Reconstructing Coral Histories Using Ancient DNA.
coraDNA is ancient DNA (aDNA) preserved in coral skeleton archives and can be used to reconstruct biological change through time. Coral cores are already well established as sediment records of past ocean conditions through geochemical and growth-based proxies. coraDNA builds on that foundation by adding a metagenomic dimension, allowing us to identify who was there across time and connect shifts in coral-associated communities to environmental history.
Call for Participation
Building a coraDNA Network
We are launching an effort to build a community around coral ancient DNA, or coraDNA: the recovery and analysis of DNA from coral skeletal archives, historical collections, and associated recent or extant coral material.
The goal of this community is to bring together researchers with complementary expertise in coral biology, paleoclimate, geochemistry, ancient DNA, genomics, museum and field collections, bioinformatics, and reef conservation. Coral skeletons and cores contain a rich environmental record, and coraDNA has the potential to add a biological and evolutionary layer to that archive. To realize this potential, we need shared methods, shared metadata standards, and a collaborative framework for analysis.
We invite interested researchers to join this emerging consortium. Participation may include contributing ideas, sharing experience with coral cores or skeletal archives, helping define best practices, identifying candidate samples, contributing geochemical or environmental context, participating in methods discussions, or joining future collaborative proposals and publications.
Initial community priorities include:
This community is intended to be inclusive.
Researchers do not need to have existing ancient DNA data to participate. We are especially interested in connecting with groups that have coral cores, skeletal archives, historical collections, paired recent and old material, existing isotope or elemental records, or access to sites with well-characterized environmental histories.
Interested participants are invited to join the coraDNA community and help shape the first shared standards, sample priorities, and collaborative research directions for this emerging field.
Methods
coraDNA combines coral core science with approaches designed for degraded and low-biomass DNA. These include contamination-aware skeletal sampling, DNA extraction, short-fragment library preparation, authentication of ancient DNA signatures, and metagenomic characterization of recovered communities. Metagenomic results are interpreted alongside coral core chronology and geochemical proxy records to place biological change in environmental context.
Extracting skeletal cores to reconstruct historical ocean conditions and coral growth dynamics.
The Process
Collection: Scientific divers use underwater pneumatic drills to extract skeletal cores from massive reef-building corals.
Sampling: Long cylindrical cores are collected along the coral’s primary growth axis. Core are sealed with inert plugs and marine epoxy to promote recovery and minimize impacts.
Scientific Value
Chronology: Annual density bands provide a high-resolution temporal record of coral growth.
Geochemistry: Skeletal proxies (e.g., Sr/Ca, δ¹⁸O) reveal past sea surface temperatures and environmental conditions.
Climate Archives: Coral cores preserve multi-decadal to centennial records of ocean and climate variability.
light (left), x-ray (center), and UV luminescence (right).
Signatures of damage in aDNA
Showing deamination
(reflected in C to T substitutions) frequency. The decreasing deamination frequency over time in samples
suggests that this pattern reflects true time damage.
Coral Core MAGs
Venn diagram showing the
overlaps in microbial taxa
assigned to MAGs from the
coral core, and from seawater and sample sediments from
Varadero Reef and Rosario
Islands (Colombia).
What coraDNA can reveal
(González-Pech et al. 2024, https://doi.org/10.1101/2024.09.02.610915).
CoraDNA Laboratory
Scenes from aDNA Laboratory , showcasing the techniques and technologies used to analyze ancient DNA and reveal insights into past environments.
Call for Collaborative Mini-Grant Proposals: coraDNA Across Thermal Stress Events
We are inviting short proposals for collaborative coraDNA mini-grants focused on coral skeletal archives that span documented thermal stress events.
The goal of this program is to generate pilot data for a collaborative consortium manuscript testing whether coral ancient DNA can recover biological, symbiont, microbial, or community-level signals across periods of extreme thermal stress. We are especially interested in samples where the timing of thermal stress is independently supported by geochemical evidence from the coral skeleton or associated environmental records.
To maximize participation across the community, we anticipate supporting up to two samples per submitting group. If additional samples are scientifically justified, applicants are encouraged to briefly explain their rationale, and these may be considered based on scientific merit and available funding.
This call is targeted toward coral cores, skeletons, or historical skeletal material that include:
A thermal stress event
The sample should span a known or inferred period of elevated temperature, bleaching stress, marine heatwave exposure, or other thermal anomaly.
Geochemical evidence of the event
Priority will be given to samples where the thermal event is supported by skeletal geochemistry, such as Sr/Ca, Li/Mg, δ18O, clumped isotopes, growth anomalies, density bands, or other temperature/stress proxies.
Temporal sampling potential
The material should allow sampling from before, during, and/or after the thermal stress event.Ideal samples include coral cores or skeletons with a clear chronology and sufficient material for destructive sampling.
Associated metadata
Proposals should describe species, location, collection history, age model, storage conditions, prior handling, exposure to any destructive reagents (e.g. Clorox or resin impregnation), and any previous processing such as slabbing, CT/CAT scanning, gamma densitometry, or other imaging.
Collaborative manuscript potential
Selected projects will contribute data, metadata, interpretation, and writing to a shared consortium paper.
Temporal sampling potential
The material should allow sampling from before, during, and/or after the thermal stress event.Ideal samples include coral cores or skeletons with a clear chronology and sufficient material for destructive sampling.
Applicants should submit a pre-proposal including:
- Project title and participating investigators;
- Coral species and collection location;
- Type of material available, such as core, skeleton, archive specimen, or paired modern material;
- Approximate age range and chronology;
- description of the thermal stress event captured by the sample;
- Geochemical or environmental evidence supporting the event;
- Proposed before/during/after sampling strategy;
- Available recent or extant comparison material, if any;
- Sample storage, handling, slabbing, and scanning history;
- Willingness to contribute to a collaborative consortium manuscript.
Priority will be given to projects where the coral archive contains a clear thermal-stress contrast, a strong geochemical record of that event, and enough contextual information to interpret coraDNA results in relation to environmental change.
Join our Network
The CoraDNA team welcomes inquiries from researchers, collaborators, organizations, and members of the public. Whether seeking additional information, exploring partnership opportunities, or requesting support, visitors are encouraged to get in touch using the contact form below. A member of the team will respond as soon as possible.