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 two
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, four were encountered on the Hawaiian breeding
ground (the primary migratory destination for whales in SEAK) and one 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.Funding
Support for this work was provided by a cooperative agreement between
Oregon State University and the National Park Service (Pacific West Region
Cooperative Ecosystems Study Unit Task Agreement #P12AC15004). Additional
funding was provided by the Mamie Markham Research Award, Joan Crebbin
Memorial Fellowship, Lylian Brucefield Reynolds Scholarship, Thomas G. Scott
Grant Scholarship and the Hatfield Marine Science Center Student Organization
Travel Grant.
Acknowledgements
We thank the SPLASH Steering Committee for access to haplotype information and
sighting records. A special thanks to Charles Jurasz for his insight and foresight in
documenting individual whales in southeastern Alaska. All research was conducted
under appropriate permits issued by the US National Marine Fisheries Service, in
accordance with the US Marine Mammal Protection Act and the US Endangered
Species Act, including no. 14122 issued to J.M.S., nos. 945-1499-02 and 473-1700-
00 issued to the Glacier Bay National Park, and no. 675 issued to C.S.B.Ye
