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Health Sciences profile

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
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:

  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.

Publications

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

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

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

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

Westbury, M., Prost, S., Seelenfreund, A., Ramirez, 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

Chapter in Book - Research

Knapp, M., & Hofreiter, M. (2014). Ancient human DNA: Phylogenetic applications. In Encyclopedia of Life Sciences. Chichester, UK: John Wiley & Sons. doi: 10.1002/9780470015902.a0005143.pub3

Knapp, M., Stiller, M., & Meyer, M. (2012). Generating barcoded libraries for multiplex high-throughput sequencing. In B. Shapiro & M. Hofreiter (Eds.), Ancient DNA: Methods and protocols: Methods in molecular biology (Vol. 840). (pp. 155-170). New York: Humana Press. doi: 10.1007/978-1-61779-516-9_19

Knapp, M., Vigilant, L., & Hofreiter, M. (2008). Ancient DNA: Phylogenetic applications. In H. Kehrer-Sawatzki (Ed.), Encyclopedia of Life Sciences. Chichester, UK: John Wiley & Sons. doi: 10.1002/9780470015902.a0005143.pub2

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Journal - Research Article

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

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

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

Westbury, M., Prost, S., Seelenfreund, A., Ramirez, 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

Knapp, M., Lalueza-Fox, C., & Hofreiter, M. (2015). Re-inventing ancient human DNA. Investigative Genetics, 6, 4. doi: 10.1186/s13323-015-0020-4

Collins, C. J., Rawlence, N. J., Prost, S., Anderson, C. N. K., Knapp, M., Scofield, R. P., Robertson, B. C., Smith, I., Matisoo-Smith, E. A., … Waters, J. M. (2014). Extinction and recolonization of coastal megafauna following human arrival in New Zealand. Proceedings of the Royal Society B, 281, 20140097. doi: 10.1098/rspb.2014.0097

Goldberg, J., Knapp, M., Emberson, R. M., Townsend, J. I., & Trewick, S. A. (2014). Species radiation of carabid beetles (Broscini: Mecodema) in New Zealand. PLoS ONE, 9(1), e86185. doi: 10.1371/journal.pone.0086185

King, T. E., Fortes, G. G., Balaresque, P., Thomas, M. G., Balding, D., Delser, P. M., … Knapp, M., … Schürer, K. (2014). Identification of the remains of King Richard III. Nature Communications, 5, 5631. doi: 10.1038/ncomms6631

Bohman, K., Evans, A., Gilbert, M. T. P., Carvalho, G. R., Creer, S., Knapp, M., … de Bruyn, M. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 29(6), 358-367. doi: 10.1016/j.tree.2014.04.003

Stiller, M., Molak, M., Prost, S., Rabeder, G., Baryshnikov, G., Rosendahl, W., … Knapp, M. (2014). Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International, 339-340, 224-231. doi: 10.1016/j.quaint.2013.09.023

Collins, C. J., Rawlence, N. J., Worthy, T. H., Scofield, R. P., Tennyson, A. J. D., Smith, I., Knapp, M., & Waters, J. M. (2014). Pre-human New Zealand sea lion (Phocarctos hookeri) rookeries on mainland New Zealand. Journal of the Royal Society of New Zealand, 44(1), 1-16. doi: 10.1080/03036758.2013.828761

Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., … Meyer, M. (2013). Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. PNAS, 110(39), 15758-15763. doi: 10.1073/pnas.1314445110

Knapp, M., Clarke, A. C., Horsburgh, K. A., & Matisoo-Smith, E. A. (2012). Setting the stage-building and working in an ancient DNA laboratory. Annals of Anatomy, 194(1), 3-6. doi: 10.1016/j.aanat.2011.03.008

Knapp, M., Horsburgh, K. A., Prost, S., Stanton, J.-A., Buckley, H. R., Walter, R. K., & Matisoo-Smith, E. A. (2012). Complete mitochondrial DNA genome sequences from the first New Zealanders. PNAS, 109(45), 18350-18354. doi: 10.1073/pnas.1209896109

Lippold, S., Knapp, M., Kuznetsova, T., Leonard, J. A., Benecke, N., Ludwig, A., … Hofreiter, M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications, 2, 450-455. doi: 10.1038/ncomms1447

Knapp, M. (2011). The next generation of genetic investigations into the Black Death. PNAS, 108(38), 15669-15670. doi: 10.1073/pnas.1112574108

Knapp, M., & Hofreiter, M. (2010). Next generation sequencing of ancient DNA: Requirements, strategies and persectives. Genes, 1(2), 227-243. doi: 10.3390/genes1020227

Prost, S., Knapp, M., Flemmig, J., Hufthammer, A. K., Kosintsev, P., Stiller, M., & Hofreiter, M. (2010). A phantom extinction? New insights into extinction dynamics of the Don-hare Lepus tanaiticus. Journal of Evolutionary Biology, 23(9), 2022-2029. doi: 10.1111/j.1420-9101.2010.02062.x

Prost, S., Smirnov, N., Fedorov, V. B., Sommer, R. S., Stiller, M., Nagel, D., Knapp, M., & Hofreiter, M. (2010). Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus. PLoS ONE, 5(5), e10447. doi: 10.1371/journal.pone.0010447

Stiller, M., Baryshnikov, G., Bocherens, H., d'Anglade, A. G., Hilpert, B., Münzel, S. C., … Knapp, M. (2010). Withering away: 25,000 years of genetic decline preceded cave bear extinction. Molecular Biology & Evolution, 27(5), 975-978. doi: 10.1093/molbev/msq083

Knapp, M., Finstermeier, K., Horn, S., Stiller, M., & Hofreiter, M. (2010). Multiplex-PCR: Neue PCR-technologien für alte DNA [Multiplex-PCR: New PCR technologies for ancient DNA]. Biospektrum, 5, 531-535.

Knapp, M., Rohland, N., Weinstock, J., Baryshnikov, G., Sher, A., Nagel, D., … Horfreiter, M. (2009). First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Molecular Ecology, 18, 1225-1238. doi: 10.1111/j.1365-294X.2009.04088.x

Stiller, M., Knapp, M., Stenzel, U., Hofreiter, M., & Meyer, M. (2009). Direct multiplex sequencing (DMPS): A novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Research, 19, 1843-1848. doi: 10.1101/gr.095760.109

Knapp, M., Mudaliar, R., Havell, D., Wagstaff, S. J., & Lockhart, P. J. (2007). The drowning of New Zealand and the problem of Agathis. Systematic Biology, 56(5), 862-870. doi: 10.1080/10635150701636412

Knapp, M., Stöckler, K., Havell, D., Delsuc, F., Sebastiani, F., & Lockhart, P. J. (2005). Relaxed molecular clock provides evidence for long-distance dispersal of Nothofagus (Southern Beech). PLoS Biology, 3(1), e14.

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