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Ivory Genetics Point to Prevalent Poaching Sites in Parts of Africa

NEW YORK (GenomeWeb) – Genetic patterns in ivory from large seizures over nearly two decades suggest elephant poaching is currently centered on two hotspots in Africa — a region in Tanzania that stretches into Mozambique and another in northeastern Gabon, the northwestern Democratic Republic of Congo, and southeastern Cameroon.

As they reported online today in Science, researchers from the University of Washington and INTERPOL used microsatellite markers to test samples from 28 seizures — each involving half a ton of ivory or more — between 1996 and 2014. They then traced the ivory back to their source elephant populations using a genetic reference created with DNA from elephant dung collected at African savannah or forest sites.

Using this approach, the team concluded that large-scale poaching of forest elephants in the Gabon-DRC-Cameroon area has been taking place since around 2006. On the other hand, almost all of the savannah elephant ivory from post-2006 seizures was genetically linked to elephant populations in Tanzania and northern Mozambique.

Those involved in the study hope their genetics-based approach will be an important step in stamping out criminal networks that obtain, trade, and transport illegal ivory across borders.

"Showing that there are really are two major hotspots … will not only stop a huge amount of the immediate [elephant] killing, which is critical to avoid bleeding the rest of Africa of its elephants," corresponding author Samuel Wasser, a conservation biologist at the University of Washington, told GenomeWeb. "But it will also choke the flow of ivory into these complex criminal networks that are so important for the ivory trade to operate."

"New hotspots may turn up," he added. "But from what our data shows, they're only going to turn up slowly because they really require a big, corrupt infrastructure to move the ivory out [of countries where poaching takes place]."

The group's analysis focused on 16 microsatellite markers, many of which were developed by Wasser and colleagues in collaboration with former Fred Hutchinson Cancer Research Center researcher Elaine Ostrander, who now heads the National Human Genome Research Institute's comparative genetics section.

Before they could use these microsatellite markers to match ivory samples back to a reference map of elephant genetic patterns, though, the researchers had to come up with reliable ways to extract DNA — much of it degraded — from ivory stored in non-temperature-controlled environments for months, years, or even decades.

In the end, the team settled on a protocol that uses liquid nitrogen and a shifting magnet field system to freeze and crush ivory into a fine powder before extracting the DNA, Wasser explained.

"In the past, people tried to get DNA out of ivory," he said, "but they were grinding it and heating it up and degrading the DNA."

Microsatellite marker patterns in seized ivory were then compared with a reference map established from dung DNA that represented 1,350 savannah or forest elephants at 71 sites, making it possible to place the seized samples to within around 300 kilometers (186 miles) of their source.

To do this, researchers relied on analytical methods built from computational strategies that members of the team first described in the Proceedings of the National Academy of Sciences in 2004 and 2007.

Rather than considering samples from each site independently, Wasser explained, the so-called Markov Chain Monte Carlo algorithm takes into account the geographical proximity of elephants with various genetic patterns, improving allele frequency estimates in areas where fewer reference samples were available.

The approach also combines genetic data from samples within same seizures, he added, which tended to involve ivory from neighboring elephant populations with higher-than-usual allele sharing.

In their Science study, for example, the researchers described seven seizures involving forest elephant ivory from 2006 to 2014. Ivory from elephants in Gabon-DRC-Cameroon area predominated in six seizures, while a seventh involved elephants from the Ghana and Ivory Coast Region.

Meanwhile, the majority of savannah elephant ivory seized since 2006 contained genetic patterns present in elephants from Tanzania and Mozambique. The data suggests poachers targeted the Selous and Nyasa Game Reserves until around 2011, when they began inching north to the Ruaha National Park/Rungwa Game Reserve area.

Before 2006, on the other hand, seized ivory tended to come from sites where elephant populations have now declined, including Zambia and the eastern DRC.

In most cases, the team's genetic data indicated that ivory was trafficked from poaching sites to other countries before being exported from Africa, hinting at a complex network that would partly obscure the source of the poaching without available genetic clues.

Wasser and his colleagues are continuing to test ivory samples using PCR amplification and Sanger sequencing methods similar to those described in the paper. They are also developing a high-throughput SNP genotyping strategy to track illegal trade in body parts from other animals, including pangolins.

In an accompanying editorial in Science, Durham University researcher Rus Hoelzel emphasized the importance of appropriate marker selection and controls when performing such genetics-based wildlife forensics, while highlighting their potential wildlife protection applications. 

"It is becoming increasingly realistic and affordable to screen hundreds or even thousands of loci at once in an automated array system that works well with degraded DNA," Hoelzel wrote. "Hopefully the DNA forensics approach exemplified by [the elephant] study, integrated with other effective approaches and these further innovations, will start to turn the tide for the African elephant and other threatened wildlife."