The grand adventures of King Rat

Commonly known as ship's rats, roof rats and house rats, black rats are major urban pests throughout the world, and in Asia, are major pests of agriculture. Black rats may all look the same on a dark night, but by day, they are typically grey or brown, and beneath the fur, turn out to be genetically diverse, according to CSIRO molecular taxonomist Dr Ken Aplin.

At February's Australian Archaeological Conference at the Australian National University, Aplin described a pattern of diversity in the rat's mitochondrial DNA that reveals it to be a complex of species or subspecies, with deep evolutionary lineages that coalesce several hundred thousand years ago, in southern and south eastern Asia.

Aplin, who works with CSIRO Sustainable Ecosystem's Australian National Mammal Collection, is the leader of an international collaboration that has studied the mitochondrial DNA (mtDNA) of black rats collected in 32 countries around the world.

The taxonomy of the group is confused, with hundreds of different names being applied to different races or ecotypes. The precise number of species or subspecies is still unknown.

Because of the black rat's synanthropic habits - its close association with humans - Apilin says the phylogeographic structure of its latter-day populations preserves a proxy record of human movements around the globe extending back many thousands of years.

Flea-ridden black rats carry a number of deadly human diseases, including bubonic plague, typhus and leptospirosis, and Seoul virus, a member of the hantavirus group, which caused a severe lung disease many soldiers in the Korean War.

Twice in the past 1500 years, flea-ridden black rats have caused deadly pandemics of bubonic plague. The 6th century Justinian Plague, which came out of Ethiopia on rat-infested grain ships, killed a quarter of the human population of the eastern Mediterranean.

The 14th century pandemic, the Black Plague, killed a third of Europeans, and half of China's population - in total, up to 100 million of the world's total population of 450 million.

Outbreaks of black rat-borne diseases are more common in some parts of the world than others, leading Aplin and his colleagues to theorise that different lineages have co-evolved with particular pathogens - for example, typhus, a rickettsial infection, is focused in East Asia.

Aplin and his colleagues have identified six distinct, deep genetic lineages or haplotypes that trace back to India, East Asia, the Himalayas, Thailand, Vietnam's Mekong Delta, and Indonesia. Aplin suspects further genetic studies of nuclear DNA will reveal the six haplotypes to be distinct species.

Rattus down under

The Middle East's black rats came from India 20,000 years ago, later spreading to Europe and Africa, before climbing aboard European sailing vessels and jumping ship in the Americas, and Australia.

Black rats arrived in Sydney with the First Fleet in 1788, and are now ubiquitous in Australian cities and towns. But Brisbane's black rats seem to have come from an east Asian lineage - they have 42 chromosomes, compared with 38 for Indian-derived European black rats.

"Black rats are just about everywhere - almost no island is free of black rats," Aplin says.

"They seem to have different impacts in different places. In some areas they are confined to human settlements and have little impact on natural ecosystems. In other places, they're out in the field, stealing bird's eggs and eating other native foods.

"The European rats that travel around on ships appear to be more ecologically conservative, while the Asian types are more penetrative in natural ecosystems.

"Back in the 1980s somebody was doing chromosome studies of Australian black rats, and found some populations - including one in Kakadu National Park - with 42 chromosomes. This provides evidence for multiple introductions in Australia."

Dutch ships that were wrecked on the coast of Western Australia in the 18th century carried cats to control ship rats. The cats appear to have survived, because Aborigines in the area regarded them as part of the native fauna - but any rats that made landfall appear not to have persisted in the absence of large human settlements.

Aplin says the East Asian Lineage moved from Taiwan to Japan Sri Lanka, the Philippines and Indonesia, and arrived in Micronesia 3500 years ago.

Its distribution closely reflects migrations by the ancestors of modern Polynesians and Micronesians in the recent prehistoric past.

Geneticists have retraced the epic Polynesian migrations into the remote eastern Pacific back through Melanesia to Indonesia, but linguistic evidence suggests that the Austronesian group of languages, which includes the Polynesian languages, originated in Taiwan.

Four haplotypes have not spread far from their centres of origin, indicating they are less adaptable.

In some parts of Asia, up to three distinct haplotypes are present. They do not interbreed, and remain morphologically distinct, leading Aplin to suspect they are distinct species.

Aplin says genetic studies need to be extended to other parts of the genome, but that as many as three distinct haplotypes are present in some parts of Asia.

"The message is that we need to have a good knowledge of these global pests, and to understand their diversity, to be prepared for the consequences of their spread, and the potential spread of rat-borne diseases."