Poaching of wildlife species is a global problem that occurs for many reasons, for example bear paws, gall bladders and bile are used in traditional Chinese medicine, elephants are killed for their ivory, and the hunting of deer out of season is considered by some to be an enjoyable sport. When the only evidence against a suspected poacher is a carcass or a body part that was found in his or her possession, prosecution is more likely to succeed if the origin of these putatively illegal samples can be established, and this is where genetic analysis comes into play.
A common application of individual genotyping in wildlife forensics is the linking of body parts with a recovered carcass. A typical example of this occurred in 2001 when the Colorado Division of Wildlife Officers received information about a bull elk that had been killed illegally for its antlers. A headless elk carcass was found on the Ute Mountain Indian Reservation, and a set of elk antlers was seized from the home of one of the suspected poachers. Analysis of DNA showed that the antlers had been taken from the recently killed elk, and this evidence helped the courts to convict two poachers (source: US Attorney's Office, District of Colorado). In another case, a motorist notified the California Department of Fish and Game (DFG) of a man who was parked by the highway with a dead deer in the back of his truck. By the time a DFG warden and a deputy sheriff had arrived at the scene, the man had driven away and two dead deer had been abandoned near the road. The suspect was later tracked down, and an examination of his truck yielded some blood samples. DNA analysis demonstrated that the blood had come from the dead deer that had been abandoned by the road, and again the prosecution was successful (source: DFG).
Convictions such as these are possible only if the prosecution can demonstrate that the probability of a genotype occurring in more than one individual is extremely small. One way to calculate this likelihood was shown by Equation 6.3 (see Box 6.5). Recall that the probability of identity (PI) can be calculated as:
Forensic investigations typically employ markers from multiple polymorphic loci in order to obtain a probability of identity that will allow prosecutors to confidently exclude extraneous individuals from the case. This was illustrated by a comparison of two randomly chosen California elk (Cervus elaphus canadensis) that, on the basis of 11 polymorphic loci, generated an estimated PI of 1.3 x 10~9. This means that the same genotype should be found in only one individual out of every 780 million elk (Jones, Levine and Banks, 2002). When probabilities are this low, individuals can be genetically identified with confidence (barring identical twins); however, probabilities as low as these are limited to species for which we have well-characterized hypervariable markers, and to populations for which we have robust estimates of allele frequencies.
Not all investigations of poaching are concerned with linking individuals to body parts. At times it may be more appropriate to ascertain which population an individual originated from, for example if only some populations are protected, or if there is a question over whether an animal was taken from a private collection such as a wildlife park. It may also be desirable to know which populations are targeted most commonly by poachers. This is particularly important when endangered or threatened species continue to be exploited, such as the African elephant (Loxodonta africana) whose total population fell from around 1.3 million to 600 000 individuals between 1979 and 1987 because of the high price of ivory.
Although a ban on ivory trade was established in 1989, the black market continues to flourish. If law enforcement officers know the origin of seized ivory goods then they may be able to identify illegal trade routes and poaching hotspots, which would benefit from additional monitoring.
With this goal in mind, researchers used 16 microsatellite markers to genotype 315 tissue samples and 84 faecal samples that were collected from elephants at 28 locations in 14 African countries. These data allowed them to map the distributions of allele frequencies across the elephants' range, and they then used assignment tests to match ivory genotypes to particular geographic origins. Preliminary analyses suggest that this method can be used to discriminate between forest and savannah elephants as the source of ivory, and in some cases to also identify specific forest blocks as the source populations (Wasser et al., 2004). In general, the use of assignment tests to pinpoint the origin of a carcass has promise, although there is currently a limited number of species for which we have adequate allele frequency information for all of the candidate populations.
There are also times when identifying which particular species a sample came from can be useful for investigations of suspected poaching. Species identifications are most commonly done using DNA sequences, because universal primers can be used to amplify and sequence a specific region of DNA that can then be aligned with existing sequences to determine which species the sample originated from. For example, one set of universal primers can amplify a portion of mitochondrial cytochrome b from at least 221 different animal species, and the sequences of these amplified fragments have so far proved to be species-specific (Verma and Singh, 2003). In one legal case, mitochondrial cytochrome b sequence was used to determine that traces of blood and tissue on a hunting knife had come from bushbuck (Tragelaphus scriptus) and not domestic cattle as the perpetrator claimed, a finding that helped prosecutors to convict the knife's owner of poaching (Pitra and Lieckfeldt, 1999). In another case, mitochondrial control region sequences that had been obtained from some hairs were shown to be from a dog and not from a wolf, thereby exonerating the suspect (Savolainen and Lundeberg, 1999).
Species can sometimes also be differentiated on the basis of microsatellite alleles. One study showed that the allele sizes of three different microsatellite loci generated genetic profiles that allowed researchers to differentiate between red deer (Cervus elaphus) and roe deer (Capreolus capreolus) (Figure 8.1), although a distinction between these two species and fallow deer (Dama dama) was less precise (Poetsch et al., 2001). Once appropriate markers have been identified, most individuals can be assigned to a particular species with a high degree of confidence without the need first to obtain population allele frequency data. The accessibility
Figure 8.1 The allele sizes at three microsatellite loci differentiate between red deer and roe deer. Adapted from Poetsch et al. (2001)
of species-specific genotypes means that they are used in several different areas of wildlife forensics, one of the most important being the fight against the illegal trade of endangered animals and plants.
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