Author: Gabrielle Genty
Genty, Gabrielle, 2024 Evolutionary genomics of Balaenopterids with a focus on the blue whale (Balaenoptera musculus), Flinders University, College of Science and Engineering
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Marine ecosystems, with their minimal physical barriers and limited opportunities for allopatry, provide a unique perspective to study evolutionary adaptations. Cetaceans—whales, dolphins, and porpoises—represent a diverse group of mammals that transitioned from terrestrial to fully aquatic life approximately 50 million years ago. While the general adaptive processes underlying this transition have been well studied, the diversification of modern cetaceans, particularly within the baleen whale family (Balaenopteridae), remains a complex and poorly understood aspect of their evolutionary history. Understanding the genomic basis of species diversification is crucial in evolutionary biology as it uncovers how genetic variations drive species formation and adaptation while also informing on species resilience or vulnerability. This thesis aims to clarify the genomic basis of diversification and evolutionary history of baleen whales, with a focus on blue whales (Balaenoptera musculus). By analysing whole-genomes from 15 cetacean species, the study detected various genomic regions associated with the diversification and adaptation of baleen whales (Chapter 2). A robust molecular phylogeny constructed with over 10,000 orthologous genes demonstrated substantial genomic changes in balaenopterids related to aging, survival, and homeostasis. Notably, positive selection was identified in immune system genes of the largest species, blue and fin whales, suggesting a link between increased body size and enhanced immune function. The thesis further explored the impact of historical environmental changes on the connectivity, demography, and diversification of blue whales (Chapter 3). An analysis of 16,661 single nucleotide polymorphisms (SNPs) from 275 individuals, representing three of the four recognised subspecies, showed that past climatic and oceanographic events have shaped blue whale subspecies. Coalescent models indicated that divergence among blue whale lineages occurred around 300,000 years ago during the Pleistocene, a period marked by major environmental shifts. Fluctuations in climate and primary productivity likely influenced the connectivity and demographic history of blue whales, shaping their current genetic diversity and distribution. There was no evidence of recent genetic bottlenecks, possibly due to limitations in detecting such signals with a reduced representation genomic dataset and the analysis used. However, in a further examination of blue whale subspecies this time using whole-genome population resequencing data from most subspecies, including three lineages and five populations, and first-generation hybrids between Antarctic and pygmy blue whales, this signal was revealed (Chapter 4). Phylogenomic analysis based on 13,041 orthologous genes, combined with population genetic analysis based on 1,520,428 SNPs, demonstrated genetic differentiation among Atlantic, Pacific, Antarctic, and pygmy blue whales, suggesting a complex interrelationship among these groups. The whole-genome analyses provided insights into recent demographic trends, highlighting a significant population decline in Antarctic blue whales during the whaling era, with no subsequent recovery. On the other hand, Atlantic and pygmy blue whales showed a similar decline but with evidence of recovery over time. Runs of homozygosity (ROH) analyses revealed generally low inbreeding levels and larger past population sizes, except in pygmy blue whales, which exhibited a greater number and longer ROHs indicating smaller historical population sizes. Despite recent overexploitation on all lineages, heterozygosity levels and genetic load analysis suggest that blue whale populations retained considerable diversity to support their recovery. The low genetic load and minimal inbreeding in the Antarctic lineage offer a promising outlook for the long-term viability of this subspecies; however, contrasting findings from the recent demographic history analysis suggest that its recovery may be slower than anticipated. This comprehensive study underscores the importance of integrating genomic and historical data to understand the complex evolutionary processes that shape baleen whales, and in particular, blue whales. The findings contribute to a deeper understanding of cetacean evolution and have major implications for conservation strategies aimed at protecting and managing blue whale lineages in their diverse habitats.
Keywords: comparative genomics, phylogenetics, population structure, genomic adaptation, population health, historical demography, conservation genomics
Subject: Biology thesis
Thesis type: Doctor of Philosophy
Completed: 2024
School: College of Science and Engineering
Supervisor: Luciana Möller