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
Loading...
Date
2014
DOI
Open Access Location
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Massey University
Rights
The Author
Abstract
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.
Description
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
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
Keywords
Corynocarpus laevigatus, Karaka, kōpi, Aotearoa, New Zealand, Research Subject Categories::NATURAL SCIENCES::Biology::Cell and molecular biology::Genetics