Reference Review: Parrots in the Early Days of Molecular Analysis
By Christopher Taylor at 11/21/2007 11:21:00 am
Ovenden, J. R., A. G. Mackinlay & R. H. Crozier. 1987. Systematics and mitochondrial genome evolution of Australian rosellas (Aves: Platycercidae). Molecular Biology and Evolution 4 (5): 526-543.
Rosellas (Platycercus) are a genus of five or more species of smallish parakeet found in more coastal areas of Australia, particularly the eastern states. Significant differences in opinion exist about just how many species there are in the genus - a number of subspecies are recognised that may be raised as separate species depending on author (I'm going to take a neutral position and treat all taxa as if they were species - see Wikipedia for a more detailed taxonomy). At least one taxon in the genus, the variable Platycercus adelaidae (the Adelaide rosella), is claimed by some to be a hybrid swarm derived from cross-breeding between two other subspecies and therefore not a valid taxon at all*. Rosellas are also possibly the most familiar parrot in New Zealand, at least in the north, due to abundant populations of introduced Platycercus eximius (the eastern rosella, shown at the top of the page in a photo from Wikipedia).
*The ICZN (in contrast to the ICBN) does not permit the recognition of taxa based on hybrids. This rule works fine when dealing with singleton hybrid specimens, which were doubtless what the ICZN had in mind when they drafted it, but is somewhat problematic when dealing with populations that have a hybrid origin, some of which may become established as new species.
The species of Platycercus can be readily divided into two groups, referred to as the "P. elegans" and "P. eximius" groups (though the latter should probably be called the P. adscitus group as that species has priority). Platycercus elegans and P. caledonicus are the blue-cheeked rosellas (P. elegans, the crimson rosella, is shown at left from Wikipedia). Platycercus adscitus, P. eximius and P. venustus are the white-cheeked rosellas. The geographically isolated P. icterotis (the western rosella) from the south-west of Western Australia has white or yellow cheeks and was once included in the P. eximius group, but is now generally excluded from either group.
At the time today's paper was published, molecular phylogenetics were still very much in their infancy. PCR, the technique that revolutionised molecular studies, was not to appear until the following year (Saiki et al., 1998). Before the advent of PCR, most molecular techniques were expensive, time-consuming, delicate and often unreliable (after the advent of PCR, they became expensive, delicate, often unreliable, and able to be done much more readily*). As such, most molecular studies in the 1980s used methods that by modern standards appear decidedly rough and ready. In the case of the one I'm looking at today, the method of choice was mitochondrial restriction fragment polymorphisms.
*It's a bit like the joke about the soldiers in the desert camp being to told by their general that there was bad news and good news. The bad news was that supplies had run so low that all they had left to eat was horseshit. The good news was that there was plenty of it.
Restriction endonucleases are enzymes that cut DNA into bits. There are a huge number of endonucleases in use at the present, and each one works by attaching to a specific sequence of bases in a DNA strand and dividing it at that point. Depending on need, there are enzymes that require relatively long sequences of bases and so would cut a given DNA strand rarely if at all, or there are enzymes that only require short sequences and so would be expected to cut strands far more readily. Probably the most familiar use of endonucleases to the general public is in DNA fingerprinting, where the resulting fragments from the endonuclease treatment of DNA samples are compared to see whether or not the samples contain the same fragment. The use of RFLPs (restriction fragment length polymorphisms) in phylogenetics is essentially a distance method - it proceeds by the assumption that samples that are most similar to each other in the resulting restriction fragment pattern are the most closely related phylogenetically. As for the use of mitochondrial DNA, there were a number of reasons why mitochondrial DNA was preferred to nuclear DNA for molecular studies at the time, but not least of them was that there is usually a lot more of it about and it is much easier to extract from a specimen than nuclear DNA. It should not be forgotten that prior to PCR, researchers only had as much sample to work with as they could directly draw out of the specimen.
There are a great many reasons why the use of RFLP for phylogenetics should not work. The assumption that genetic distance is equivalent to phylogenetic distance is simply not reliable, because evolution does not always occur at the same rate in separate lineages. Add to that the fact that in an ideal phylogenetic data set changes in one character state should not affect the state of other characters - a requirement blatantly violated by RFLP data, as the loss of a restriction site causes the resulting data set to "lose" two fragments and gain a whole "new" fragment. Fortunately for this case, the results actually make a certain degree of sense. Ovenden et al. recovered the same two species groups that had already been identified on the basis of morphological data. The only exception was that Platycercus icterotis, rather than clustering with the P. eximius group, came out as the most divergent species of all. However, this, too, had already been suggested on morphological grounds.
Unfortunately, the phylogeny of Platycercus does not appear to have been re-examined since the advent of more reliable analytical methods. There are no obvious reasons not to believe Ovenden et al.'s results, but considering the methodology they can hardly be said to not be worth a further look.
Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horm, K. B. Mullis & H. A. Ehrlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.