naturally elevated water temperatures year-round (up to 2°C) compared to nearby classic sites. Seasonal temperature ranges at extreme sites were ~29-32 °C, compared to ~28-31 °C at classic sites (Rivera et al., 2022). Sites were selected to ensure that, aside from the contrast in terms of temperature between classic and extreme sites, variability was minimal: they were all comparable in terms of depth (1 - 6 m), proximity to land (~10 - 20 m from land), and wave exposure (calm, on the leeward side of the archipelago or in a lagoon).
Water temperatures were measured every 30 minutes u..., , # Holobiont traits shape climate change responses in cryptic coral lineages

[https://doi.org/10.5061/dryad.1g1jwsv65](https://doi.org/10.5061/dryad.1g1jwsv65)

## Description of the data and file structure

This submission contains 9 datafiles from a study in Chelbacheb (the Rock Islands of Palau) studying the genetic diversity, microbial partners, physiology, and thermal tolerance of massive *Porites* inhabiting extreme and non-extreme (classic) reefs. Datafiles 1 and 2 contain temperature and light data at six study sites (N=3 extreme, N=3 classic sites) in Chelbacheb, respectively. Datafiles 3 and 4 contain data on dinoflagellate symbiont and bacterial diversity associated with colonies of massive* Porites* corals at these sites, respectively. Datasets 5 and 6 contain data on polyp densities and light harvesting mechanisms of these corals, respectively. Datasets 7-9 contain data from a thermal challenge experiment with the coral colonies: Dataset 7 contains colony mortality rates; ...