Humboldtians in Focus

Farewell to the Phylogenetic Tree

By Karen Sieber

For generations of researchers into evolution, phylogenetic trees were an ideal way of presenting the relationships between species and how they developed. However, a new kind of genetic analysis has revealed that evolution is often far less linear than we had assumed. The phylogenetic tree is being supplanted by the network.

41 species of buttercup have been recorded in New Zealand. Ranunculus nivicola is one of them.
41 species of buttercup have been
recorded in New Zealand.
Ranunculus nivicola is one of
them.

Photo: private

Peter Lockhart is glad to be back on firm ground. It has taken the evolutionary biologist more than 36 hours to get from Auckland in New Zealand to Frankfurt. He has come to Germany to meet collaborative partners and discuss joint projects. Since his stay in Germany in 1996, when he was a Humboldt Research Fellow, he has travelled round the world twice every year, working together with researchers from various disciplines and diverse countries and using state of the art technology for his purpose. Peter Lockhart wants to throw light on the evolution of species. And to this end, he investigates the motor of evolution: the genome.

Lockhart isolates deoxyribonucleic acid (DNA) from the nucleus of plants, animals and bacteria for his investigations and unravels their secret code: the precise sequence of the four decisive DNA building blocks. “To sequence DNA you have to set off several chemical reactions one after the other. You have to follow a sort of recipe, the only difference being that the amounts are much smaller in molecular biology than they are in the kitchen,” Lockhart explains. When the recipe has been completed, he gets the DNA sequence in the form of a computer file which he examines in minute detail. “If we study the evolution of molecules we’ll learn how today’s biodiversity has arisen.”

The unfaithful buttercup

“If we study the evolution of molecules we’ll learn how today’s biodiversity has arisen.”

In the mid-1990s, Lockhart started investigating the DNA ofNew Zealand’s buttercups. 41 species of the Ranunculus genus have been recorded on the archipelago; it set off on its journeyto conquer the world all of 25 million years ago. Pollen and fossil remains give a rough idea of the evolution of this group of plants. But DNA has provided scientists with a much moredetailed picture. Lockhart’s investigations show that the buttercup has only been indigenous to the country for a relatively short time. He suspects that the seeds were brought across the sea to New Zealand some five million years ago by the wind or in bird feathers. The new arrival produced offspring which managed to find various biological niches. Lockhart refers to a phylogenetic tree. “The short branches indicate that all the species living today are very closely related. Many of them have only developed in the last million years – ingeological terms, a very short time.” Nevertheless, in this veryshort time, many very different forms have emerged. Amongst the Alpine experts there are species that even bloom at icy temperatures above the snowline. Others manage to find a hold on slippery scree or defy the flooding in boggy terrain.

“If you want to compare closely-related organisms, DNA sequences are not always very effective, unless you find sections of the genome that change very quickly.” Lockhart sought and found these sections, but soon faced a surprising set-back: many of the plants he examined had a hybrid genome. Although their external characteristics identified them as members of a certain species, their genome revealed that some of their parents or grandparents had been unfaithful: the specimens under investigation were crossbreeds!

Networks and phylogenetic trees

“When you draw up an evolutionary tree you work on the assumption that relationships between species evolve in a tree-like process,” Lockhart emphasises. For evolutionary biologists, “tree-like” means that species can be traced back in a simple line of descent. However, if today’s forms are the result of crossing and backcrossing, then it follows that evolution is not linear. Relationships become complex, and a simple phylogenetic tree turns into a network. “This finding was what made scientists start developing methods for computing phylogenetic networks.” Lockhart points to a network graph with plant names at either end which he can use to illustrate genetic indications of hybridisation events.

Evolutionary biologist Peter Lockhart
Evolutionary biologist Peter Lock-
hart
Photo: Karen Sieber

Nowadays, DNA sequences can be prepared in no time, but processing the molecular data is still a challenge. This is why Lockhart works closely together with mathematicians and computer scientists who have embraced this task. Humboldt Research Fellow Michael Steel, head of the Biomathematics Research Centre at the University of Canterbury, New Zealand, is one of his collaborative partners. Steel is an expert at turning biological processes into mathematical formulae. Initially, Lockhart had to learn how to describe his biological problems so that mathematicians could understand and implement them. Since 1994, he has been cooperating with Daniel Huson, Steel’s Humboldt Host at Tübingen University. Huson develops computer programmes on the basis of mathematical algorithms, which even make it possible to present processes in evolutionary biology in graphic form. “As a scientist engaged in biocomputer research, I rely on people not only giving me the datasets but also describing the biological processes hidden behind them,” he says.

The fact that they live and work at opposite ends of the world is not a problem in the age of email, telephones and video conferences. “Still, it is important to get together regularly nonetheless,” Huson comments. That is why he, too, arranges annual trips to New Zealand and combines visits to Palmerston North, where Lockhart is doing research at Massey University, with conferences “down under”. Neither of them complains about the amount of time they spend travelling: 36 hours en route to the other side of the earth are, after all, an important investment in their global academic network.


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Karen Sieber Karen Sieber
Photo: F. Wagenseil

Dr. Karen Sieber teaches biotechnology at the Straubing Center of Science and works freelance as a journalist. She is fascinated by networks – not just in evolutionary biology but also in interhuman relations.

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