Ngā uri o karaka : a genetic study of the karaka/kōpi tree in Aotearoa/New Zealand : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University/Te Kunenga ki Pūrehuroa, Palmerston North/Te Papaioea, New Zealand/Aotearoa

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Polynesians translocated a number of plant species around the Pacific region. Many of these tropical crops were probably introduced to New Zealand, however, only a few survived owing to the cooler climate. Compensating for the loss of introduced crops, Maori cultivated endemic species they discovered in New Zealand. This project focuses on cultural and evolutionary aspects of the cultivation of one of these, karaka (Corynocarpus laevigatus Forst. & Forst.), which was cultivated for its highly nutritious kernel. Originally it is thought to have been restricted to the northern North Island. Its occurrence in the southern North Island, the South Island, Chatham and Kermadec Islands is strongly associated with Maori and Moriori archaeological sites and considered to have resulted from translocations as part of its cultivation. For this project, hypotheses were formulated based on existing written accounts of oral histories, published studies on karaka and informal observations and recollections. Oral histories exist regarding the origins of some translocated populations and have the potential to play an important role in tracing the history of karaka. The relationships among the five Corynocarpus species were investigated by analyzing DNA sequences amplified using universal nuclear and chloroplast markers to test hypotheses of the inter- and intraspecific relationships of the genus. Nuclear markers suggest a closer relationship between C. laevigatus and C. dissimilis whereas the interpretation from chloroplast markers is less clear. This is indicated by the rbcL and trnL-trnF networks, which both show a reticulation suggesting support for both C. laevigatus and C. similis being more closely related to each other and C. laevigatus and C. dissimilis being more closely related. Nevertheless, in all cases, all markers suggest a close relationship between C. laevigatus and Corynocarpus species to the north of New Zealand (C. dissimilis in New Caledonia and C. similis in Vanuatu). Using universal primers, intraspecific variation within karaka was found to be too low for studying translocation histories within New Zealand and extensive marker development was necessary. The first step in the development of chloroplast markers was characterisation of the chloroplast genome as a reference for different strategies in molecular marker identification. A protocol was developed for the isolation of chloroplasts and the sequencing of the chloroplast genome using the Illumina Genome Analyser II. This protocol was also shown to be effective in the characterisation of chloroplast genomes in other elements of the New Zealand flora. The sequence variability of the karaka chloroplast genome was investigated as a potential source for seed dispersal markers. A set of seven chloroplast molecular markers was developed and evaluated in terms of their potential for elucidating the history of karaka translocation during Maori settlement of New Zealand. Long-range polymerase chain reaction products were amplified from the chloroplast genome sequenced using Illumina Genome Analyser II, which enabled the identification of 48 putative chloroplast single nucleotide polymorphisms (SNPs). Sanger sequencing validated 16 of these detected SNPs. High resolution melting (HRM) was evaluated as an accurate, sensitive and fast PCR-based method to screen SNP variations in the chloroplast genome of karaka. Sufficient resolution in the data enabled an evaluation of the phylogeographic distribution of karaka to provide insight into the extent of human-mediated dispersal of the tree in New Zealand. The results of the analysis of species-specific markers show the potential of the chloroplast genome to study recent events in plant history, and the use of HRM to assay several hundred accessions for a suite of chloroplast SNPs. They show an interesting relationship between Kermadec Island karaka and mainland karaka, and between Rekohu/Chatham Islands karaka and mainland karaka. To be able to pinpoint the location of the source for Rekohu/Chatham Islands karaka, more genetic work is required. However, these results are promising in their ability to trace the translocation of one of New Zealand’s most important ethnobotanical species. By developing a more detailed picture of the genetic variation of karaka, this work has the potential to be the foundation for a deeper study into the translocation of the species. This has implications for further understanding the level of domestication in karaka, which at present cannot be ascertained.
Content removed for copyright reasons: Appendix 8. Goremykin, V. V., Nikiforova, S. V., Biggs, P. J., Zhong, B., Delange, P., Martin, W. ...Lockhart, P. J. (2013). The evolutionary root of flowering plants. Systematic Biology, 62(1), 50-61. doi:10.1093/sysbio/sys070
Appendix 9: Nexus files used to generate SplitsGraphs for Chapter Two and Chapter Four. Appendix 10: FASTA sequence alignment files for SNPs 1, 2, 3, 8, 16, 41 and 49
Corynocarpus laevigatus, Karaka, kōpi, Aotearoa, New Zealand, Research Subject Categories::NATURAL SCIENCES::Biology::Cell and molecular biology::Genetics