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MASSEY is published by Massey University, Private Bag 11-222, Palmerston North, New Zealand

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Groundbreaking research

The DNA of long-dead penguins IS making researchers rethink the pace of evolution

Summer 2001. A group of labourers quarry away at the Antarctic permafrost. Only now, at summer’s height, has the ground softened enough to be workable. The miners are a team of scientists, headed by Massey University’s Professor David Lambert. Their paydirt – the frozen confection of guano, feathers, bones, sand, pebbles and rocks beneath an Adélie penguin rookery – will lead to a rethink of the pace of evolution.

Adélies are the emblematic Antarctic penguin. They feature in every Antarctic documentary, are the stars of advertising campaigns, and are the most popular penguins with researchers. Around present-day Antarctica the Adélie population is estimated at 2.5 million pairs. Their colonies occupy islands, beaches and headlands at particular places around the Antarctic coastline Some colonies of Adélies number in the hundreds of thousands. Year after year the birds return to the same sites, nesting in dense colonies, each nest no more than a shallow depression in the ground lined with carefully chosen pebbles. Here in the rookeries, they court, reproduce, defecate – and die. Beneath them the residue of generations – air-dried and deep frozen – can be metres deep and the lowest layers thousands of years old.

How rapidly does evolution occur? The long- established method has been to compare two living species, then go back through the fossil record to find when it was that they shared an ancestor. More recently, with the arrival of gene sequencing techniques, attention has turned to DNA as a far more precise means of finding out how fast the evolutionary clock ticks. Most DNA is not much good for timekeeping. This is because of the garbling effect of sex: the recombination of the mother’s and father’s DNA. There are, however, two sets of DNA that remain largely intact down the generations: the male Y chromosome and the DNA contained in the cell compartments called mitochondria. Mitochondrial DNA is passed down from mother to child. Your mitochondrial DNA came from your mother who inherited it from your grandmother and so forth. The genetic alphabet is restricted to four letters: the bases adenine (A), thymine (T), cytosine (C), and guanine (G). On the odd and infrequent occasion, copying mistakes – or mutations – occur as the genes are passed down through the generations. In one generation a sequence might run ATTCGA and in the next, after a mutation, ACTCGA. The attraction of this for evolutionary scientists is that if you know the rate at which mutations accumulate you can compare two sets of DNA and determine when there was a common ancestor. If – it bears repeating – you know the rate at which mutations accumulate.

This is where the Adélie colonies come in. For here you have an unsurpassed source of well-preserved DNA held in datable sequences. Lambert’s team was able to take the DNA of 380 living birds and compare these sequences with DNA samples from 96 radiocarbon-aged bones ranging from 88 to 6424 years old.

In the laboratory each gene fragment was multiplied – or ‘amplified’ – using a process called Polymerase Chain Reaction. In the course of a few hours each fragment became several million copies, allowing its constituent bases can be mapped out.

As part of his Massey PhD programme, team member Dr Peter Ritchie was able to isolate and analyse a 1600 base pair (each base is paired with another as part of the DNA helix) sequence from the mitochondrial control region of a bone dating back to 523 years before present. A 390 base pair fragment could be sequenced from 66 percent of all of the subfossil bones.

With the sequences known, the next set of problems called for advanced mathematical techniques. If you have a two similar sequences of bases, how do you know that they came from a common ancestor and are not just coincidental and separately derived. This problem -- known as homoplasy – and others like it had to be resolved by looking at the statistical likelihoods.

The conclusion? That the evolutionary clock is ticking unexpectedly quickly, two-to-seven times faster than had been thought.

Two groups of Adélie penguins – the Antarctica lineage and the Ross Sea lineage – that differ genetically by about 8 percent have been shown to have accumulated these differences over 60,000 years rather than the 200,000 years of earlier estimates.

According to Lambert, the 60,000 year mark fits perfectly with the Last Glacial Maximum, a time when there were “few if any, ice-free areas in the Ross Sea, and Adélie penguins were likely to have been restricted to refugia”. Isolated from one another by the ice, this was the time for the two Adélie lineages to diverge genetically. “This is the first time anyone has measured the rate of evolution using ancient DNA,” he says. “It’s the first time anyone has been able to apply confidence intervals to an estimate.

We are 95 percent confident the rate of evolution in Adélie penguins is two to seven times faster than originally thought.”

If this is so of penguins, then how far out of whack are our estimates for human origins? The rates of change for birds and mammals have been commonly accepted to have similar values. In the 1980s, Allan Wilson – the Allan Wilson Centre’s namesake – famously looked at the mitochondrial DNA of 135 women from all around the world. After comparing the number of copying mistakes separating each woman from each other woman, he concluded that we all share the same maternal ancestor, a woman who lived around 150,000 years ago, swiftly dubbed Eve by the media. (This does not mean that we do not have other female ancestors who were contemporaries of Eve.) Could the rate of change for mammalian mitochondrial DNA has been underestimated as it has for penguins? Do we and our primate relatives share a more recent common ancestry than has been thought? The ancient DNA from Adélie penguin colonies raises all sorts of questions.

As well as Dr Peter Ritchie, Professor Lambert’s team includes Dr Craig Millar, Lara Shepherd and masters student Gillian Gibb, based at The Allan Wilson Centre for Molecular Ecology and Evolution. They have worked in collaboration with Barbara Holland of Massey’s Institute of Fundamental Sciences, A J Drummond of Auckland University and Carlo Baroni of Pisa University, Italy.