[caption id="attachment_290" align="alignleft" width="222" caption="Rattus rattus, via alexfiles on Flickr (click image)"][/caption]

It seems that everywhere you find a group of humans, you'll find a clan of rats hiding in the shadows. This history seems born out of opportunity for the rat, but we've done our part to help them get around the world rather easily. This commensalism - a relationship where one species benefits, but the other receives little or no harm - is probably the result of the sloppy nature of humans. It appears we've never been very good at properly stowing our trash!

The flagship rat species, Rattus rattus, originated in India. While some of its cousins hung around on forest edges and fields, many found a living chasing down humans and loitering around their encampments for scraps. About 1 million years ago a split occurred among rats and what consistently separates the black rat from the wide variety of other Rattus species, including the infamous norwegian rat R. norvegicus, is its cozy relationship with humans. Though we may provide the rat with a treasure trove of our trash, it doesn't always repay us in kind! Plague, typhus and wrecking agricultural havoc aren't very nice ways to say thank you.

Perhaps surprising for such a widespread nemesis, but black rat biogeography - the study of how organisms are distributed on this planet - is relatively unknown. The first step, though, in determining the history of the rat's tracks is figuring out what exactly a black rat is. In a study published last week in the open access journal PLoS ONE, Ken Aplin and colleagues set out to find how intimate our connection is with this feared and reviled co-inhabitant.

Looking closely at a set of genetic markers that allow a deeper historical context, Aplin and colleagues discovered that several other species of rats were genetically similar to the common black rat, thus forming a complex of species that share a close ancestry. In fact, the black rat complex split off from its closest relative around 1 million years ago and is composed of at least 6 distinct lineages that appear to have diversified around 200,000 years ago, which coincides with the second to last glacial period during the middle of the Pleistocene.

[caption id="attachment_287" align="alignright" width="220" caption="Figure 4 from Alpin et al. (2011): a) Distribution of lineages I and II. b) Natural ranges of lineages I-VI. c) Distribution and movement of lineages I, II and IV."][/caption]

Of the six black rat lineages, two are particularly widespread. The most ancestral individuals of lineage I live in India, supporting an out-of-India hypothesis for European and African black rats. On the other hand, lineage II stayed in southeast Asia, hanging around the Mekong River basin. These two widespread lineages separated ~200,000 years ago and now occupy distinct, non-overlapping ranges.

Lineages I and II dominate the global distribution of black rats, but there are much finer-scale patterns among the other lineages residing in southeast Asia. Lineage III is restricted to the Himalayas and lineages V is hypothesized to be a different species of Rattus, showing consistent morphological differences from the species that it coexists with. Likewise, lineage VI is composed of two previously described Rattus species that are distributed similarly to the black rat and show consistent morphological differences and are generally not found at human settlements. Lastly, lineage IV is restricted to the lower Mekong River and just barely overlaps in its northern range with lineage II.

Perhaps most striking, we can see from the maps at right that there were likely several origins of commensalism. The split of lineages I, II and IV occurred over 500,000 years, well before evidence of human settlement. Fossil evidence of humans are evident between 50-60 thousand years ago in Asia, yet permanent human settlements didn't really occur until the Holocene, or within the last 10,000 years. Thus, these black rat lineages were established prior to human arrival. Modern black rats are very keen to exploit disturbed habitats, though. It seems probable that as humans swept through the area, burned forests and fields, and settled into an agricultural society, ancestral black rats would have done well to take advantage of this - commencing the commensalism.

Another feature of Alpin's analysis shows clearly how lineages I and II in particular - but also lineage IV - had a little bit of help getting around during the Age of Exploration, especially in traditional port towns. But some individuals have a genetic signal dating their arrival to the southeast Asian islands in the mid to late Holocene, or around 5-10 thousands years ago. This would have occurred after the last glaciation when sea levels were tens of meters lower and there were intermittent connections between the Asian mainland and what is now Malaysia, Taiwan, and Indonesia. So for earlier-than-boat-transport, it is conceivable that rats in lineages II and IV, scampered across the formerly well-connected landscape.

Humans were also migrating during this time, though. Rats, being lovers of disturbed habitats and human waste, trailed along the path of destruction and found their way into these new environs. Once sea level rose they were trapped and couldn't breed with other populations. This isolation would have promoted the high diversity of species and within-species lineages that we now see in southeast Asia. And this is only the beginning of the process - it's only a few thousand years in. The outcome of further speciation will ultimately depend on the degree of contact between lineages, which appears accelerated by people. While the rats might seem like they are tagging along in our footsteps. It is evident that we are being used as a vehicle in the rats' quest for global domination!

A final take home message is that different rat vector-borne diseases are also associated with the various lineages. Thus, it is recommended that it would be prudent to type the host lineage to understand the context of the disease vector. For introduced rats away from their ancestral southeast Asian or Indian homelands, one can retrace the geography from where the diseases might have come from. This could actually be a simple, yet useful way to quickly determine responses to various rat-carried diseases.

Aplin, K., Suzuki, H., Chinen, A., Chesser, R., ten Have, J., Donnellan, S., Austin, J., Frost, A., Gonzalez, J., Herbreteau, V., Catzeflis, F., Soubrier, J., Fang, Y., Robins, J., Matisoo-Smith, E., Bastos, A., Maryanto, I., Sinaga, M., Denys, C., Van Den Bussche, R., Conroy, C., Rowe, K., & Cooper, A. (2011). Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats PLoS ONE, 6 (11) DOI: 10.1371/journal.pone.0026357