Assigning African elephant DNA to geographic region of origin: applications to the ivory trade - PubMed (original) (raw)

Assigning African elephant DNA to geographic region of origin: applications to the ivory trade

Samuel K Wasser et al. Proc Natl Acad Sci U S A. 2004.

Abstract

Resurgence of illicit trade in African elephant ivory is placing the elephant at renewed risk. Regulation of this trade could be vastly improved by the ability to verify the geographic origin of tusks. We address this need by developing a combined genetic and statistical method to determine the origin of poached ivory. Our statistical approach exploits a smoothing method to estimate geographic-specific allele frequencies over the entire African elephants' range for 16 microsatellite loci, using 315 tissue and 84 scat samples from forest (Loxodonta africana cyclotis) and savannah (Loxodonta africana africana) elephants at 28 locations. These geographic-specific allele frequency estimates are used to infer the geographic origin of DNA samples, such as could be obtained from tusks of unknown origin. We demonstrate that our method alleviates several problems associated with standard assignment methods in this context, and the absolute accuracy of our method is high. Continent-wide, 50% of samples were located within 500 km, and 80% within 932 km of their actual place of origin. Accuracy varied by region (median accuracies: West Africa, 135 km; Central Savannah, 286 km; Central Forest, 411 km; South, 535 km; and East, 697 km). In some cases, allele frequencies vary considerably over small geographic regions, making much finer discriminations possible and suggesting that resolution could be further improved by collection of samples from locations not represented in our study.

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Figures

Fig. 1.

Map of Africa showing the collection sites divided into five regions: West Africa (cyan), Central forest (red), and Central (black), South (green), and East (blue) savannah.

Fig. 2.

Estimated locations of elephant tissue and fecal samples from across Africa when assignments are allowed to vary anywhere within the elephants' range. All tissue and scat samples (n = 399) successfully amplified at seven or more loci. Sampling locations are indicated by a cross and are color-coded according to actual broad geographic region of origin: West Africa, Central forest, and Central, South, and East savannah (color-coded as in the Fig. 1 legend). Assigned location of each individual sample is shown by a circle and is color-coded according to its actual region of origin. The closer each circle is to crosses of the same color, the more accurate is that individual's assignment.

Fig. 3.

Representation of confidence of assignments when all neighboring samples from that subpopulation (represented by a single cross) were included (A) vs. excluded (B) from the calculation of geographic-specific allele frequencies for ET (green), Bia (cyan), and Mikumi (blue). The 100 color-coded circles are random draws from the set of all possible locations weighted according to their probability. The concentration of these 100 circles in any given area gives a guide to the probability that the sample arose from that area under each condition.

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Assigning African elephant DNA to geographic region of origin: applications to the ivory trade - PubMed (original) (raw)