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Battelle Life Sciences Research CRO+ Today

Battelle Applied Genomics Today

January 2016 - Issue 4

Using Next Generation Sequencing to Detect and Classify Environmental Species

Battelle has proven and unique capabilities that have been successfully applied to microbial ecology, human forensics and wildlife population biology investigations. Equivalent DNA analysis methods have been used by others to discriminate between domestically produced and illegally hunted pork products based on species of origin[i]. Similarly, the types of DNA analysis capabilities at Battelle have been used to determine the species of origin of artifacts and mementos such as meat and medicinal animal parts, tusks, and horns[ii].

The Gray Whale Story: Gray whales feed in the summer off the northeastern coast of Sakhalin Island, Russia, in areas near oil and gas facilities and occupying a general range known to be within the historic distribution of the western stock of North Pacific gray whales. This population is of great interest to conservationists as it is considered to be the last surviving remnant of the western gray whale which was hunted along the coastal areas of Japan and Korea during the 19th and early 20th centuries. The western gray whale was previously reported to be extinct. Now, the western gray whale is considered as critically endangered by the International Union for Conservation of Nature (IUCN). The oil and gas industry expends considerable effort to monitor the population including its movements, feeding and population size.

Solving the problem: Battelle worked with an international oil company in 2014 to evaluate the use of environmental DNA (eDNA) methods to detect and type gray whales using sloughed DNA that is suspended in sea water. The study extended species detection abilities reported in recent eDNA studies[iii] by also providing evidence of maternal lineage (haplotypes) through analysis of variable regions of the recovered mitochondrial DNA (mtDNA).

Study Results: Water samples were collected offshore of Sakhalin Island in the vicinity of known gray whale habitat. Filtered water samples were shipped to and analyzed by Battelle’s Genomic Sequence Analysis Laboratory in Columbus, Ohio. Results confirmed the presence of gray whale DNA and the sequence was confirmed to be haplotype B, which is the second most common among the 22 gray whale haplotypes in the Sakhalin Island range. 

Significance: This study demonstrated the recovery and analysis of DNA, specifically western gray whale mtDNA, of sufficient quality and quantity to enable haplotyping for determination of lineage. Similar methodologies could be applied to forensic analysis of animals or animal products and to survey areas for the presence of threatened, endangered or otherwise controlled species.

[i]Sanches et al., 2012.  Illegal hunting cases detected with molecular forensics in Brazil. Investigative Genetics 3:17.
[ii] Linacre and Tobe, 2011. An overview to the investigative approach to species testing in wildlife forensic science. Investigative Genetics 2:2.
[iii] Kelly, et al., 2014. Using environmental DNA to census marine fishes in a large mesocosm. PloS one 9(1):e86175.