Abstract:
Coral reefs are an important natural resource that need to be appropriately conserved and
managed. Drivers that have affected reef species in the past are still poorly known, but
inferences of population history based on genetic data can help with their identification,
providing that it is used in combination with a good calibration of the molecular clock.
Traditional calibrations based on fossils or biogeographic divergence events (>1 million years)
are known to cause inflation of the time and population parameter estimates, which creates a
disconnect that can only be solved by using appropriate mutation rates derived over recent
timescales.
To identify environmental drivers that affected the demographic history of coral reef species,
I proposed the development of a new molecular clock calibration that would provide accurate
genetic inferences. First, the literature review helped identify appropriate genetic approaches
and study models for reconstructing the population history of reef species. Second, the new
calibration method based on an appropriate environmental factor was validated using a
simulation study. Finally, the utility of the calibration method was explored and evaluated by
applying it to populations of an iconic reef species.
The literature review highlighted the lack of a calibration method that would be suitable for reef
species over recent timescales. Because the Last Glacial Maximum (LGM) and associated
sea-level low stands led to major local extinctions and bottlenecks in reef species, it represents
an excellent environmental factor for the calibration. These assumptions, together with an
expected post-LGM expansion, helped me develop and validate the LGM calibration method
using simulations and inferences based on Bayesian Skyline plots. The literature review also
highlighted the Crown-of-Thorns Starfish (COTS) as an ideal study model. The five COTS
populations studied had different mutation rates, but all provided the expected pattern of postLGM expansion. A specifically designed similarity index further indicated that sea-level change
and reef development have been the main drivers of COTS demography. An additional
simulation study showed the limits of the LGM calibration method for datasets with low genetic
content. Based on these results, I would recommend using a minimum of 50 individuals with
2500 nucleotides each in a dataset to get accurate inferences when applying the LGM
calibration method. The new method opens new opportunities to understand the dynamics of
reef species that can be used to inform management decisions.
