Secrets of the Deep: The Molecular Genetics of Cryptic Beaked Whales
Thompson, Kirsten Freja
Thesis or dissertation
University of Exeter
Beaked whales are comparatively unknown social mammals due to their deep-ocean distribution and elusive habits. The deep-ocean is the largest biome on Earth and the final frontier for human expansion. Since their first discovery, beaked whales have remained largely hidden from science. In this era of rapid technological advancement, genetic and genomic methods are key tools for population biologists and are particularly useful in describing rarely seen species. Using DNA-barcoding and nuclear markers, the publications in this thesis provide data on the distribution and external appearance of two species of beaked whale: the spade-toothed (Mesoplodon traversii) and Derinayagala’s whale (Mesoplodon hotaula). These whales were previously known from only a handful of tissue and bone specimens. Long-term efforts have facilitated the collection of samples of Gray’s beaked whale (Mesoplodon grayi) and we have used shot-gun sequencing to characterise the mitochondrial genome and isolate species-specific nuclear microsatellite loci. Using genetic species and sex identification, together with museum specimens and multivariate analyses, we provide clear evidence of sexual dimorphism in cranial dimensions and geographic variation in external morphology. No genetic differentiation was evident in Gray’s beaked whales across a large study area (~ 6,000 km). With a large female effective population size (Ne) and genetic homogeneity, we hypothesise that gene flow is facilitated by large-scale oceanographic features, such as the sub-tropical convergence. Genetic kinship analyses within Gray’s beaked whale groups suggest that the whales that strand together are not related. Both sexes disperse from their parents and these groups are not formed through the retention of kin. These results are consistent with a ‘fission-fusion’ social system that has been observed in some oceanic dolphin species. Taken together, these data provide the first insights into the population dynamics, dispersal and social organisation in Gray’s beaked whales. These publications highlight the value of using genetics alongside other techniques to describe inter- and intraspecific diversity. For beaked whales, the dead can tell us much about the living.
University of Auckland
National Geographic Society
US Marine Mammal Commision
Thompson K, Baker S, van Helden A, Patel S, Millar C, Constantine R. (2012). The world’s rarest whale. Current Biology 22: 905–906.
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: 641- 647.
Dalebout ML, Baker CS, Steel D, Thompson KF, Robertson K, Chivers SJ, Perrin WF, Goonatilake M, Anderson RC, Mead JG, Potter CW, Yamada TK, Thompson TK, Jupiter D. (2013). Resurrection of Mesoplodon hotaula Deraniyagala 1963: A new species of beaked whale in the tropical Indo-Pacific. Marine Mammal Science 30: 1081-1108.
Thompson KF, Patel S, Williams L, Tsai P, Constantine R, Millar CD. (2016). High coverage of the complete mitochondrial genome of the rare Gray’s beaked whale (Mesoplodon grayi) using Illumina next generation sequencing. Mitochondrial DNA Part A 27.
Patel S, Thompson KF, Williams L, Tsai P, Constantine R, Millar CD. (2014). Mining microsatellites for Gray’s beaked whale from next generation sequencing data. Conservation Genetics Resources 6: 657-659.
Thompson KF, Ruggiero, K, Millar CD, Constantine R, van Helden A. (2014). Large-scale multivariate analysis reveals sexual dimorphism and geographic differences in the Gray’s beaked whale. Journal of Zoology 294: 13-21.
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: 287–115.
Patel S, Thompson KF, Santure A, Constantine R, Millar CD. (2017). Genetic kinship analyses reveal that Gray’s beaked whale strands in unrelated groups. Journal of Heredity
Stevens, Jamie R.
Millar, Craig D.
PhD by Publication in Biological Sciences