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RESEARCH ARTICLE (Open Access)

Genetic differentiation and population connectivity of humpback whales migrating through Aotearoa New Zealand waters

Debbie J. Steel https://orcid.org/0000-0001-5898-2850 A B , Emma L. Carroll B C , C. Scott Baker https://orcid.org/0000-0003-2183-2036 A B , Susana Caballero B D , Simon Childerhouse https://orcid.org/0000-0002-4161-037X B E , Chloe Corne https://orcid.org/0009-0008-3595-2067 F , Claire Garrigue https://orcid.org/0000-0002-8117-3370 B G , Nadine Gibbs B H , Richard Kinsey F , Ngāti Kuri I , Mike Ogle J , Carlos Olavarría B K , Daniel Palacios https://orcid.org/0000-0001-7069-7913 A L , M. Michael Poole https://orcid.org/0009-0008-4942-2243 B M , Kristin Rasmussen https://orcid.org/0000-0003-4758-5010 N , Leena Riekkola https://orcid.org/0000-0002-9653-7106 B C , Jooke Robbins B L and Rochelle Constantine https://orcid.org/0000-0003-3260-539X B C *
+ Author Affiliations
- Author Affiliations

A Marine Mammal Institute, Oregon State University, Newport, OR, USA.

B South Pacific Whale Research Consortium, Avarua, Cook Islands.

C School of Biological Sciences, University of Auckland – Waipapa Taumata Rau, Auckland, New Zealand.

D Aquatic Vertebrate Integrative Conservation Laboratory, Department of Marine and Environmental Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.

E Blue Planet Marine, Nelson, New Zealand.

F Department of Conservation – Te Papa Atawhai, Te Anau, New Zealand.

G Institut de Recherche pour le Développement, Noumea, New Caledonia.

H Cook Strait Whale Project, Takaka, New Zealand.

I Ngāti Kuri Trust Board, Ngataki, Kaitaia, New Zealand.

J Department of Conservation – Te Papa Atawhai, Golden Bay, New Zealand.

K Centro de Estudios Avanzados en Zonas Aridas (CEAZA), Coquimbo, Chile.

L Center for Coastal Studies, Provincetown, MA, USA.

M Marine Mammal Research Program, Moorea, French Polynesia.

N Panacetacea, St Paul, MN, USA.

* Correspondence to: r.constantine@auckland.ac.nz

Handling Editor: Graham Wallis

Pacific Conservation Biology 31, PC25026 https://doi.org/10.1071/PC25026
Submitted: 5 April 2025  Accepted: 14 August 2025  Published: 2 September 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

Context

Historically, humpback whales migrating past Aotearoa New Zealand (NZ) were linked to western South Pacific wintering grounds and Antarctic feeding grounds. As populations have recovered, research has focused on contemporary connectivity patterns throughout the South Pacific.

Aims

To determine the contemporary connectivity of winter breeding grounds for humpback whales on their northern and southern migrations past NZ, and those at the Kermadec Islands (Rangitāhua) migratory stopover.

Methods

We generated DNA profiles (mitochondrial DNA (mtDNA) haplotypes, genetic sex and microsatellite genotypes) using skin samples collected from whales between 1998 and 2021. We used comparisons of DNA profiles and a mixed-stock analysis of mtDNA haplotypes to determine the most likely wintering grounds of genetically identified individuals.

Key results

DNA profiles of 350 individual whales from NZ were compared to profiles from Oceania (n > 2000), Central and South America (n = 452) and East Australia (n = 809). This comparison revealed 35 genotype matches, mainly to New Caledonia and East Australia. The mixed-stock analysis showed that northbound whales (n = 145) had approximately equal assignment proportions to East Australia and New Caledonia whereas southbound whales (n = 74) showed a two-fold higher assignment to East Australia. In contrast, whales passing Rangitāhua (n = 112) assigned to New Caledonia and other Pacific wintering grounds but not to East Australia.

Conclusions

Humpback whales passing mainland NZ on their north and southbound migrations are strongly associated with East Australia and New Caledonia wintering grounds. Those migrating south past Rangitāhua have a broader range of wintering ground destinations, including a connection to Central America.

Keywords: connectivity, genetics, humpback whale, migration, mixed stock assignment, mtDNA, New Zealand, Pacific Ocean.

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