PhD Project: Fire and Ice: Genomic insights into the evolution, biogeography and extinction of modern penguins

2019, University of Otago.

Supervisors: Jon Waters, Janet Wilmshurst

Abstract

Islands of the vast Southern Ocean host abundant endemic wildlife populations representing important breeding grounds for many seabirds. With contrasting geological, glacial and human-impact histories, these islands represent strong systems for inferring evolutionary processes. Although penguins (Sphenisciformes) spend much of their lives at sea, most taxa require ice-free terrain for breeding, inhabiting every major landmass and archipelago in the Southern Ocean. While many penguin species are distributed widely across sub-Antarctic and Antarctic coastlines, nearly a third of all taxa are endemic to geologically young islands, especially in the New Zealand region. Penguins therefore represent an ideal group of seabirds with which to study the biogeographic and evolutionary effects of island history. This thesis extends classic approaches in island biology research to the Southern Ocean islands, using penguins as the focal system. The various analyses include evidence from near-complete mitochondrial genomes, thousands of genome-wide single nucleotide polymorphisms, together with mitochondrial cytochrome oxidase subunit 1 and control region sequences, generated to examine spatial and temporal evolutionary patterns across all extant and recently extinct taxa. First, this thesis generates a broad framework for understanding penguin evolution by providing the first time-calibrated phylogeny to encompass all modern taxa (Chapter 2). Divergence-time estimates demonstrate that many island-endemic taxa diverged following the geological emergence of their natal islands. This study provides the first molecular demographic analyses to encompass all sub-Antarctic and Antarctic penguin taxa (Chapter 3). Genome-wide single nucleotide polymorphisms yielded signatures of concerted demographic expansions following the Last Glacial Maximum, suggesting taxa inhabiting islands south of the Last Glacial Maximum sea-ice limit underwent rapid post-glacial expansion associated with rapid climate change. This thesis also provides the first multi-species genetic assessment of the impacts of Polynesian and European arrival on New Zealand and Chatham Island penguin assemblages (Chapter 2 and Chapter 4). Phylogenetic analyses of modern and ancient mitochondrial genomes, together with cytochrome oxidase subunit 1 and control region sequences, revealed the presence of two recently extinct penguin taxa from the Chatham Islands (Eudyptes warhami and Megadyptes antipodes richdalei), that are formally described here using genetic and morphological comparisons (Chapter 2). Recent extinction of these island-endemic lineages was likely a direct result of human pressure. By contrast, phylogenetic and demographic analyses of cytochrome oxidase subunit 1 and control region revealed limited evidence for demographic reductions in mainland New Zealand Eudyptes penguins, with ecological preferences possibly buffering those taxa from human impacts (Chapter 4). This thesis also provides new systematic insights for ‘extinct’ prehistoric penguins elsewhere, demonstrating that the so-called Hunter Island penguin is actually an artificial assemblage of three extant taxa (Chapter 5). Furthermore, this study concludes that rockhopper penguins comprise three species, that extant and extinct Megadyptes penguins comprise three subspecies, and that royal and macaroni penguins are probably incipient species. The results of this thesis are synthesised and discussed in the broader context of island biology (Chapter 6). Overall, this study provides a global assessment of recent penguin biogeography, evolution and extinction, providing a comprehensive basis for ongoing management and conservation of penguin biodiversity.

Google scholar: https://scholar.google.co.nz/citations?user=trX_cyYAAAAJ&hl=en&oi=ao