Research
My research focus is on marine megafauna ecology, primarily looking at the effects of climate change on local adaptation and population dynamics.
Assembling high-quality sea turtle reference genomes to aid conservation
Advances in sequencing technologies are aiding the assembly and analysis of high-quality reference genomes for non-model organisms. Our research aims to assemble and analyse high-quality reference genomes for all extant species of sea turtle, with genomes of the leatherback (Dermochelys coriacea) and green turtles (Chelonia mydas) already assembled in collaboration with the Vertebrate Genomes Project (VGP). The outputs for these two genome assemblies and the corresponding analyses are currently under review in PNAS, while the preprint is on bioRxiv: doi.org/10.1101/2022.01.10.475373.
These two initial platinum-quality reference genomes showed high genome synteny and collinearity between the two remaining extant sea turtle families that have been evolutionarily separated for over 60 million years. Our analyses showed regions of reduced collinearity (RRCs), where there were breaks in the similarities between the two species, and these were invariably associated with higher gene copy numbers in the green turtle, relative to the leatherback. Within these RRCs, olfactory receptor (OR), immune-related, and zinc finger protein genes were found in higher numbers in the green turtle. We postulated that habitat differences and different ecological roles have driven divergences in these gene groups, with green turtles relying more heavily on olfaction for foraging and navigation than the leatherback turtle, while also being exposed to a higher, and more variable, pathogen load due to their proximity to anthropogenically altered nearshore habitats.
We also showed that the leatherback turtle possesses very low genome-wide diversity compared to the green turtle, including within protein coding regions, raising concerns for future persistence as adaptive potential may be limited. This concern was furthered by the observation of a higher proportion of variants being annotated as potentially high impact (e.g., gain or loss of stop-codon) in the leatherback turtle relative to the green. Our investigation into runs of homozygosity (ROHs) also showed a high accumulated length and total number of ROHs in the leatherback turtle, with many short ROHs suggesting sustained low population sizes over evolutionary history. In contrast, ROHs were far less prevalent in the green turtle, although we did find long ROHs in the reference green turtle individual, indicating recent inbreeding events, which is consistent with the Mediterranean population where the samples were sourced, as this represents a relatively small nesting population. Finally, PSMC analyses supported our previous findings, with low, sustained Ne for the leatherback turtle over the last 10 million years, and relatively higher and fluctuating Ne for the green turtles.
In addition to these initial two genomes, we have secured funding through the Wild Genomes Project by Revive and Restore to assemble and analyze the genomes of the remaining five species of sea turtle, with sequencing currently underway and genomes expected to be available for public use in 2023.
These two initial platinum-quality reference genomes showed high genome synteny and collinearity between the two remaining extant sea turtle families that have been evolutionarily separated for over 60 million years. Our analyses showed regions of reduced collinearity (RRCs), where there were breaks in the similarities between the two species, and these were invariably associated with higher gene copy numbers in the green turtle, relative to the leatherback. Within these RRCs, olfactory receptor (OR), immune-related, and zinc finger protein genes were found in higher numbers in the green turtle. We postulated that habitat differences and different ecological roles have driven divergences in these gene groups, with green turtles relying more heavily on olfaction for foraging and navigation than the leatherback turtle, while also being exposed to a higher, and more variable, pathogen load due to their proximity to anthropogenically altered nearshore habitats.
We also showed that the leatherback turtle possesses very low genome-wide diversity compared to the green turtle, including within protein coding regions, raising concerns for future persistence as adaptive potential may be limited. This concern was furthered by the observation of a higher proportion of variants being annotated as potentially high impact (e.g., gain or loss of stop-codon) in the leatherback turtle relative to the green. Our investigation into runs of homozygosity (ROHs) also showed a high accumulated length and total number of ROHs in the leatherback turtle, with many short ROHs suggesting sustained low population sizes over evolutionary history. In contrast, ROHs were far less prevalent in the green turtle, although we did find long ROHs in the reference green turtle individual, indicating recent inbreeding events, which is consistent with the Mediterranean population where the samples were sourced, as this represents a relatively small nesting population. Finally, PSMC analyses supported our previous findings, with low, sustained Ne for the leatherback turtle over the last 10 million years, and relatively higher and fluctuating Ne for the green turtles.
In addition to these initial two genomes, we have secured funding through the Wild Genomes Project by Revive and Restore to assemble and analyze the genomes of the remaining five species of sea turtle, with sequencing currently underway and genomes expected to be available for public use in 2023.
Modelling sex-ratios and embryonic mortality of sea turtles in Western Australia
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The main focus of my PhD thesis (completed Aug 2018) was to determine how climate change will impact the development of sea turtles in Western Australia. In particular, in examined how rising ambient temperatures will influence the sex-ratios and embryonic mortality of flatback (Natator depressus) and green (Chelonia mydas) sea turtles at rookeries throughout the Kimberley and Pilbara region of WA. This research entailed three separate, yet interlinking projects. Initial steps involved developing the NicheMapR (Kearney & Porter, 2017) microclimate model to perform at predicting below-surface sand temperatures on Australian beaches. This research was published in the Journal of Thermal Biology (see Publications), and demonstrated a high correspondence between predicted and observed sand temperatures, thus validating its' use for predictive studies.
Due to the high levels of philopatry exhibited by sea turtles, populations are expected to be locally adapted to thermal environments at rookeries. The second component of my thesis compared development rates (and inferred thermal tolerances), as well as parameters defining the temperature-dependent sex determination (TSD) reaction norm parameters between and within the species. These parameters varied greatly within N. depressus, suggesting that while some populations (e.g. Cape Domett) have adapted to warming climates by shifting nesting phenology to cooler periods, others (such as Eighty Mile Beach) have undergone evolution of the sex-determining mechanism to ensure production of mixed sexes. This research is currently (April 2020) under review in Functional Ecology. To assess how climate change will impact these populations, the third aspect of my thesis was to integrate the mechanistic microclimate model with the population-specific thermal thresholds. I applied a suite of climate change scenarios (low to high emission scenarios) to macro-scale climate inputs for NicheMapR and ran models for future scenarios (2030, 2050, 2070 and 2090). My results suggest populations will be differentially impacted by climate change due to existing and future environmental heterogeneity, spatially explicit changes in climate, and existing differences in thermal thresholds, coupled with differences in nesting phenology. In brief, the results showed that winter nesting populations of N. depressus are at the greatest risk of rising ambient temperatures as they lack the ability to shift nesting to a cooler time of year. Should summer nesting populations also be unable to shift nesting phenology, or shift nesting ranges polewards, they are also at risk of local extinctions. Management plans should therefore consider sea turtles at a population-level to ensure continued survival of these species. This component is still in preparation for publication. |
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Exploring gene expression changes in developing sea turtles under thermal stress
The ability to survive stressful conditions begins at the molecular level, with a suite of mechanisms initiated by the cell when stress is detected. Building on previous work on heat shock proteins (HSPs) in sea turtle embryos, our focus is to explore what mechanisms are initiated in sea turtles, and more importantly, find out how these differ between populations and species. By exposing some turtles to a biologically realistic heat stress, we can compare gene expression with embryos at "comfortable temperatures" and identify genes important in this tolerance. Preliminary results in loggerhead sea turtles (Caretta caretta) demonstrate that a number of HSPs and other protein editing and chaperone molecules are heavily upregulated to clear away clusters of detrimental proteins. This appears to come at a cost, with developmental genes downregulated under stress.
Following the success of the pilot study on C. caretta embryos, this project was expanded to incorporate populations of Natator depressus and Chelonia mydas. Analysis is currently underway to determine if species exhibit the same molecular response to biologically realistic thermal stress, and whether there is a difference between and within species that may provide insight into local adaptation and resilience to thermal stress.
Following the success of the pilot study on C. caretta embryos, this project was expanded to incorporate populations of Natator depressus and Chelonia mydas. Analysis is currently underway to determine if species exhibit the same molecular response to biologically realistic thermal stress, and whether there is a difference between and within species that may provide insight into local adaptation and resilience to thermal stress.
Assessing fitness costs of anomalous development in sea turtles
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My postdoctoral study at the Florida Atlantic University aimed to assess how anomalous scute (carapace and plastron scales) development may impact individual survival. Using a 25-year photo data set, we explore how the prevalence of scute anomalies fluctuates within populations of sea turtle as they grow. We compared frequencies of anomalies with the size of loggerhead (Caretta caretta) and green (Chelonia mydas) sea turtles captured off the east coast of Florida. Our findings suggest that anomalous scute arrangements have no survival costs for individuals, with frequencies remaining fairly consistent of the size range of our individuals (~20 - 120cm). The findings of this study were published in the Journal of Morphology in 2021.
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