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Mitochondrial Study Provides Clues to East Asian Pig Evolution and Domestication

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a paper appearing in the early, online edition of the Proceedings of the National Academy of Sciences this week, an international research team reported on their use of ancient and modern mitochondrial DNA for gaining insights into pig domestication and evolution in East Asia.

"The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East," senior author Ning Li, an agrobiotechnology researcher at the China Agricultural University in Beijing, and colleagues wrote.

By comparing 18 ancient mitochondrial DNA sequences from pig remains unearthed at six archeological sites in northern China with mitochondrial sequence data on nearly 2,000 modern pig samples, the team found evidence suggesting domestic pigs in China descended from ancient domestic pigs in the country's Yellow River regions. They also found genetic clues for additional domestication events in India and Southeast Asia.

Past research suggests wild boar domestication occurred in both Europe and Asia, with human migration contributing to mixing between various sub-populations.

In an effort to clarify pig domestication patterns in East Asia, the team integrated genetic data on modern pigs with information from ancient pig DNA isolated from pig remains in the Yellow River region of China, where archeological evidence for agriculture and domestication appears at least 8,000 years ago.

The researchers sequenced a 185 base pair region of the mitochondrial genome from 48 ancient pig specimens. Of these, the team was able to get usable sequence from 18 of the samples, estimated to be between 3,100 and 9,000 years old.

They then compared these ancient sequences with data on a 698 base pair region from mitochondrial DNA for 151 present day wild and domestic pigs, along with 1,390 sequences from GenBank.

Consistent with past studies of pig populations, their phylogenetic analyses revealed distinct wild boar clades in western Eurasia and the islands of Southeast Asia, with the Southeast Asian group appearing in a more basal position.

The team also identified 45 distinct haplotypes representing only the wild populations. The domestic pigs, meanwhile, formed 92 haplotypes. Another 21 haplotypes contained both wild and domestic pigs.

Using this information, the researchers were able to tease apart geographic patterns associated with phylogeny and establish another network incorporating ancient mitochondrial sequence data.

Within the ancient samples, for example, the team detected five of seven common haplotypes that are shared by present day wild and domestic pigs in East Asia.

With a few exceptions, the team found that most geographic regions tested corresponded to a single wild boar population, suggesting domesticated pigs originated from local boar populations in most cases.

Overall, the researchers' findings were consistent with East Asian pig domestication, suggesting domestic pigs in China today descended from ancient domesticated animals in and around the Yellow River site.

"[T]he most common modern domestic haplotypes found in Central China are also the most common Asian haplotypes found across East Asia, in Australian feral pigs, and in modern European and American breeds — the latter as a consequence of the 18th century drive to improve European breeds by hybridizing them with imported Asian pigs," Li and her co-authors wrote.

Even so, their findings hint at four independent domestication events in Southeast Asia, India, and off the coast of Taiwan, which the researchers dubbed "cryptic domestication" events.

Down the road, the researchers noted, additional analyses involving both mitochondrial and nuclear markers, combined with archeological information, are expected to produce an even more refined view of pig domestication, evolution, and human migration events.

"[T]he evidence presented here strongly suggests an intriguingly complex pattern of local domestication and regional turnover," the team concluded, "and underscores the need for further integrated archeological and genetic research."