Genetic analysis has been critical for understanding population structure, gene flow, relatedness, paternity, and more broadly, conservation. Genetic data have been collected since 1997, when shark bay researchers developed a novel biopsy system for small cetaceans, whereby adult dolphins were darted in order to obtain a small skin sample for genetic analysis. The research team had already identified several highly polymorphic regions of interest (Krützen et al. 2001), and these samples allowed for microsatellite and d-loop analysis in 95.8% and for genetic sexing in 99% cases. This was a novel method for reliable and safe tissue sampling of free-ranging cetaceans, with wounds healing completely in about three weeks (Krützen et al. 2002).
Being able to obtain genetic data from our dolphins allowed us to test several interesting questions, such as whether the formation of male alliances was based on relatedness. It turned out that males in stable first-order alliances tend to be highly related, while males in super-alliances with labile first-order alliances aren’t any more related than one would expect by chance alone (see male alliances). This suggested that within one population and one sex there are multiple ways to form groups (Krützen et al. 2003).
Genetic data has also given support for natal philopatry, with males retaining their natal home ranges within slightly larger adult ones, which makes sense if they want to obtain inclusive fitness benefits from alliance formation. For females the data showed that adjacent localities were genetically similar for mtDNA, with a gradual shift in haplotype frequencies with increasing distance. Data which supported the existence of a network in which all females were connected to each other, and where dispersal in female is more restricted than that of male dolphins (Krützen et al. 2004a).
Examination of female association patterns in conjunction with genetic data has also shown support for the recognition of biparental kin. While females showed a preference for forming close bonds with matrilineal kin, they also showed a preference for having casual relationships with biparental kin outside their matriline, independent of the level of home range overlap. (Frère et al. 2010a).
Genetic data also allows us to answer questions about the possibility of dolphin culture. Using mitochondrial DNA analyses, our research has shown that the use of marine sponges as foraging tools demonstrates an almost exclusive vertical social transmission within a single matriline from mother to female offspring. Also significant genetic relatedness at the nuclear level suggests that all modern spongers have close coancestry, which may be the result of descendance from a single female, a “Sponging Eve.” However, despite their close relatedness, sponging is unlikely to be the result of a genetic propensity. It’s unlikely to be explained by any single-locus mode of inheritance, with any sex limitation or other special expression pattern, and multilocus inheritance is equally unlikely because they would have to be so tightly linked that they behaved as one gene or there would have to be strong assortative mating. Likewise assortative mating, assortative mating is unlikely because since adult males virtually never sponge, any assortment would have to be based on some other (unknown) correlated trait, and sponging females have been shown to conceive from nonsponging males and almost all offspring of spongers are sired by nonsponging males, and there was no observed heterozygosity deficit among all 13 spongers that would be predicted by such assortative mating (Krützen et al. 2005). Further research tested the hypothesis that the propensity for sponging may be a result of enhanced respiratory and diving abilities, but it was found that the regions of mitochondrial DNA that predicted sponging were non-coding and thus wouldn’t result in any phenotypic differences between spongers and non-spongers, which again supported the view that genetic transmission was not responsible for this form of tool use (Bacher et al. 2010).
Genetic data allowed for paternity assessment and therefore for us to examine male reproductive success. Such assessments showed that while alliance membership increased a male’s chance of fathering offspring, some juvenile males were able to obtain paternities without being a member of an alliance. Reproductive success was skewed within some stable first order alliances, suggesting that the alliances were hierarchically arranged with more dominant males obtaining more matings than others (Krützen et al. 2004b). The data also demonstrated that at least one mating was incestuous, leading our team to later investigate the occurrence and effects of inbreeding within the population.
Levels of inbreeding in Shark Bay dolphins are indeed higher than expected. However, it is not without negative effects. Inbred females have been shown to have lower calving success (Figure 1) and inbred calves take longer to be weaned (Figure 2). While inbreeding has deleterious effects on female reproductive success, the lack of male dispersal and high level of sexual coercion by male alliances may be allowing inbreeding to occur regardless (Frère et al. 2010b).
One of the most exciting new developments in the field of cetacean genetics is a new technique known as blow sampling. This method allows DNA to be collected from the epithelial cells present in the dolphins’ exhalations. It’s an exciting and much less invasive alternative to skin biopsying, and will be able to be more ethically applied to young animals and members of more vulnerable populations (Frère et al. 2010c).