Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics.

In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.

A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies.

The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.

Population structure of pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales in the Southern Hemisphere may reflect foraging ecology and dispersal patterns.

Little is known about the biology of pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales as these animals are difficult to observe in the wild. However, both species strand frequently along the South African, Australian and New Zealand coastlines, providing samples for these otherwise inaccessible species. The use of DNA samples from tissue and DNA extracted from historical material, such as teeth and bone, allowed a first analysis of the population structure of both species in the Southern Hemisphere. A 279 base pair consensus region of the mitochondrial cytochrome b gene was sequenced for 96 K. breviceps (53 tissue and 43 teeth or bone samples) and 29 K. sima (3 tissue and 26 teeth or bone samples), and 26 and 12 unique haplotypes were identified, respectively. K. breviceps showed a higher nucleotide diversity of 0.82% compared to 0.40% in K. sima. Significant genetic differentiation was detected in the Southern Hemisphere between K. breviceps from South Africa and New Zealand (ФST = 0.042, p < 0.05). Mitochondrial control region sequences (505 bp) were available for 44 individuals (41 K. breviceps and 3 K. sima) for comparative purposes. A comprehensive global phylogenetic analysis (maternal lineage) of our sequences together with all available Kogia mtDNA sequences largely supported previously published phylogenetic findings, but highlighted some changed inferences about oceanic divergences within both species. The higher nucleotide diversity and low population differentiation observed in K. breviceps may result from its broad foraging ecology and wide distribution, which may indicate a more opportunistic feeding behaviour and tolerance towards a larger range of water temperatures than K. sima.

Using epigenetic clocks to investigate changes in the age structure of critically endangered Maui dolphins.

The age of an individual is an essential demographic parameter but is difficult to estimate without long-term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including nonmodel organisms such as cetaceans. Maui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Maui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training data set, the optimal model required only eight methylation sites, provided an age correlation of .95, and had a median absolute age error of 1.54 years. A leave-one-out cross-validation analysis with the same parameters resulted in an age correlation of .87 and median absolute age error of 2.09 years. To improve age estimation, we included previously published beluga whale (Delphinapterus leucas) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Maui dolphins revealed a shift from a median age of 8-9 years to a younger population aged 7-8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species.

DNA methylation networks underlying mammalian traits.

Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.

Diversity of mitochondrial DNA in 3 species of great whales before and after modern whaling.

The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere.

Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes.

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.

Carbon, nitrogen, and oxygen stable isotope ratios of striped dolphins and short-finned pilot whales stranded in Hokkaido, northern Japan, compared with those of other cetaceans stranded and hunted in Japan.

Strandings of striped dolphins (SD) and short-finned pilot whales (PW) in Hokkaido, northern Japan, are rare but have recently increased, probably due to global warming. We quantified δ13C, δ15N, and δ18O in muscles of SD (n = 7) and PW (n = 3) stranded in Hokkaido and compared these values with those in muscles (red meat products) of hunted SD and PW in three areas of central and southern Japan. δ18O in stranded SD, except for the calf, decreased with increasing body length (BL), whereas δ13C increased, with no BL-related changes in δ15N. The variability of δ18O (range of maximum and minimum) was larger in the stranded SD (7.5 ‰) than of the hunted SD in three areas (0.9, 1.9, and 1.4 ‰), whereas that of δ15N was smaller in the stranded SD than in the hunted SD. Similarly, the variability of δ18O was larger in the stranded PW in Hokkaido (3.3 ‰) than in the hunted PW in central Japan (1.4 ‰). The larger variability of δ18O and smaller variability of δ15N in stranded SD imply long-term sojourning in coastal waters and feeding on small amounts of limited prey species at low trophic levels before death.

Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales.

Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.

Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change.

Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (>60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (>60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

A surplus no more? Variation in krill availability impacts reproductive rates of Antarctic baleen whales.

The krill surplus hypothesis of unlimited prey resources available for Antarctic predators due to commercial whaling in the 20th century has remained largely untested since the 1970s. Rapid warming of the Western Antarctic Peninsula (WAP) over the past 50 years has resulted in decreased seasonal ice cover and a reduction of krill. The latter is being exacerbated by a commercial krill fishery in the region. Despite this, humpback whale populations have increased but may be at a threshold for growth based on these human-induced changes. Understanding how climate-mediated variation in prey availability influences humpback whale population dynamics is critical for focused management and conservation actions. Using an 8-year dataset (2013-2020), we show that inter-annual humpback whale pregnancy rates, as determined from skin-blubber biopsy samples (n = 616), are positively correlated with krill availability and fluctuations in ice cover in the previous year. Pregnancy rates showed significant inter-annual variability, between 29% and 86%. Our results indicate that krill availability is in fact limiting and affecting reproductive rates, in contrast to the krill surplus hypothesis. This suggests that this population of humpback whales may be at a threshold for population growth due to prey limitations. As a result, continued warming and increased fishing along the WAP, which continue to reduce krill stocks, will likely impact this humpback whale population and other krill predators in the region. Humpback whales are sentinel species of ecosystem health, and changes in pregnancy rates can provide quantifiable signals of the impact of environmental change at the population level. Our findings must be considered paramount in developing new and more restrictive conservation and management plans for the Antarctic marine ecosystem and minimizing the negative impacts of human activities in the region.

mtDNA heteroplasmy gives rise to a new maternal lineage in North Pacific humpback whales (Megaptera novaeangliae).

Heteroplasmy in the mitochondrial genome offers a rare opportunity to track the evolution of a newly arising maternal lineage in populations of non-model species. Here, we identified a previously unreported mitochondrial DNA haplotype while assembling an integrated database of DNA profiles and photo-identification records from humpback whales in southeastern Alaska (SEAK). The haplotype, referred to as A8, was shared by only 2 individuals, a mature female with her female calf, and differed by only a single base pair from a common haplotype in the North Pacific, referred to as A-. To investigate the origins of the A8 haplotype, we reviewed n = 1,089 electropherograms (including replicate samples) of n = 710 individuals with A- haplotypes from an existing collection. From this review, we found 20 individuals with clear evidence of heteroplasmy for A-/A8 (parental/derived) haplotypes. Of these, 15 were encountered in SEAK, 4 were encountered on the Hawaiian breeding ground (the primary migratory destination for whales in SEAK), and 1 was encountered in the northern Gulf of Alaska. We used genotype exclusion and likelihood to identify one of the heteroplasmic females as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. The mutation leading to this heteroplasmy and the fixation of the A8 haplotype provide an opportunity to document the population dynamics and regional fidelity of a newly arising maternal lineage in a population recovering from exploitation.

Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean.

The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.

Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu.

The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic diversity and much about their natural history remain poorly understood. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous peoples of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and True's beaked whale (M. mirus) from the North Atlantic, with which it was previously subsumed. Morphometric analyses of skulls also distinguish the two species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began circa 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous peoples offers a model for broadening the cultural scope of the scientific naming process.

An epigenetic clock to estimate the age of living beluga whales.

DNA methylation data facilitate the development of accurate molecular estimators of chronological age or "epigenetic clocks." We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine-guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R 2 = 0.92 for the training data; and an R 2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross-validation. We applied the epigenetic clock to an independent dataset of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.

Correction: Satellite derived offshore migratory movements of southern right whales (Eubalaena australis) from Australian and New Zealand wintering grounds.

[This corrects the article DOI: 10.1371/journal.pone.0231577.].

Satellite derived offshore migratory movements of southern right whales (Eubalaena australis) from Australian and New Zealand wintering grounds.

Southern right whales (Eubalaena australis) migrate between Austral-winter calving and socialising grounds to offshore mid- to high latitude Austral-summer feeding grounds. In Australasia, winter calving grounds used by southern right whales extend from Western Australia across southern Australia to the New Zealand sub-Antarctic Islands. During the Austral-summer these whales are thought to migrate away from coastal waters to feed, but the location of these feeding grounds is only inferred from historical whaling data. We present new information on the satellite derived offshore migratory movements of six southern right whales from Australasian wintering grounds. Two whales were tagged at the Auckland Islands, New Zealand, and the remaining four at Australian wintering grounds, one at Pirates Bay, Tasmania, and three at Head of Bight, South Australia. The six whales were tracked for an average of 78.5 days (range: 29 to 150) with average individual distance of 38 km per day (range: 20 to 61 km). The length of individually derived tracks ranged from 645-6,381 km. Three likely foraging grounds were identified: south-west Western Australia, the Subtropical Front, and Antarctic waters, with the Subtropical Front appearing to be a feeding ground for both New Zealand and Australian southern right whales. In contrast, the individual tagged in Tasmania, from a sub-population that is not showing evidence of post-whaling recovery, displayed a distinct movement pattern to much higher latitude waters, potentially reflecting a different foraging strategy. Variable population growth rates between wintering grounds in Australasia could reflect fidelity to different quality feeding grounds. Unlike some species of baleen whale populations that show movement along migratory corridors, the new satellite tracking data presented here indicate variability in the migratory pathways taken by southern right whales from Australia and New Zealand, as well as differences in potential Austral summer foraging grounds.

Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground.

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru.

Low mtDNA diversity in a highly differentiated population of spinner dolphins (Stenella longirostris) from the Fernando de Noronha Archipelago, Brazil.

Spinner dolphins (Stenella longirostris, Gray 1828) are widely distributed in tropical waters around the world. Although they occur in large, pelagic groups in the Eastern Tropical Pacific, elsewhere in the Pacific they are found in small and genetically isolated populations associated with islands. This species is considered to be "Least Concern" (LC) by the World Conservation Union (IUCN). To assess genetic diversity and population structure of an island-associated population in the South Atlantic Ocean we surveyed 162 spinner dolphins throughout the Fernando de Noronha Archipelago of the northeast coast of Brazil using ten microsatellite loci and sequencing a 413-bp section of the mitochondrial DNA (mtDNA) control region. Eleven mtDNA haplotypes were identified and haplotype diversity (h) and nucleotide diversity (π) were 0.3747 and 0.0060, respectively. Median-Joining Network revealed the presence of two very divergent haplotypes and F-statistics indicated some heterogeneity between two sampling years. All microsatellite loci were polymorphic (Ho: 0.767; He: 0,764) but, revealed no detectable substructure. We also compared the mtDNA haplotypes from Noronha to 159 haplotypes representing 893 individuals from 14 locations worldwide. We found that the two common haplotypes from the Fernando de Noronha Archipelago were absent in all other populations. These comparisons showed that Noronha spinner dolphins are likely more differentiated than other island populations, suggesting that they form societies with strong site fidelity mediated by females.

Whales in warming water: Assessing breeding habitat diversity and adaptability in Oceania's changing climate.

In the context of a changing climate, understanding the environmental drivers of marine megafauna distribution is important for conservation success. The extent of humpback whale breeding habitats and the impact of temperature variation on their availability are both unknown. We used 19 years of dedicated survey data from seven countries and territories of Oceania (1,376 survey days), to investigate humpback whale breeding habitat diversity and adaptability to climate change. At a fine scale (1 km resolution), seabed topography was identified as an important influence on humpback whale distribution. The shallowest waters close to shore or in lagoons were favored, although humpback whales also showed flexible habitat use patterns with respect to shallow offshore features such as seamounts. At a coarse scale (1° resolution), humpback whale breeding habitats in Oceania spanned a thermal range of 22.3-27.8°C in August, with interannual variation up to 2.0°C. Within this range, both fine and coarse scale analyses of humpback whale distribution suggested local responses to temperature. Notably, the most detailed dataset was available from New Caledonia (774 survey days, 1996-2017), where encounter rates showed a negative relationship to sea surface temperature, but were not related to the El Niño Southern Oscillation or the Antarctic Oscillation from previous summer, a proxy for feeding conditions that may impact breeding patterns. Many breeding sites that are currently occupied are predicted to become unsuitably warm for this species (>28°C) by the end of the 21st century. Based on modeled ecological relationships, there are suitable habitats for relocation in archipelagos and seamounts of southern Oceania. Although distribution shifts might be restrained by philopatry, the apparent plasticity of humpback whale habitat use patterns and the extent of suitable habitats support an adaptive capacity to ocean warming in Oceania breeding grounds.