Common genes form new family tree for animals

Looking deep within the genes of three very different kinds of animals, scientists have found enough molecular evidence to finally fell the animal kingdom’s old family tree.

Writing this week in the British journal Nature, scientists from UW–Madison, the University of Paris, Cambridge University and St. Petersburg University in Russia report the discovery of a common genetic theme that provides powerful new evidence to firmly place nearly all animals — from mollusks to humans — on a simplified, three-limbed tree of life.

For more than a hundred years, scientist have depended on morphology, the form and structure of animals, to determine their place on the family tree. But over the past few years, a new tree has been proposed based on comparisons of themes found in animal genes.

“In the last four or five years, this tree has been totally reorganized and if you’re interested in evolutionary relationships, that’s really important,” said Sean B. Carroll, a professor of molecular biology at the Howard Hughes Medical Institute at the UW–Madison and a co-author of the report in Nature.

The new genetic evidence suggests that in the animal kingdom there are three primary lines of descent that first diverged from a common ancestor at least 540 million years ago, and that gave rise to most animals (with the exception of jellyfish and sponges) living today, said Jennifer K. Grenier, a Howard Hughes Medical Institute Fellow, UW–Madison graduate student and a lead author of the report. (Story continues below.)

The new study was based on exploration of so-called Hox genes in three distinct kinds of animals: an unsegmented marine worm related to insects, an unusual marine animal called a lamp shell, and a segmented worm related to earthworms

By studying the Hox genes in three distinct kinds of animals – including an unsegmented priapulid worm (above) – scientists can infer what critical body-organizing genes were present in a common ancestor 540 million years ago.

and leeches. Hox genes comprise part of a toolbox that is central to animal development. They help organize cells into the different body parts and determine such things as number and placement of legs, wings and other appendages.

By looking for, and finding, essentially the same critical organizing genes in seemingly unrelated animals, the groups from Wisconsin, Paris and Cambridge could, in essence, look far back in time and infer what critical body-organizing genes were present in a common ancestor.

“The point is we’re trying to find out the early history of animal evolution,” said Carroll, and what we’ve found is that “the genetic toolbox was pretty sophisticated in the earliest animals. That toolbox has been called on and expressed in many different ways.”

It’s possible, Carroll explained, to infer the past existence of some genes by looking at fossils, which may reflect those genes in the anatomy of the fossil animal. It is also possible to determine what critical genes were at work hundreds of millions of years ago by analyzing the genes of the living descendants of animals found in the fossil record.

“When you actually look at the genes, the three-branched tree is supported,” Carroll said.

All of the animals involved in the new study, although from widely divergent parts of the animal kingdom, have similar Hox genes, although with slight but significant variations, said Grenier. The upshot, she said, is that an ancient common ancestor conferred these genes on animals that subsequently evolved in dramatically different directions.

“Before these (modern) animals existed, these genes were around. There was a common ancestor 600 million years ago that had all these genes,” Grenier said.

The new, three-limbed tree simplifies the previous animal kingdom family tree by substituting one branch in place of many offshoots first suggested through anatomical comparison.

“Similar (anatomical) traits don’t necessarily reflect a closer relationship,” Grenier explained. “We think there are fewer problems using molecular data” to map kinship among animals.

One intriguing upshot of the new study and others is that scientists, through genetic analysis, may learn something about the genes of an animal for which no fossil exists. Beyond 600 million years ago, the fossil record is skimpy at best, and scientists have no clue as to what the common ancestor of all animals actually looked like.

“There’s no fossil. Five-hundred and forty million years ago is just about the end of the animal fossil record,” said Grenier. “We don’t know what (the common ancestor) looked like, but we think we know what its genes were.”