Dr. Allison Miller

Hello/Hafa adai/ Kia Ora! 

I received my undergraduate degree (B.Sc.) from the University of California San Diego, my master’s (M.Sc.) degree from the University of Guam, and my doctorate (PhD) degree from the University of Otago (New Zealand). My interests include ecology, evolution, population genetics, marine invertebrate biology, and reef biology. I am also passionate about conservation and biodiversity management, and I practiced these as a biological technician (US National Park Service, Guam) during the time between my master’s and doctorate degrees.

I studied sea cucumber (Holothuroidea, Echinodermata) phylogenetics for my master’s work and I investigated the use of genomic methods (e.g., population genetics and transcriptomics) for understanding enigmatic species for my PhD thesis work. My PhD work primarily focused on the pouched lamprey (called kanakana/piharau in New Zealand) and could not have been completed without the support of kaitiaki (guardians), Dr. Jane Kitson, my supervisors, and multiple international collaborators. During this work I also created two citizen science pages to find out more information about this unique taonga (treasured) species – please see info below on how you can help.

As a current postdoc in the Gemmell lab I am excited to be continuing my past work and to be starting my new work on the Toka Ākau Toitū Kaitiakitanga project (https://taukiakau.org/). For this project our team will be using environmental DNA (eDNA) methods to better understand coastal reef ecosystems and how they may be affected by climate change/land development. We will also work towards optimising marine monitoring methods to enrich the management of these systems so that they will persist long into the future. 

Allison Miller in a trip to Glenorchy.

Southern Hemisphere lamprey information and citizen science

You can help our research on lamprey/kanakana by getting involved! 

Do you, or others you know, spend time near rivers or streams? If yes, there are two citizen science projects you might be able to contribute to! Citizen science projects are activities sponsored by a wide variety of organizations so non-scientists can meaningfully contribute to scientific research. In our case, sightings of kanakana around the country are valuable pieces of information!

Lamps_for_champs is a site for collecting vital Southern Hemisphere kanakana distribution data. Where are kanakana found in the Southern Hemisphere? iNaturalist Lamps_for_champs citizen scientists are asked to “Add an Observation” about a kanakana they find in the wild to help answer this question.

Alongside this project, FISHYbites is another citizens science project for collecting much-needed information about the health and feeding preferences of Southern Hemisphere fishes. Have you see something FISHY in your backyard stream? For example, an odd bite mark on a fish, or red markings on a kanakana? This could be a lamprey bite or Lamprey Reddening Syndrome. FISHYbites citizen scientists are asked to keep a look out for these marks on fishes and lampreys and to “log the bite” if they see them.

Information on these projects will be used by natural resource managers to improve their management strategies and better protect the species. This protection is particularly important now, since kanakana numbers are decreasing due to habit alteration, disease, and climate change.

Read more about this curious creature and the work we are doing on it here:


Keep up with all the hard mahi (work) that kaitiaki are doing here:



  • Urban, L., Miller, A.K., Eason, D., Vercoe D., … Digby, A. (2023). Genomic monitoring of the critically endangered kākāpō by real-time targeted nanopore sequencing of environmental DNA. eLife. 1–25. http://dx.doi.org/10.2139/ssrn.3977260
  • Koch, N.M, Tilic, E., Miller, A.K., Stiller, J., A.K., Rouse, G.W. (2023). Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea. Proceedings of the Royal Society B. (In Press). https://doi.org/10.1098/rspb.2023.0988.
  • Phillips, R.A., Waluda, C.M., Miller, A.K. (2023). Distribution, host, and long-term decline in abundance of the Patagonian lamprey inferred from diet assessment of albatrosses. Reviews in Fish Biology and Fisheries. 1–22. https://doi.org/10.1007/s11160-023-09786-3
  • Miller, A.K., Baker, Brosnahan, C.L., Pande, A., Baker, C., Kitson, J., Gemmell, N.J., Dowle, E. (2023). Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease. Molecular Ecology Resources. 2023;001–18. https://doi.org/10.1111/1755-0998.13805
  • Timoshevskaya, N., Eskut, K.I., Timoshevskiy, V.A., … Miller, A.K., … Smith, J.J. (2023). An improved sea lamprey germline genome assembly illuminates the evolution of germline-specific chromosomes. Cell Reports. 42(3). https://doi.org/10.1016/j.celrep.2023.112263
  • Komai, T., Miller, A.K., Malay, M.C. (2022). A new species of diogenid hermit crab genus Pseudopaguristes McLaughlin, from the Northern Mariana Islands, Micronesia. Zootaxa. 5175(5), 570–582.  DOI: 10.11646/zootaxa.5175.5.6
  • Miller, A.K., Timoshevskaya, N., Smith, J., Gillum, J., Sharif, S., Shannon, C., Baker, C., Kitson, J., Gemmell, N.J., Alexander, A. (2022). Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). Journal of Heredity. 113, 380–397. https://doi.org/10.1093/jhered/esac014
  • Komai, T.*, Miller, A.K.*, Malay, M.C. (2022). Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia. Zootaxa. 5099(5), 563–585.*Authors contributed equally
  • Malay, M.C.*, Miller, A.K.*, Komai, T. (2021). Hermit crabs (Crustacea: Decapoda: Anomura: Paguroidea) of the Northern Marianas, including new records and an updated checklist. Micronesica. 2021-01: 1–29. *Authors contributed equally
  • Miller, A.K., Mifsud, J. C., Costa, V. A., Grimwood, R. M., … Geoghegan, J. L. (2021). Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evolution. 7(2), 1–10. https://doi.org/10.1093/ve/veab050
  • Miller, A.K., Baker, C., Kitson, J.C., Yick, J.L., Manquel, P.E.I., Alexander, A., Gemmell, N.J. (2021). The Southern Hemisphere lampreys (Geotriidae and Mordaciidae). Reviews in Fish Biology and Fisheries. 1–32.
  • Clemens, B., Arakawa, C., Baker, C., Miller, A.K., Coghlan, S., Kucheryavyy, … Mateus, C. (2020). Management of anadromous lampreys: common challenges, different approaches. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2020.09.005
  • Lichangco, G., Foltz, D., Reid, R., Williams, J., Nodzak, C., Kerr, A.M., Miller, A.K., Hunter, R., Wilson, N.G., Williams, J.N., Mah, C.L., Rouse, G.W., Wray, G.A., Janies, D.A. (2017). The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics. Molecular Phylogenetics and Evolution. 115, 161–170. DOI: 10.1016/j.ympev.2017.07.022
  • Kerr, A.M., Miller, A.K., Brunson, C., Gawel, A.M. (2017). Commercially valuable sea cucumbers of Guam. University of Guam Marine Laboratory Technical Report 162.
  • Miller, A.K., Kerr, A.M., Paulay G., Reich M., Pawson, D.L., Pawson D.J., Carvajal J.I., Rouse, G.W. (2017). Molecular phylogeny of extant Holothuroidea (Echinodermata). Molecular Phylogenetics and Evolution. 111, 110–131. https://doi.org/10.1016/j.ympev.2017.02.014
  • Janies, D.A., Witter, Z., Linchangco, G.V., Foltz, D.W., Miller, A.K., Kerr, A.M., Jay, J., Reid, R.W., Wray, G.A. (2016). EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics. 17:48. https://doi.org/10.1186/s12859-016-0883-2
  • Kim, S.W., Miller, A.K., Brunson, C., Netchy, K., Clouse, R.M., Janies, D., Tardy, E., Kerr, A.M. (2014). Shallow-water holothuroids (Echinodermata) of Yap, Federated States of Micronesia. Pacific Science. 68(3), 397–420. https://doi.org/10.2984/68.3.8
  • Kerr, A.M., Kim, S.W., Miller, A.K. (2013). The Shallow-water Holothuroids of Chuuk, Federated States of Micronesia. University of Guam Marine Laboratory Technical Report. 155.
  • Michonneau, F., Borrero-Perez, G.H., Honey, M., Kamarudin, K.R., Kerr, A.M., Menez, M.A., Miller, A.K., Ochoa J.A., Olavides, R.D., Paulay, G., Samyn, Y., Setyastuti, A. Solis-Marin, F., Starmer, J., VandenSpiegel, D. (2013). The littoral sea cucumber (Echinodermata: Holothuroidea) fauna of Guam re-assessed – a diversity curve that still does not asymptote. Cahiers de Biologie Marine. 54, 531–540.
  • Goodbody-Gringley, G., Wetzel, D.L., Pulster, E., Gillion, D., Miller, A.K., Ritchie, K.R. (2013) Toxicity of Deepwater Horizon Source Oil and the Chemical Dispersant, Corexit 9500, to Coral Larvae. PLOS ONE. 8, 1–10. https://doi.org/10.1371/journal.pone.0045574
  • Raymundo, L., Diaz, R., Miller, A.K., Reynolds, T. (2011). Baseline Surveys of Proposed and Established Marine Sanctuaries on Bantayan Island, Northern Cebu. University of Guam Technical Report 141.
  • Whittaker D., Richmond, K., Miller, A.K., Kiley, R., Burns, C., Atwell, J., Ketterson, E. (2011). Intraspecific preen oil odor preferences in dark-eyed juncos (Junco hyemalis). Behavioral Ecology. 22, 1–8. https://doi.org/10.1093/beheco/arr122
  • Ritchie, B.K. Miller, A.K. (2011). A rapid response to cold water stress on corals – Monitoring coral health and immunity across habitat gradients in the lower Florida Keys. TNC Final Report. (MML 197–548).