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Health Sciences staff profiles

Dr Michael Knapp

PositionSenior Lecturer in Biological Anthropology / Rutherford Discovery Fellow
DepartmentDepartment of Anatomy
QualificationsDiplom(Saarland) PhD(Massey)
Research summaryEvolutionary genomics and conservation genomics; biological anthropology
  • BIOA 101 Introduction to Biological Anthropology
  • BIOA 201 Biocultural Human Skeletal Biology
  • BIOA 301 Biological Anthropology of the Human Skeleton
  • Editorial Board Member: PLOS ONE
  • Editorial Board Member: Scientific Reports


Brief description of research

My group focuses on how species interact with their environment both on the molecular and on the population level and on how human activity shapes biodiversity. This interdisciplinary work aims at addressing a number of key questions including:

  1. How did past environmental change and human migration shape our present day biodiversity?
  2. How do modern conservation measures influence biodiversity?
  3. What is the genetic basis of evolutionary adaptation to new environments?

Our work integrates genomic, phylogenetic, biogeographic and environmental data to address these questions from a multi-disciplinary angle.

This research will contribute to protecting New Zealand's natural heritage, build capacity for genome scale projects in New Zealand, and help establish New Zealand at the cutting edge of the rapidly growing field of conservation genomics.

Research interests

New projects include:

1. The evolution and extinction of New Zealand's Haast's eagle. Haast's eagle is a characteristic example of island gigantism. The largest raptor in the world, it went through the most extreme size increase relative to time known of any vertebrate species in the world. The causes for its extinction about 600 years ago are likely related to human arrival, but otherwise unclear. The two key objectives of this project are 1) to reconstruct the possible causes for Haast's eagle extinction and 2) to identify the functional genomic basis of island gigantism in Haast's eagle.

2. Conservation genomics. Due to their adaptions to a mammal free environment, New Zealand birds have suffered dramatic losses through introduced mammalian predators and their conservation is a major challenge. Next generation sequencing technology now allows us to address these challenges in a new way. Instead of using random and often neutral genetic markers to guide conservation efforts, complete genome data will be used to evaluate how populations of threatened bird species differ on a functional genomic level and to develop targeted conservation strategies based on these data.

Project 1 will focus on the evolution and speciation of kea, North Island kaka and South Island kaka and will investigate the feasibility of kaka translocation between the islands as a conservation strategy.

Project 2 will study the world's rarest wading bird, the endemic, critically endangered black stilt (kakī), and the threat it faces from interbreeding with its common, recently introduced sister species, the pied stilt.

Project 3 will use the genomes from all sequenced New Zealand birds to reconstruct the population dynamics of these species throughout the late Pleistocene glacial-interglacial cycles and evaluate the potential threat to each species from climate warming.

Existing projects include:

1. Reconstructing the settlement of the Pacific. The Pacific is the last frontier of human settlement. As part of the Biological Anthropology team at the University of Otago my group contributes to investigating questions relating to human migration into Remote Oceania, including: Who were the Lapita people that first moved into Remote Oceania around 3500 years ago and were they the biological ancestors of indigenous people in the Pacific today? Was there prehistoric contact between Polynesia and South America? To address these questions we are reconstructing the ancestry of early Pacific settlers using ancient DNA extracted from human remains from across the South Pacific.

2. What killed cave bear, mammoth and great auk? Before a species goes extinct it must go through a time of declining population size. The timing and mode of this final decline can be informative for identifying its cause(s). Did a species decline rapidly or slowly and what contemporaneous factors could have facilitated the decline? Are there any potential stressors that correlate strongly with the timing of the decline? To address these questions we are reconstructing the population dynamics of extinct species such as cave bear, mammoth and great auk throughout the past 50,000 years using temporal genetic analysis of radiocarbon dated subfossil remains. We are then correlating these data with known contemporary environmental parameters and potential human interference. These studies do not only give us insights into potential causes of extinct, but also help us to evaluate what makes a species particularly susceptible to extinction.


Thomas, J. E., Carvalho, G. R., Haile, J., Martin, M. D., Samaniego Castruita, J. A., Niemann, J., … Rawlence, N. J., … Knapp, M. (2017). An Aukward' tale: A genetic approach to discover the whereabouts of the last Great Auks. Genes, 8(6), 164. doi: 10.3390/genes8060164

Chang, D., Knapp, M., Enk, J., Lippold, S., Kircher, M., Lister, A., … Shapiro, B. (2017). The evolutionary and phylogeographic history of woolly mammoths: A comprehensive mitogenomic analysis. Scientific Reports, 7, 44585. doi: 10.1038/srep44585

Westbury, M., Prost, S., Seelenfreund, A., Ramírez, J.-M., Matisoo-Smith, E. A., & Knapp, M. (2016). First complete mitochondrial genome data from ancient South American camelids: The mystery of the chilihueques from Isla Mocha (Chile). Scientific Reports, 6, 38708. doi: 10.1038/srep38708

Galla, S. J., Buckley, T. R., Elshire, R., Hale, M. L., Knapp, M., McCallum, J., … Wilcox, P., & Steeves, T. E. (2016). Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Molecular Ecology, 25(21), 5267-5281. doi: 10.1111/mec.13837

Rawlence, N. J., Collins, C. J., Anderson, C. N. K., Maxwell, J. J., Smith, I. W. G., Robertson, B. C., Knapp, M., Horsburgh, K. A., Stanton, J.-A. L., Scofield, R. P., … Matisoo-Smith, E. A., & Waters, J. M. (2016). Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations. Molecular Ecology, 25(16), 3950-3961. doi: 10.1111/mec.13726