Quantification and genetic profiling of DNA isolated from free-floating feces of the North Atlantic right whale (Eubalaena glacialis)

R. M. Gillett, B. N. White, R. M. Rolland

Fecal analysis from the highly endangered North Atlantic right whale provides valuable information about health and reproductive parameters of individual animals. Genetically profiling the feces facilitates this connection when the sample originator is unknown. Although genetic analysis of feces collected in terrestrial systems has become well established, genetic studies of cetacean DNA are rare. Here, the use of free-floating feces as a source of right whale DNA and the reliability of the genotypes produced are examined. On average, fecal extracts yielded 25 ng of DNA/mg dry weight, but less than 1% was right whale DNA. Although all samples were amplified using genus-specific mitochondrial control region primers, the quantity of right whale DNA present was over estimated when compared to amplifications using nuclear primers. No correlation was found between the quantity of right whale DNA recovered and the duration the sample sat in the water. Composite microsatellite profiles from multiple amplifications of 28 fecal samples of known origin were consistent with profiles of the same individuals obtained from skin biopsies, however, the rate of allelic dropout varied depending on the amount of right whale DNA added. A screening and genotyping protocol for reliable genetic profiling based on fecal DNA quantification is presented.


Molecular identification of individual North Atlantic right whales (Eubalaena glacialis) using free-floating feces

Roxanne M. Gillett, Timothy R. Frasier, Rosalind M. Rolland, Bradley N. White

During the 1990s, North Atlantic right whales had significantly decreased reproduction and showed signs of compromised health, prompting the initiation of noninvasive fecal-based studies to investigate potential causal factors. The interpretation of these studies is enhanced when the defecator is identified, as data can then be linked to individual life history information. Fecal samples (n= 118) were either collected from single photoidentified whales, associated with several individuals by photoidentification of whales in the vicinity upon sample collection, or were collected when no whales were in the vicinity. Genetic profiles from fecal DNA comprising sex, mitochondrial haplotype, and five microsatellite loci helped assign specific samples to individual right whales based on existing genetic profiles. Profiles were informative in assigning 61 fecal samples to known individuals, 24 of which were collected when no whales were in the vicinity. Whales identified genetically were typically photographed in the same habitat area and on the same day of sample collection (n= 35/48). Twelve profiles new to the genetic database were identified, suggesting fecal sampling provides a means to obtain genetic profiles from previously unsampled individuals, which may help refine estimates of population size and habitat use patterns if annual fecal sampling continues.


Characterization of alleles of class I and II-like major histocompatibility complex loci in the highly endangered North Atlantic right whale (Eubalaena glacialis)

R. M. Gillett, B. N. White

The North Atlantic right whale (Eubalaena glacialis) has low levels of genetic variation, which are comparable to the levels of genetic diversity found in other endangered species experiencing reduced population fitness. Here, functional variation was assessed by characterising class I and II loci of the major histocompatibility complex (MHC). Amplification of the peptide binding region (PBR) of class II DRβ-like genes identified four loci. Transmission analysis of known family groups enabled us to assign six alleles to the locus EuglDRβ*01, and five alleles to the locus EuglDRβ*02. These loci were in linkage disequilibrium and 12 haplotypes were inferred based on the segregation of genotypes from parents to calves. Two DRβ-like pseudogenes were also identified, containing one and three alleles respectively. Amplification of the PBR of class I MHC identified two functional MHC-I-like loci (EuglI*01 and EuglI*03), and two pseudogenes (EuglI*02 and EuglI*04). EuglI*01 and EuglI*02 were monomorphic, while multiple alleles were identified at the EuglI*03 and EuglI*04 loci. Pairwise comparisons indicated that the number of non-synonymous substitutions was significantly greater than number of synonymous substitutions at codons involved in peptide binding for EuglDRβ*01 and EuglDRβ*02, and approached significance over the entire PBR for EuglI*01 and EuglI*03, suggesting these loci may be under the influence of balancing selection. Some alleles were similar to those described in other cetaceans, indicating that there has been a long-term retention of these alleles across speciation events. The characterization of MHC loci described here represents the first step in determining the relationship between genetic variability at loci under the influence of selection and factors affecting health and reproduction in this highly endangered species.


DNA profile of a sixteenth century western North Atlantic right whale (Eubalaena glacialis)

Brenna A. McLeod, Moira W. Brown,Timothy R. Frasier, Bradley N. White

Low levels of genetic variability identified within the North Atlantic right whale (Eubalaena glacialis), when compared to the Southern right whale (E. australis) and other large whales, have been suggested to result from population reductions due to whaling. Previous genetic analysis of 218 whale bones from sixteenth century Basque whaling sites in the western North Atlantic revealed only a single right whale bone. We determined the genotypes of 27 microsatellite loci using DNA isolated from this bone. All alleles from the historic specimen occur in the extant western North Atlantic population and both the probability of identity of the specimen and the number of heterozygous loci are similar to that in the extant population. Assessments of how genetically different the historical population might have been suggest genetic characteristics have not changed substantially over four centuries of whaling.


Discovery of North Atlantic right whale mating grounds

Tim Cole, Philip Hamilton, Allison Glass Henry, Peter Duley, Richard M. Pace, III, Bradley N. White, Tim Frasier

The location of the mating grounds of the endangered North Atlantic right whale (Eubalanea glacialis) has eluded discovery despite centuries of whaling and, more recently, decades of research. This remnant population lives adjacent to the industrialized east coast of North America, and is the most extensively studied whale species in the world. Gestation period estimates from the closely related southern right whale (E. australis) suggest that conception for their northern hemisphere cousins occurs in the boreal winter. Between 2002 and 2008, aerial surveys found half the North Atlantic population in the central Gulf of Maine between November and January. Generalized linear models indicated that significantly higher proportions of both known fathers and conceptive females were present in this region compared to other areas seasonally inhabited by right whales. The significantly higher proportions of reproductively successful individuals sighted in the central Gulf of Maine during the likely period of conception strongly suggest that this area is a mating ground. Roseway Basin, on the southwest Scotian Shelf, may also be the site of some conceptions if right whale gestation extends to 14 months. The identification of right whale mating grounds is an important step in their conservation as collisions with ships and entanglement in commercial fishing gear threaten this species’ survival.

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