Ancient DNA profile

An article by science writer Henry Nicholls in PLoS Biology covers a lot of ground. Most of the attention goes to Alan Cooper, with Svante Pääbo in a supporting role. There is this on the hobbits:

aDNA could also, in principle, be used to shed light on the evolutionary position of the 18,000-year-old "hobbit" recently unearthed on the Indonesian island of Flores [8]. Both Cooper and Pääbo have offered to have a go at isolating DNA from the "hominid" skeleton, but the early signs are that DNA has not survived. "The somewhat moist and tropical preservation conditions make the recovery of DNA improbable," says Peter Brown, the paleoanthropologist at the University of New England in Armidale, Australia, who led the hobbit study. Efforts to extract DNA from other bones collected at the same site as this tiny hominid have not produced results. "We have made attempts with Stegodon molars," he says, "but so far without success."

I am most impressed with studies that survey many ancient specimens to make conclusions about ancient population dynamics, such as local extinctions and recolonizations. The recent arctic fox paper is a great example. This article mentions two more: a study of ancient bison fossils from Beringia, and a study of arctic brown bears. Here's a paragraph about the bison study:

Cooper's latest work has analysed DNA from over 400 bison fossils from Beringia—the frozen wastes between eastern Siberia and the Canadian Northwest Territories [3]. "What we've done is carbon-date a shitload [JH --is that a metric shitload?] of bison and get DNA out of them." It's the largest aDNA study to date, he says (Figure 1). The icy conditions mean that good quality mitochondrial DNA could be extracted from most of the specimens. The bison could also be dated accurately. This allowed Cooper and his colleagues to trace the changes in the bison genetic diversity from 150,000 years ago to the present. It was even possible to predict the effective population size throughout this period of bison evolution. "Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically," they note.

The main drawback of these studies has been their limitation to mitochondrial DNA. The story of that one molecule is informative, but it is not the whole story -- and in particular, it may reflect selection associated with climate change, not just extinction and population expansion.

That is the main reason the Neanderthal genome is so important -- it allows us to compare the vast majority of the genome to find evidence of functional changes. Likewise, the ability to look at many genetic regions is a highlight of the described work on early maize domestication:

Pääbo's analysis suggests that the alleles typical of contemporary maize were already present in Mexican maize 4,400 years ago, so just a couple of thousand years after its initial domestication from the wild grass teosinte (Figure 3). "Quite early on, properties were selected that were not only the structure of the plant but also the biochemistry," he says.

There is really a light year of difference between the labs bringing out nuclear genomic sequences and those working exclusively with mtDNA. There is so much more information to be had from the full genome that these datasets will keep PhD's busy for decades.

But for the time being, labs that limit to mtDNA are able to bring out more and more sequences from different individuals. This adds the essential component of population variability, which is essential to understanding the dynamics of evolutionary change. So it's like we are getting a third of the story from each of these sides -- with the other third coming, of course, from traditional morphological comparisons.

References:

Nicholls H. 2005. Ancient DNA Comes of Age. PLoS Biol 3: e56. doi:10.1371/journal.pbio.0030056