RECONSTRUCTING CORAL HISTORIES USING ANCIENT DNA
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.
Photo credit Julia E. Cole.
Coral colony coring on SCUBA using a pneumatic drill.
Photo credit Julia E. Cole.
Coral colony coring on SCUBA using a pne
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
preserving dated records through sclerochronology and geochemical tracers. Integrating metagenomic data extends these archives by adding a biological layer, allowing environmental reconstructions to be examined alongside preserved signatures of past coral-associated communities. Metagenomic analysis of aDNA from coral cores provides insights into the coral microbiome, allowing us to identify coral-associated prokaryotes and eukaryotes through time.
(González-Pech et al. 2024, https://doi.org/10.1101/2024.09.02.610915).
faveolata coral core according to the top right legend. Columns represent the core
subsamples and rows the 36 MAGs.
calculated from the relative abundance of the 36 MAGs. Each data point
corresponds to a subsample (i.e., timepoint) and its color to the maximum annual
temperature of the previous year following the legend on top. (c) Loading plot of
the PCA in (b) showing the MAGs driving the separation of subsamples along PC1
and PC2 bases on their contribution in both axes.
CoraDNA Laboratory.
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.
This call is targeted toward coral cores, skeletons, or historical skeletal material that include:
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.