I think I first woke up to the potential of ancient DNA (aDNA) research when I was part of the team developing the Evolution for Teaching website. My friend Dave Lambert, who was then with the Allan Wilson Centre at Massey (Albany) was working with aDNA to study microevolution in Adelie penguins in Antarctica, and he gave us some material to put on our site. More recently Dave & his research team applied the same techniques to moa, revealing that in at least some cases what were thought to be pairs of species (one large, one small) were in fact female and male of the same species (Huynen et al. 2003). Now they've turned their focus to kiwi (Shepherd & Lambert, 2008).
Researchers working with rare species, such as kiwi, face a number of hard-to-answer questions: was the species once common, or has it always been rare? How much genetic variation is there in the species - and were things any different in the past? What was the species' distribution like in the past? Are we looking at remains from a single species, or from two or more cryptic species that are very difficult to distinguish on the basis of physical appearance?
It seems that aDNA techniques have the potential to answer at least some of these questions. For example, aDNA can give an estimate of past genetic variation in a population, which in turn allows for a measure o fhow much genetic diversity has been lost in that contemporary population. This is important, as there may be a link between the long-term survival of a population and its level of genetic diversity.
Also, because many (if not all) endangered species live in fragments of their original range, it's hard to tell if they have always been isolated from other related species, or whether they might have been sympatric in the past. This has management implications - if they've never been sympatric, we can't guarantee that they'll possess effective reproductive isolating mechanisms, & so putting two such species in the same conservation reserve might not be such a good idea. Having such information about species distribution is also useful when considering species re-introductions - these are more likely to be successful if the chosen sites are within the historical range of that species.
Shepherd & Lambert (2008) used ancient DNA to examine past ranges, species boundaries and loss of genetic diversity in five species of the endangered kiwi (Apteryx). Kiwi taxonomy is reasonably complex: there are two spotted kiwi species ('great' & 'little') and three brown kiwi species (all allopatric): North Island brown, Okarito brown (rowi) & tokoeka - plus a possible 4th, extinct species, the 'eastern' brown kiwi. The three extant brown kiwi are morphologically very similar but genetically distinct. (In fact, of all the kiwi species only the little spotted kiwi (A. owenii) can be distinguished by bone morphology, because it's significantly smaller than any of the others. This makes determination of past distributions on the basis of fossil remains, quite a challenge.)
The researchers obtained aDNA sequences from 46 'large' kiwi remains (either subfossil bones, or skins) kept in museums. The aDNA samples were obtained & analysed in a dedicated & regularly decontaminated laboratory, to minimise the likelihood of contamination. Shepherd & Lambert used kiwi-specific primers for the mitochondrial cytyochrome b gene & also part of the mitochondrial control region. and used PCR to amplify the DNA prior to sequencing. They obtained 28 complete sequences, which were then compared with published modern sequences from 1 little spotted kiwi, one great spotted kiwi, & 58 bown kiwi (including rowi & tokoeka).
And what did they find? aDNA from samples identified as 'eastern' brown kiwi fell within the tokoeka range, suggesting that the 'eastern' brown was not a separate species. The samples also clearly distinguished between North Island brown, rowi, & tokoeka, which suggests that these taxa have been have been reproductively separated for some considerable period. The data also identified a number of allopatric subgroups in both rowi & tokoeka, but Shepherd & Lambert caution that this is not sufficient basis for describing the subgroups as separate species.
The ancient mtDNA also provided information about the previous ranges of kiwi: Great spotted kiwi seem to have a prehuman distribution very similar to their current distribution ie the northwest of the South Island. In contrast, brown kiwi were previously more widespread in both the North and South Islands... the past distribution of rowi included the west coast of the South Island and the lower North Island...while tokoeka were found on the east coast of the South Island - & there was no overlap in the species' distributions. This information can be used to decide on sites for re-introduction of the different species, within their past ranges.
As for the species' genetic diversity - samples from almost all ancient locations contained unique genetic variation. This means that extinction of ancient populations eg of rowi & tokoeka has had a significant negative impact on genetic diversity in those species (something confirmed by statistical comparisons). And again, this has implications for species conservation. Modern North Island brown kiwi retained much more genetic diversity.
Ancient bones really do have a story to tell.
L. Huynen, C.D. millar, R.P. Schofield & D.M. Lambert (2003) Nuclear DNA sequences detect species limits in ancient moa. Nature 425: 175-178
L.D Shepherd & D.M. Lambert (2008) Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand. Molecular Ecology 17:2174-2184