Coral biology and evolution through the lens of genomics and population genetics
Restricted (Penn State Only)
- Author:
- Stankiewicz, Kathryn
- Graduate Program:
- Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- May 18, 2022
- Committee Members:
- David Toews, Major Field Member
Istvan Albert, Outside Unit & Field Member
Iliana Baums, Major Field Member & Dissertation Advisor
Todd Lajeunesse, Chair of Committee
Stephen Wade Schaeffer, Professor in Charge/Director of Graduate Studies - Keywords:
- genomics
bioinformatics
corals
population genetics
hybridization
recombination
comparative genomics
Delta K
STRUCTURE - Abstract:
- Coral reefs are some of the most diverse ecosystems on the planet. While corals are ecologically and economically important, many species are in sharp decline due to the impacts of anthropogenic climate change. As members of the class Anthozoa, they also represent one of the oldest clades of metazoans. Thus, there is a pressing need to study the biology of these organisms from the standpoint of conservation and, at the same time, we may gain novel insight into ancient features of basal animals to better understand evolution of the higher metazoans. A critical underpinning of effective conservation is to delineate barriers to gene flow that may prevent the spread of adaptive alleles. The discovery of such barriers relies on theoretical population genetic models with assumptions that are frequently violated in real world datasets. Here, we investigated the impact of different population genetic methodologies through a re-estimation of genetic structure in empirical microsatellite datasets from both coral and non-coral species. Recent work showed that the ΔK statistic, when applied to the output of the program STRUCTURE, often underestimates the true number of populations and proposed four alternative estimators. In comparing these newer K estimators with traditional (ΔK and posterior probability) estimates in the empirical datasets re-analyzed here, we found widespread disagreement between estimators. Thus, we determined that a multi-tool approach, including a combination of all estimators and visual inspection of STRUCTURE plots, is always warranted in inferring the number of populations. Scleractinian corals have successfully adapted to a wide range of habitats from sunlit, tropical shallow waters to the dark and cold of the deep sea. By comparing genomic features of species from diverse habitats, we can gain insights into coral evolution. While several genomes of tropical corals now exist, temperate species remain understudied. I, thus, focused on developing a chromosome-scale genome assembly for the facultatively symbiotic, temperate coral Astrangia poculata. In comparison to the tropical coral Acropora millepora, we discovered a gene family with putative functions in circadian sleep/wake cycle, feeding suppression, and sleep promotion that was significantly bigger in Astrangia poculata. This finding highlights the potential role of gene expansion in the remarkable dormancy state A. poculata enters to survive the harsh, cold conditions of winter in the northern part of its range. In contrast, gene families that were significantly larger in Acropora millepora had functions relating to meiosis and sperm hyperactivation, consistent with the extreme requirements of sperm competition during mass spawning events in this species. Finally, in the fourth and fifth chapter, I studied how existing genetic variation is recombined and passed on from the current generation to the next – a critical step in how corals may adapt to changing environments. We built a genetic linkage map for Acropora palmata and characterized the recombination landscape in a coral for the first time. We discovered pronounced heterochiasmy in A. palmata and suggest this may be due to female meiotic drive. We further confirm that coral recombination rates are high compared to other animals, which is a necessary prerequisite for fast adaptation to changing conditions. We then turned to studying how the genome of A. palmata recombines with the genome of its sister species, A. cervicornis when they form an F1 hybrid. We profiled the local ancestry of F1 hybrids between the two species and found regions of loss of heterozygosity (LOH) despite the expectation of heterozygosity at all loci in an F1 interspecific hybrid. These LOH regions were biased for the A. palmata ancestry and could contribute to the commonly observed sterility of the F1 hybrid. However, we did not find an association between local recombination in A. palmata and the LOH regions in the F1 hybrids, therefore the mechanisms underlying excess parentage of A. palmata in F1 hybrids remains unknown and deserves further study. Overall, this dissertation aims to develop and implement genomic resources and population genetic approaches to aid conservation efforts and to enhance our understanding of these threatened animals at the base of the Tree of Life. The results found here emphasize the importance of including genomic resources for a diversity of taxa during the study of core concepts in biology. Particularly, these findings demonstrate the value of high-quality genomic resources in non-model systems, such as corals.