Biology subjects

Rippe, J. P.

Publications and source records attributed to Rippe, J. P..

4 recordsLinked to original sources

bioRxiv2025

Environmental drivers of genetic adaptation in two corals from the Florida Keys

Increasingly frequent marine heatwaves devastate coral reefs around the world, so there is great interest in finding warm-adapted coral populations that could be used as sources for assisted gene flow and restoration. Here, we evaluated the relative power of various environmental factors to explain coral genetic variation, suggestive of differential local adaptation to these factors, across the Florida Keys Reef Tract. We applied a machine learning population genomic method (RDAforest) to two coral species - the mustard hill coral Porites astreoides and the lettuce coral Agaricia agaricites - sampled from 65 sites covering the whole reef tract. Both species comprised three genetically distinct lineages distributed across depths in a remarkably similar way. Within these lineages, there was additional genetic variation explained by depth, but even more within-lineage variation was cumulatively explained by water chemistry parameters related to nitrogen, phosphorus, silicate, and salinity. Visualizing the predicted environment-associated genetic variation on a geographic map suggests that these associations reflect adaptation to certain aspects of the inshore-offshore environmental gradient, and, to a lesser extent, to difference of Middle and Lower Keys from the rest of the reef tract. Thermal parameters, most notably maximal monthly thermal anomaly, were also consistently identified as putative drivers of genetic divergence, but had a relatively low explanatory power compared to depth and water chemistry. Overall, our results indicate that temperature is not the most important driver of differential coral adaptation in the Florida Keys, and underscore depth and water chemistry as more important environmental factors from the corals perspective. These findings are relevant for planning assisted gene flow and restoration efforts: not just any warmer reef would be an optimal source of transplants to promote thermal adaptation within the local coral population.

evolutionary biology↗

bioRxiv2024

Cryptic diversity shapes coral symbioses, physiology, and response to thermal challenge

Coral persistence in the Anthropocene is shaped by interactions among holobiont partners (coral animals, microbial symbionts) and their environment. Cryptic coral lineages-genetically distinct yet morphologically similar groups-are critically important as they often exhibit functional diversity relevant to thermal tolerance. Additionally, environmental parameters such as thermal variability may promote tolerance, but how variability interacts with holobiont partners to shape responses to thermal challenge remains unclear. Here, we identified three cryptic lineages of Siderastrea siderea in Bocas del Toro, Panama that differ in distributions across inshore and offshore reefs, microbial associations, holobiont phenomes, and skeleton morphologies. A thermal variability experiment failed to increase thermal tolerance, but subsequent thermal challenge and recovery revealed one lineage maintained elevated energetic reserves, photochemical efficiency, and growth. Lastly, coral cores highlighted that this lineage also exhibited faster growth historically. Functional variation among cryptic lineages highlights their importance in predicting coral reef responses to climate change. TeaserCryptic host diversity drives coral phenotypes relevant to climate change.

evolutionary biology↗

bioRxiv2023

Decrypting corals: Does regulatory evolution underlie environmental specialization of coral cryptic lineages?

A recent study has shown that two common Caribbean corals, Montastrea cavernosa and Siderastrea siderea, in the Florida Keys each consist of four genetically distinct lineages. These lineages are strongly specialized to a certain depth and, to a lesser extent, to nearshore or offshore habitat. We hypothesized that the lineages environmental specialization is at least in part due to regulatory evolution, which would be manifested as the emergence of groups of coregulated genes ("modules") demonstrating lineage-specific responses to different reef environments. Our hypothesis also predicted that genes belonging to such modules would show greater genetic divergence between lineages than other genes. Contrary to these expectations, responses of cryptic lineages to natural environmental variation were essentially the same at the genome-wide gene coexpression network level. Moreover, none of the identified coregulated gene modules exhibit elevated between-lineage divergence. The environmental specialization of cryptic lineages must, therefore, come from relatively subtle adjustments to gene function or regulation that are not detectable at the gene network level and/or involve other constituents of the coral holobiont rather than the coral host.

evolutionary biology↗

bioRxiv2020

Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract

Broadcast-spawning coral species have wide geographic ranges, spanning strong environmental gradients, but it is unclear how much spatially varying selection these gradients actually impose. Strong divergent selection might present a considerable barrier for demographic exchange between disparate reef habitats. We investigated whether the cross-shelf gradient (nearshore - offshore - deep) is associated with spatially varying selection in two common coral species, Montastraea cavernosa and Siderastrea siderea, in the Florida Keys. Toward this end, we generated a de novo genome assembly for M. cavernosa and used 2bRAD to genotype 20 juveniles and 20 adults of both species from each of the three reef zones to identify signatures of selection occurring within a single generation. Unexpectedly, each species was found to be composed of four genetically distinct lineages, with gene flow between them still ongoing but highly reduced in 13.0-54.7% of the genome. Each species includes two sympatric lineages that are only found in the deep (20 m) habitat, while the other lineages are found almost exclusively on the shallower reefs (3-10 m). The two "shallow" lineages of M. cavernosa are also specialized for either nearshore or offshore: comparison between adult and juvenile cohorts indicates that cross-shelf migrants are more than twice as likely to die before reaching adulthood than local recruits. Siderastrea siderea and M. cavernosa are among the most ecologically successful species on the degraded Florida Keys Reef Tract, and this work offers important insight on the genomic background of divergent selection and environmental specialization that may in part explain their resilience and broad environmental range.

evolutionary biology↗