So I got to choose my PhD project today, well at least somewhat. It’s nailed down a little more than it was a week ago. I had pretty much any Australian rodent species to choose from, and could look at anything from phylogenetics and phylogeography, to other areas of genomics (i.e. chromosomal rearrangements) and next generation sequencing (NGS) techniques.
I had a long hard think about what I wanted to achieve from my project, did I want to repeat what I’d done for my Masters of Science (MSc) and specialise in that specific area, or move onto new areas to get a broader skill set from? To me it was an easy choice, I wanted to leave the MSc behind and move onto other areas and improve my skill set.
I’ve decided to work on a genus of Australian rodents of which I’m sure most of you will know the name of, Rattus, aka rats! Now for a bit of background, Australia actually has at least 65 different species of rodents here, including the Old “Endemic” and New “Endemic” groups. Endemic meaning they’re only found here in Australia, with Old referring to an old wave of colonisation from South East Asia ~4-million-years-ago (MYA) and New referring to a later wave of colonisation ~1MYA. The genus Rattus makes up the New Endemics, with all other remaining Australian rodents making up the Old Endemics. Both these groups fall into the family Muridae, and from my limited knowledge obtained so far on this subject it has sequentially colonised Australia via South East Asia via Asia, with many endemic species also found in Africa and Europe, and introduced species found effectively everywhere now (i.e. Rattus rattus, the Black rat).
Anyway, I’ve chosen to work on the New “Endemics”, the genus Rattus here found throughout the Australian continent, which includes Papua New Guinea (together Australia and Papua New Guinea make up the landmass known as technically as Sahul). So my project will involve:
1. Piecing together a phylogeny of the New “Endemics” using either nuclear and mitochondrial sequencing, and maybe using NGS as well. So this will allow me to resolve how each species within the Rattus genus is related to one another, which are close, which are distant, which species actually comprise a species complex (i.e. multiple species grouped into a single species). I will also be able to move out from this and add other Rattus species from throughout South East Asia and hopefully piece together their path of colonisation from Asia through South East Asia and into Sahul. I’ll be doing field work in Sulawesi in Indonesia, and Papua New Guinea!
2. I’ll be examining the phylogeography of each species as well. That involves the sequencing of multiple individuals covering each species distribution and examining genetic relationships between them to elucidate any genetic breaks caused by biogeographic barriers. So in layman’s terms, how has each species evolved to fill out its current range? Has it been blocked by physical barriers like rivers or mountain ranges, or habitats barriers like dense rain forest or arid deserts?
3. I’ll be focusing in on examining the evolutionary genetics of two species in particular. Rattus villosissimus (the Long-haired rat) and Rattus fuscipes (the Bush rat). Rattus villosissimus is interesting to me, and captured my attention right from the start, because it normally exists in 2 or 3 disjunct populations in northern central Australia. In times of flooding, and subsequent productivity for its food source of native grass species, it goes through a huge population expansion rapidly erupting into billions of individuals that end up expanding the range to cover most of the Northern Territory and some of Queensland and Western Australia. After the flooding ends and the arid environment returns back to normal the species suffers a huge crash in numbers with the population retracting its range back to the disjunct pockets of perhaps only a few 1000 individuals. Because this has happened periodically following seasons of flooding, and because rats exhibit chromosomal rearrangements, this species might be going through periodic linear speciation or diversification. That is, that its genome is changing drastically due to these chromosomal rearrangements, and maybe in part due to genetic drift. Crazy huh? And Rattus fuscipes because it has a really cool distributions covering the coastal outline of Australia, inhabiting its mesic (wet forest) environments. It’s expected that this species colonised the mainland when a land bridge joined Papua New Guinea to Australia and then rapidly expanded along the coastline in a clockwise fashion throughout its current range. So it’ll be interesting to see what’s going on there too.
I’m sure, too, that many of you will have squirmed as soon as I mentioned rats! However, these guys are amazingly beautiful animals, and I’m dying to get out into the field and get my hands on a few of them soon! I’ll leave you with a few pictures.
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