Ancient DNA of New Zealand's extinct avifauna

Abstract

As a direct result of human activity and other environmental changes, considerable ecological changes and species extinctions have occurred on most terrestrial environments during the last 50,000 years. Therefore, correctly interpreting naturally occurring biogeography or ecology is limited without including historical information. Detailed insights into past environments or extinct species can be provided by ancient DNA (aDNA), yet this field has long been limited by the degraded nature of ancient genetic material. Recent developments and the increasing availability of next-generation sequencing (NGS), is now allowing for a breakthrough in aDNA studies. It is now possible to obtain entire genomes from long-extinct organisms, and sequence high-depth ‘environmental DNA’ representative of prehistoric environments. New Zealand (NZ) was the last of the large landmasses (except Antarctica) to be colonised by humans, approximately 700 years ago. Furthermore, the long isolation of NZ from Gondwana (from which it separated between ~85-52 Ma) resulted in an ancient, ecologically complex and biogeographically unique biota. Due to a near-absence of mammals this biota was dominated by a diverse array of endemic bird species, of which nearly 50% are now extinct due to human activity. Nonetheless, the recent age of NZ’s extinctions, combined with a temperate climate, has permitted an unparalleled degree of preservation of the pre-human ecosystem. By use of aDNA and NGS methods, NZ’s biota may now be understood in relative completion. This thesis uses aDNA NGS methods to research a select number extinct bird species. Chapters Two and Three investigate environmental DNA of avian coprolites (paleofaeces), most of which originate from four species of the megaherbivore ratite moa (Dinornithiformes). It is identified for the first time that the extinct moa consumed and dispersed species of mycorrhizal fungi important in natural forest dynamics. Phylogenetics of sequenced moa parasite DNA found rare evidence for a higher taxonomic level co-extinction event: between moa, and an identified genus or family of moa-specific nematodes. Finally, differences in parasite, plant and fungal DNA assemblages greatly support divergent behaviour strategies between each moa species. I also analyse shotgun DNA and DNA-RNA hybridization enrichment data on avian coprolites representative of rich deposits in semi-arid areas of the central South Island. I find that these samples have been greatly affected by thermal-based DNA damage and/or formation of organic compounds inhibiting DNA amplification. Future approaches aiming to resolve these issues are discussed. Chapter Four investigates the phylogeny one of NZ’s most poorly understood large bird taxa, the adzebills (Aptornis, Aptornithidae). Sequencing of near-complete complete mitochondrial genomes of both recently extinct species, resolves placement of these birds within the superfamily Ralloidea (Gruiformes). This in turn elucidates evolutionary details into the global radiation of Ralloid birds and the Aptornis lineage in NZ. The final Fifth chapter summarizes the results of these diverse studies and how they interrelate, and concludes the thesis by discussing future related aDNA projects to be undertaken on NZ’s ancient ecosystem.