Associate Professor Michael Knapp

Contact Details

Phone: 64 3 479 5169
Email: michael.knapp@otago.ac.nz

University Links

Position

Associate Professor

Department

Department of Anatomy

Qualifications

Diplom(Saarland) PhD(Massey)

Research summary

Evolutionary genomics and conservation genomics; biological anthropology

Teaching

BIOA 101 Introduction to Biological Anthropology
BIOA 201 Biocultural Human Skeletal Biology
BIOA 301 Biological Anthropology of the Human Skeleton

Memberships

Editorial Board Member: PLOS ONE
Editorial Board Member: Scientific Reports

Research

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:

How did past environmental change and human migration shape our present day biodiversity?
How do modern conservation measures influence biodiversity?
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.

I am also a member of the Coastal People: Southern Skies collaboration that connects communities with world-leading, cross-discipline research to rebuild coastal ecosystems.
Coastal People: Southern Skies

He Kitenga: eDNA's species snapshot describes recent work detecting species in the diverse marine environments of Doubtful Sound and Aramoana.

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.

Publications

Adams, C. I. M., Jeunen, G.-J., Cross, H., Taylor, H. R., Bagnaro, A., Currie, K., Hepburn, C., Gemmell, N. J., … Knapp, M. (2023). Environmental DNA metabarcoding describes biodiversity across marine gradients. ICES Journal of Marine Science, fsad017. Advance online publication. doi: 10.1093/icesjms/fsad017

Grosser, S., Dutoit, L., Foster, Y., Robertson, F., Fidler, A. E., Martini, D., Knapp, M., & Robertson, B. C. (2023). Genomic evidence of a functional RH2 opsin in New Zealand parrots and implications for pest control. New Zealand Journal of Zoology, 50(2), 341-349. doi: 10.1080/03014223.2022.2053554

Dussex, N., & Knapp, M. (2022). Back from the brink: How genome research is helping the recovery of the Chatham Island black robin. The Conversation. Retrieved from https://theconversation.com/back-from-the-brink-how-genome-research-is-helping-the-recovery-of-the-chatham-island-black-robin-194319

von Seth, J., van der Valk, T., Lord, E., Sigeman, H., Olsen, R.-A., Knapp, M., Kardailsky, O., Robertson, F., … Robertson, B. C., & Dussex, N. (2022). Genomic trajectories of a near-extinction event in the Chatham Island black robin. BMC Genomics, 23, 747. doi: 10.1186/s12864-022-08963-1

Czechowski, P., de Lange, M., Knapp, M., Terauds, A., & Stevens, M. I. (2022). Antarctic biodiversity predictions through substrate qualities and environmental DNA. Frontiers in Ecology & the Environment, 20(10), 550-557. doi: 10.1002/fee.2560

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Associate Professor Michael Knapp

Contact Details

University Links

Research

Brief description of research

Research interests

New projects include:

Existing projects include:

Publications