MARINE MAMMAL SCIENCE, 26(3): 716–732 (July 2010)
2010 by the Society for Marine Mammalogy
Published 2010. This article is a US Government work and is in the public domain in the USA.
DOI: 10.1111/j.1748-7692.2009.00362.x
Characterization of 42 single nucleotide polymorphism (SNP)
markers for the bowhead whale (Balaena mysticetus) for use in
discriminating populations
PHILLIP A. MORIN
VICTORIA L. PEASE
BRITTANY L. HANCOCK
KELLY M. ROBERTSON
CAROLINE W. ANTOLIK
Southwest Fisheries Science Center,
National Marine Fisheries Service,
3333 N. Torrey Pines Court,
La Jolla, California 92037, U.S.A.
E-mail: phillip.morin@noaa.gov
RYAN M. HUEBINGER1
Purdue University,
503 Northwestern Avenue,
West Lafayette, Indiana 47907-2966, U.S.A.
The bowhead whale was hunted extensively in the North Pacific and Atlantic.
Historic abundance is estimated to have been at least 30,000 (Burns et al. 1993)
in the North Pacific and 12,000 in the western North Atlantic (Hudson Bay and
Davis Strait stocks; Rugh et al. 2003). By the end of commercial whaling, each
population was estimated to have numbered fewer than 1000 individuals. Since
“economic extinction” in the early 1900s, populations have generally rebounded,
now reaching approximately 11,000 in the Bering/Chukchi/Beaufort seas (BCB)
stock of the North Pacific (George et al. 2004) and conservatively estimated at
5,000 in the western North Atlantic (Dueck et al. 2007). A small population in the
Sea of Okhotsk (Russia) was reduced from an estimated 3,000–6,000 to probably
fewer than 500 (Endangered in the International Union for the Conservation of
Nature [IUCN] Red List; IUCN 2008), and a population in the eastern North
Atlantic, called the Spitsbergen stock (Critically Endangered), was reduced from
>25,000 to probably fewer than 100 surviving today (Rugh et al. 2003). BCB
bowhead whales remain listed as Endangered under the U.S. Endangered Species Act
and are currently protected from commercial hunting under International Whaling
Commission treaties. Subsistence hunting continues in Alaska, Russia, and Canada
with an annual permitted biological removal (PBR) set by the International Whaling
Commission of 95 whales in the western Arctic (BCB and Okhotsk stocks), although
1Current address: University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard,
Dallas, Texas 75390-9160, U.S.A.
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NOTES 717
annual take is usually less than 40 in the BCB stock (Angliss and Outlaw 2007), and
fewer in other regions.
Several genetics studies have been completed to investigate population struc-
ture within and between existing bowhead populations and to examine changes in
population structure due to the recent severe bottlenecks in populations caused by
19th century whaling. These studies, using mitochondrial DNA (mtDNA) sequence
(LeDuc et al. 2005, 2008) and nuclear microsatellites (Givens et al., in press) indicated
significant differences between recognized populations in the Sea of Okhotsk, the
BCB stock, and the Hudson Bay and Davis Strait stocks of eastern Canada. Within
the BCB population there was no indication of spatial population structure, but there
was an indication of temporal changes in structure due to the very severe bottleneck
in the population about 100 yr ago and subsequent rapid expansion (LeDuc et al.
2008). Temporal shifts in genetic structure violate assumptions of some analytical
methods for spatial population structure, thereby complicating analysis of extant
populations. To further investigate whether this temporal shift in genetic structure
exists and to increase statistical power to detect genetic structure, analysis of a greater
number of samples is needed from both poorly represented regions of the sampling
range, and from samples known to be from whales born prior to the population
nadir. The use of historical samples, even if they were only collected 30–40 yr ago,
can increase the sample size of animals born before the population nadir because
bowheads are known to live to at least 100 yr, and it is believed they may live to over
150 yr (George et al. 1999). To obtain a sufficient number and type of samples for
this analysis to be completed, we will need to use a combination of samples obtained
by dart biopsy, samples from animals harvested in the annual aboriginal subsistence
hunts in Alaska and samples from historical bone and baleen obtained between 10
and 40 yr ago from remains of subsistence hunt animals left on the shore, kept by
hunting villages, or in museums.
Historical samples pose particular problems for use of microsatellites because of
the level of DNA degradation. To complement existing mtDNA and microsatellite
markers for population structure studies of this species, and to make effective use
of historical samples, we have undertaken the development of single nucleotide
polymorphims (SNPs) for bowhead whale genetic studies. SNPs are simple changes
in the single nucleotides in the DNA sequence and represent the most common
type of genetic variation in most genomes (Morin et al. 2004). Because SNPs are
typically bi-allelic (e.g., a change of a G to an A in the DNA sequence), each locus
provides lower statistical power for population analysis than highly polymorphic
loci such as microsatellites, so larger numbers of SNPs and/or samples are needed
to increase statistical power (Krawczak 1999; Kuhner et al. 2000; Ryyna¨nen et al.
2007; Morin et al. 2009). However, there are potential benefits to using SNPs instead
of or in addition to microsatellites. SNPs can be genotyped using a large and ever
growing range of technologies, several of which allow genotyping of many loci
and/or many samples simultaneously, thereby increasing efficiency and significantly
decreasing genotyping cost per sample (e.g., Morin et al. 1999; Taylor et al. 2001;
Morin et al. 2004; Narum et al. 2008). SNPs can also be genotyped accurately and
efficiently from poor-quality and historical DNA samples, such as tooth, bone, and