esac014.pdf (7.17 MB)

Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis)

Download (7.17 MB)
journal contribution
posted on 2023-05-03, 18:22 authored by Allison Miller, Nataliya Timoshevskaya, Jeramiah Smith, Joanne Gillum, Saeed Sharif, Shannon ClarkeShannon Clarke, Cindy Baker, Jane Kitson, Neil Gemmell, Alana Alexander
Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft Geotria australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16,000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n=186) and sequence data from Cyt-b (766 bp, n=94) and COI (589 bp, n=20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.


Rights statement

© The American Genetic Association. 2022.||This is an Open Access article distributed under the terms of the Creative Commons AttributionNonCommercial License (, which permits noncommercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.


  • English

Does this contain Māori information or data?

  • No


Oxford University Press

Journal title

Journal of Heredity




Miller, A. K., Timoshevskaya, N., Smith, J. J., Gillum, J., Sharif, S., Clarke, S., 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(4), 380–397.

Usage metrics


    Ref. manager