Potent new strategy for mapping animal species shakes up tree of life

Since the 1859 publication of Charles Darwin’s “Origin of Species,” efforts to trace evolutionary relationships among different classes of organisms have largely relied on external morphological observations.

But a new study — published in Nature by a team including Gonzalo Giribet, professor of organismic and evolutionary biology in the Faculty of Arts and Sciences — has introduced a potent new strategy for mapping the family tree of animal species. Giribet and colleagues present, for the first time, a wide-ranging DNA-based survey of 77 species of animals, yielding a handful of surprises for evolutionary biologists.

New data from 29 species representing 21 important phyla in the animal kingdom — more than half of which had never been examined using the group’s method of genomic analysis — were studied alongside better-characterized specimens. The newcomers consisted mostly of protostomes — or, as Giribet calls them, “the squeezies and the creepy crawlies.”

After incorporating data from the likes of worms, sea spiders, squids, snails, and comb jellies into the mix, Giribet and his colleagues found that the resulting taxonomic trees — charts that scientists construct to illustrate the relationships among various organisms — were reshuffled in unexpected ways.

The researchers were startled to discover evidence contradicting a long-held hypothesis that placed sponges on the most primitive branch of the taxonomic tree. Instead, they found strong support for an alternative animal ancestor: comb jellies — fragile, often colorless plankton that move via the action of shiny, beating cilia.

There were more surprises in store: An entire taxonomic group, Coelomata, consisting of animals with fluid-filled body cavities, disappeared. “It now seems clear that this [group was] an artifact of poor taxon sampling,” the authors comment in the paper.

A long-standing debate about the relationships among centipedes and millipedes, arachnids, and jawed insects (such as ants and beetles) was dispatched with ease: The spiders, not the insects, clustered more closely with their leggier cousins.

Giribet finds the clarifications and upsets resulting from the study particularly satisfying.

“Some biologists believed it would never be possible to confidently reconstruct the major groups in the animal kingdom,” he says. “They thought that the metazoan radiation was too rapid during the Cambrian explosion — that the genetic lineages were too closely spaced and had too much in common to untangle.”

The Cambrian explosion, which took place roughly 530 million years ago, witnessed the sudden appearance and evolution of major groups of animals, or metazoans, according to the fossil record.

However, say Giribet and his co-authors, it is now clear that previous attempts to use DNA data to construct a taxonomic tree were hobbled by inadequately diverse sampling.

Furthermore, sequences were clumsily targeted. Researchers attempted to select sets of genes that were roughly analogous in function across different species — a strategy that constrained the data to only a fraction of the lengths of the genomes under investigation. Giribet and his colleagues, by contrast, used random sampling to generate a large database of 150 genes that were shared to varying extents by all the species represented in the study.

The team then analyzed the degree of commonality among the different sets of genes in each taxa — a computational task requiring 120 processors and several months to complete.

“Certainly the enhanced computational technology in recent years has made this research possible,” says Giribet. “The technology has changed a great deal in the last five years — and sequencing is cheaper and faster. I don’t think this kind of project would have been possible five years ago.”

Giribet’s co-authors hailed from Brown University, the University of Hawaii, Yale University, the Scripps Institution of Oceanography, the Kristineberg Marine Research Station in Sweden, the Natural History Museum in London, the University of Copenhagen, the Monterey Bay Aquarium Research Institute, the Zoological Museum at the University of Hamburg, Simmons College, and the American Museum of Natural History.

The group’s work was funded by two collaborative grants from the National Science Foundation’s Protostome Assembling the Tree of Life Project.