Publications by year
2021
Westbury MV, Thompson KF, Louis M, Cabrera AA, Skovrind M, Castruita JAS, Constantine R, Stevens JR, Lorenzen ED (2021). Ocean-wide genomic variation in Gray's beaked whales. Mesoplodon grayi.
Royal Society Open Science,
8(3).
Abstract:
Ocean-wide genomic variation in Gray's beaked whales. Mesoplodon grayi
. The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale (
. Mesoplodon grayi
. ) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa (
. n
. = 2) and South Australia (
. n
. = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.
.
Abstract.
2019
Azoulay D, Villa P, Arellano Y, Gordon M, Moon D, Miller K, Thompson K (2019). Plastic is a global health crisis hiding in plain sight. Renewable Resources Journal, 33(3), 10-13.
Abreo NAS, Thompson KF, Arabejo GFP, Superio MDA (2019). Social media as a novel source of data on the impact of marine litter on megafauna: the Philippines as a case study.
Marine Pollution Bulletin,
140, 51-59.
Abstract:
Social media as a novel source of data on the impact of marine litter on megafauna: the Philippines as a case study
Marine litter is a global threat to marine biodiversity. However, there is a key knowledge gap on the impacts of marine litter in the Philippines – a country of high marine biodiversity and large exclusive economic zone. This gap is addressed here by using information shared on the internet by citizen scientists and conservation groups to assess the impacts of marine litter on megafauna. Facebook, presently the largest social media platform, was scanned for posts concerning the interaction between litter and marine species in the Philippines. Results showed thirty-two individuals from 17 species were affected by marine litter in the country. Furthermore, ingestion (61%) was the most frequent interaction reported. Mindanao was also identified as a hotspot for marine litter interactions. The study highlights the utility of social media in providing data to create an inventory of marine species adversely affected by litter and the spatial distribution of these interactions.
Abstract.
2018
Miller KA, Thompson KF, Johnston P, Santillo D (2018). An overview of seabed mining including the current state of development, environmental impacts, and knowledge gaps.
Frontiers in Marine Science,
4(JAN).
Abstract:
An overview of seabed mining including the current state of development, environmental impacts, and knowledge gaps
Rising demand for minerals and metals, including for use in the technology sector, has led to a resurgence of interest in exploration of mineral resources located on the seabed. Such resources, whether seafloor massive (polymetallic) sulfides around hydrothermal vents, cobalt-rich crusts (CRCs) on the flanks of seamounts or fields of manganese (polymetallic) nodules on the abyssal plains, cannot be considered in isolation of the distinctive, in some cases unique, assemblages of marine species associated with the same habitats and structures. In addition to mineral deposits, there is interest in extracting methane from gas hydrates on continental slopes and rises. Many of the regions identified for future seabed mining are already recognized as vulnerable marine ecosystems (VMEs). Since its inception in 1982, the International Seabed Authority (ISA), charged with regulating human activities on the deep-sea floor beyond the continental shelf, has issued 27 contracts for mineral exploration, encompassing a combined area of more than 1.4 million km , and continues to develop rules for commercial mining. At the same time, some seabed mining operations are already taking place within continental shelf areas of nation states, generally at relatively shallow depths, and with others at advanced stages of planning. The first commercial enterprise, expected to target mineral-rich sulfides in deeper waters, at depths between 1,500 and 2,000 m on the continental shelf of Papua New Guinea, is scheduled to begin early in 2019. In this review, we explore three broad aspects relating to the exploration and exploitation of seabed mineral resources: (1) the current state of development of such activities in areas both within and beyond national jurisdictions, (2) possible environmental impacts both close to and more distant from mining activities and (3) the uncertainties and gaps in scientific knowledge and understanding which render baseline and impact assessments particularly difficult for the deep sea. We also consider whether there are alternative approaches to the management of existing mineral reserves and resources, which may reduce incentives for seabed mining. 2
Abstract.
Thompson KF, Miller KA, Currie D, Johnston P, Santillo D (2018). Seabed mining and approaches to governance of the deep seabed.
Frontiers in Marine Science,
5(DEC).
Abstract:
Seabed mining and approaches to governance of the deep seabed
Commercial seabed mining seems imminent, highlighting the urgent need for coherent, effective policy to safeguard the marine environment. Reconciling seabed mining with the United Nations Sustainable Development Goals will be difficult because minerals extraction will have irreversible consequences that could lead to the loss of habitats, species and ecosystems services. A dialog needs to take place around social, cultural, environmental and economic costs and benefits. Governance of human interactions with the seabed is fragmented and lacks transparency, with a heavy focus on facilitating exploitation rather than ensuring protection. In the light of high uncertainties and high stakes, we present a critical review of proposed policy options for the regulation of seabed mining activities, recommend actions to improve seabed governance and outline the alternatives to mining fragile deep-sea ecosystems.
Abstract.
2017
Patel S, Thompson KF, Santure AW, Constantine R, Millar CD (2017). Genetic kinship analyses reveal that gray's beaked whales strand in unrelated groups.
Journal of Heredity,
108(4), 456-461.
Abstract:
Genetic kinship analyses reveal that gray's beaked whales strand in unrelated groups
Some marine mammals are so rarely seen that their life history and social structure remain a mystery. Around New Zealand, Gray's beaked whales (Mesoplodon grayi) are almost never seen alive, yet they are a commonly stranded species. Gray's are unique among the beaked whales in that they frequently strand in groups, providing an opportunity to investigate their social organization. We examined group composition and genetic kinship in 113 Gray's beaked whales with samples collected over a 20-year period. Fifty-six individuals stranded in 19 groups (2 or more individuals), and 57 whales stranded individually. Mitochondrial control region haplotypes and microsatellite genotypes (16 loci) were obtained for 103 whales. We estimated pairwise relatedness between all pairs of individuals and average relatedness within, and between, groups. We identified 6 mother- calf pairs and 2 half-siblings, including 2 whales in different strandings 17 years and 1500 km apart. Surprisingly, none of the adults stranding together were related suggesting that groups are not formed through the retention of kin. These data suggest that both sexes may disperse from their mothers, and groups consisting of unrelated subadults are common. We also found no instances of paternity within the groups. Our results provide the first insights into dispersal, social organization, and the mating system in this rarely sighted species. Why whales strand is still unknown but, in Gray's beaked whales, the dead can tell us much about the living.
Abstract.
2016
Thompson KF, Patel S, Baker CS, Constantine R, Millar CD (2016). Bucking the trend: Genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean.
Heredity,
116(3), 277-285.
Abstract:
Bucking the trend: Genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean
Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (∼6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and R =4.22-4.37, H =0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat. s e
Abstract.
Thompson KF, Patel S, Williams L, Tsai P, Constantine R, Baker CS, Millar CD (2016). High coverage of the complete mitochondrial genome of the rare Grays beaked whale (Mesoplodon grayi) using Illumina next generation sequencing.
Mitochondrial DNA,
27(1), 128-129.
Abstract:
High coverage of the complete mitochondrial genome of the rare Grays beaked whale (Mesoplodon grayi) using Illumina next generation sequencing
Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genome of Grays beaked whale (Mesoplodon grayi) to an average coverage of 152X. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome length to be 16,347 bp. The nucleotide composition was asymmetric (33.3% A, 24.6% C, 12.6% G, 29.5% T) with an overall GC content of 37.2%. The gene organization was similar to that of other cetaceans with 13 protein-coding genes, 2 rRNAs (12S and 16S), 22 predicted tRNAs and 1 control region or D-loop. We found no evidence of heteroplasmy or nuclear copies of mitochondrial DNA in this individual. Beaked whales within the genus Mesoplodon are rarely seen at sea and their basic biology is poorly understood. These data will contribute to resolving the phylogeography and population ecology of this speciose group.
Abstract.
2014
Thompson KF, Ruggiero K, Millar CD, Constantine R, van Helden AL (2014). Large-scale multivariate analysis reveals sexual dimorphism and geographic differences in the Gray's beaked whale.
Journal of Zoology,
294(1), 13-21.
Abstract:
Large-scale multivariate analysis reveals sexual dimorphism and geographic differences in the Gray's beaked whale
Gray's beaked whales (Mesoplodon grayi) are medium-sized odontocete (toothed) cetaceans that are members of the family Ziphiidae. These animals inhabit deep oceanic waters and are rarely seen at sea. Most information is derived from stranded animals and there has been no systematic study of their morphology. We present a multivariate analysis of the morphology of Gray's beaked whales using 80 cranial measurements from 22 individuals and 13 external measurements from 50 individuals. Sparse principal component and linear discriminant function analyses were used to classify samples into sexes. Males and females have markedly different cranial morphology. In particular, females have longer skulls with longer more slender rostra (beaks) in comparison to males. Two variables, depth of the rostrum at mid-length and tip of rostrum to the right temporal fossa, can classify sex with 100% accuracy. The external body measurements used in this study are more prone to error as they were recorded by a number of observers on carcasses in differing states of decomposition and this is reflected in the level of variance in most measurements. However, analyses of these measurements showed a significant difference between sexes in the distance between (1) the tip of the rostrum to the genital slit, (2) the tip of the rostrum to the blowhole, as found in the cranial analyses and (3) tail fluke width where males have absolutely wider tail flukes than females. Differences in these same measurements were also found between animals stranded on the east and west coasts suggesting a degree of population separation across New Zealand. Finally, we present two linear models that enable the assignment of sex from either skull or external measurements. These models will be useful for future studies as well as the management of these whales and can be applied to archived data where genetic sex assignment is not possible. © 2014 the Zoological Society of London.
Abstract.
Patel S, Thompson K, Williams L, Tsai P, Constantine R, Millar C (2014). Mining microsatellites for Gray's beaked whale from second-generation sequencing data.
Conservation Genetics Resources,
6(3), 657-659.
Abstract:
Mining microsatellites for Gray's beaked whale from second-generation sequencing data
We used three second-generation sequencing platforms to develop 12 microsatellite markers for Gray's beaked whale (Mesoplodon grayi). There was a strong correlation between the amount of sequence obtained from each platform and the number of microsatellites recovered. In order to design reliable primers we found that it was important in all cases to eliminate low quality reads and trim sequences so that 80 % of each sequence had a PHRED score of >20. We found that tri- and tetranucleotide repeats produced less stutter enabling robust peak-calling and consistent genotyping. The microsatellites developed here will be useful for the population genetics and conservation studies of Gray's beaked whales. © 2014 Springer Science+Business Media Dordrecht.
Abstract.
Constantine R, Steel D, Allen J, Anderson M, Andrews O, Baker CS, Beeman P, Burns D, Charrassin JB, Childerhouse S, et al (2014). Remote Antarctic feeding ground important for east Australian humpback whales.
Marine Biology,
161(5), 1087-1093.
Abstract:
Remote Antarctic feeding ground important for east Australian humpback whales
Understanding the dynamics of population recovery is particularly complex when an organism has multiple, remote breeding and feeding grounds separated by one of the longest known migration routes. This study reports on the most comprehensive assessment of humpback whale (Megaptera novaeangliae) movements between remote Antarctic waters south of New Zealand and east Australia (EA), and the migratory corridors and breeding grounds of Australia and Oceania. A total of 112 individual whales were identified; 57 from microsatellites and 61 by fluke with 23 % (n = 26) matched to sites outside Antarctica. Despite large datasets from other southern regions being included in the comparison, the whales were predominantly linked to EA (n = 24). Only two matches to the Oceania catalogues directly north was surprising; therefore the primary feeding grounds of these endangered whales still remain unknown. The confirmation of the Balleny Islands as an important feeding ground for EA whales could provide an insight into reasons behind the rapid recovery of this population. Determining the feeding grounds of Oceania's whales may explain whether prey energetics or migration length are limiting factors to their recovery and will allow an understanding of future ecosystem changes in these whales. © 2014 Springer-Verlag Berlin Heidelberg.
Abstract.
Dalebout ML, Scott Baker C, Steel D, Thompson K, Robertson KM, Chivers SJ, Perrin WF, Goonatilake M, Charles Anderson R, Mead JG, et al (2014). Resurrection of Mesoplodon hotaula Deraniyagala 1963: a new species of beaked whale in the tropical Indo-Pacific.
Marine Mammal Science,
30(3), 1081-1108.
Abstract:
Resurrection of Mesoplodon hotaula Deraniyagala 1963: a new species of beaked whale in the tropical Indo-Pacific
We present genetic and morphological evidence supporting the recognition of a previously synonymized species of Mesoplodon beaked whale in the tropical Indo-Pacific, Mesoplodon hotaula. Although the new species is closely-related to the rare ginkgo-toothed beaked whale M. ginkgodens, we show that these two lineages can be differentiated by maternally (mitochondrial DNA), biparentally (autosomal), and paternally (Y chromosome) inherited DNA sequences, as well as by morphological features. The reciprocal monophyly of the mtDNA genealogies and the largely parapatric distribution of these lineages is consistent with reproductive isolation. The new lineage is currently known from at least seven specimens: Sri Lanka (1), Gilbert Islands, Republic of Kiribati (1+), Palmyra Atoll, Northern Line Islands, U.S.A. (3), Maldives (1), and Seychelles (1). The type specimen (Sri Lanka) was described as a new species, M. hotaula, in 1963, but later synonymized with M. ginkgodens. This discovery brings the total number of Mesoplodon species to 15, making it, by far, the most speciose yet least known genus of cetaceans. © 2014 Society for Marine Mammalogy.
Abstract.
2013
Thompson KF, Millar CD, Scott Baker C, Dalebout M, Steel D, van Helden AL, Constantine R (2013). A novel conservation approach provides insights into the management of rare cetaceans.
Biological Conservation,
157, 331-340.
Abstract:
A novel conservation approach provides insights into the management of rare cetaceans
The conservation of rare or cryptic species in inaccessible habitats represents a particular challenge to biologists. Since 1991, a collaborative research program involving members of the public, indigenous communities, the Museum of New Zealand Te Papa Tongarewa (NMNZ) and the Department of Conservation has provided tissue samples for genetic analysis of stranded, or beach-cast cetaceans. The New Zealand Cetacean Tissue Archive (NZCeTA), initiated and maintained by the University of Auckland, is now one of the largest archives of its kind in the world, with tissue samples or extracted DNA from 1982 individuals. Species identity has been confirmed by DNA barcoding, using mtDNA control region sequences for 65% of the samples representing 35 species, 11 of which are from the poorly known beaked whale family, Ziphiidae. Although these animals regularly strand around the coastline of New Zealand there are no known areas at sea where they can be reliably found and very few reported live sightings. Samples collected from strandings of three species: Gray's (Mesoplodon grayi); straptoothed (Mesoplodon layardii) and Cuvier's beaked whale (Ziphius cavirostris), represent 83% (n= 225) of all ziphiids in the NZCeTA (n= 272). As an example of the archives utility, we used the spatial and temporal distribution of these records to provide new evidence for key habitat of these cryptic species and for seasonal and sex-biased patterns of stranding mortality. As beaked whales are known to be threatened by anthropogenic activity in other parts of the world, these records provide a critical baseline for understanding the future impacts of planned development in New Zealand's near and offshore waters. © 2012 Elsevier Ltd.
Abstract.
Baker CS, Hutt A, Thompson K, Dalebout ML, Robins J, Brownell RL, Stone GS (2013). Species identity and human consumption of beaked whales in the Gilbert Islands, Republic of Kiribati.
Animal Conservation,
16(6), 641-647.
Abstract:
Species identity and human consumption of beaked whales in the Gilbert Islands, Republic of Kiribati
We investigated the species identity and local use of cetaceans on the Gilbert Islands, Republic of Kiribati. Working with the Kiribati Ministry of Environment, Lands and Agricultural Development and Fisheries Division, we visited the islands of Tarawa, Tabiteuea (North), Butaritari and Onotoa from June to July 2009, and collected 24 bones, bone fragments or teeth attributed to recent strandings. The mitochondrial DNA control region or cytochrome b was successfully amplified from 12 bones or bone fragments and used to identify four species: Mesoplodonsp. representing a new species or subspecies of beaked whale, the dense-beaked whale Mesoplodon densirostris, Cuvier's beaked whale Ziphius cavirostris and the pygmy sperm whale Kogia breviceps. This is the first confirmed identification of the dense-beaked, Cuvier's and pygmy sperm whales from the Gilbert Islands. All specimens were reportedly used for human consumption. © 2013 the Zoological Society of London.
Abstract.
2012
Constantine R, Jackson JA, Steel D, Scott Baker C, Brooks L, Burns D, Clapham P, Hauser N, Madon B, Mattila D, et al (2012). Abundance of humpback whales in Oceania using photo-identification and microsatellite genotyping.
Marine Ecology Progress Series,
453, 249-261.
Abstract:
Abundance of humpback whales in Oceania using photo-identification and microsatellite genotyping
Estimating the abundance of long-lived, migratory animals is challenging but essential for managing populations. We provide the first abundance estimates of endangered humpback whales Megaptera novaeangliae from their breeding grounds in Oceania, South Pacific. Using fluke photo-identification (1999-2004, n = 660 individuals) and microsatellite genotypes (1999-2005, n = 840 individuals), we estimated abundance with open capture-recapture statistical models. Total Oceania abundance and trends were estimated from 4 primary and 5 secondary sampling sites across the region. Sex-specific genotype data enabled us to account for the difference in capturability of males and females, by doubling male-specific estimates of abundance derived from genotypes. Abundance estimates were congruent between primary- and secondaryregion data sets, suggesting that the primary regions are representative of all Oceania. The best estimate of total abundance was 4329 whales (3345-5313) in 2005, from a sex-specific POPAN super-population model, which includes resident whales and those migrating through the surveyed areas. A doubled-male POPAN abundance estimate from 2003 (n = 2941, 95% CI = 1648-4234) was considered the most plausible for the 4 primary survey areas and was similar to the 2003 doubled-male estimate derived from Pradel capture probabilities (n = 2952, 95% CI = 2043-4325). Our results confirm that Oceania is the least abundant humpback whale breeding population in the southern hemisphere. Pradel models showed no significant trend in abundance, which contradicts the recovery seen in most other populations throughout the world. Thus we suggest that the whales in this area warrant continued study and management attention. © 2012 Inter-Research.
Abstract.
Constantine R, Jackson JA, Steel D, Baker CS, Brooks L, Burns D, Clapham P, Hauser N, Madon B, Mattila D, et al (2012). Abundance of humpback whales in Oceania using photo-identification and microsatellite genotyping.
MARINE ECOLOGY PROGRESS SERIES,
453 Author URL.
Thompson K, Baker CS, Van Helden A, Patel S, Millar C, Constantine R (2012). Erratum: the world's rarest whale (Current Biology (2012) 22 (R905-R906)). Current Biology, 22(23).
Thompson K, Baker CS, Van Helden A, Patel S, Millar C, Constantine R (2012). The world's rarest whale.
Current Biology,
22(21).
Abstract:
The world's rarest whale
The vast expanses of the South Pacific Ocean have, until recently, concealed the identity of the world's rarest whale, the spade-toothed beaked whale (Mesoplodon traversii). Based on the scarcity of records and the total absence of previous sightings, this species is the least known species of whale and one of the world's rarest living mammals. Two individuals of this species, previously known from only two skull fragments and a mandible, were recently discovered beach-cast in New Zealand. Although initially misidentified, we have used DNA analysis to reveal their true identity. We provide the first morphological description and images of this enigmatic species. This study highlights the importance of DNA typing and reference collections for the identification of rare species. © 2012 Elsevier Ltd.
Abstract.
