Microbe genes help scientists reconstruct animal origins

Without the help of fossils or any other record from the distant past, scientists have identified what they believe represents a common ancestor of all animals on Earth, a microscopic organism with key genetic traits that, until now, have been found only in true animals.

Writing in the Dec. 18 Proceedings of the National Academy of Sciences, a team of scientists from the Howard Hughes Medical Institute at UW–Madison reports the discovery of a key cell communication gene in modern, single-celled microbes known as choanoflagellates.

Long suspected to be close relatives of animals, choanoflagellates have a lineage that dates to more than 600 million years ago, the time when animals – multicellular organisms with distinct body plans and systems of organs -are believed to have evolved in the ancient stew of microscopic protozoan life

Ancient microbes eventually gave rise not only to animals, but also plants, fungi, bacteria, and other living things, each going their separate ways to make up the tree of life as we know it today. The evolution of multicellular animals from a unicellular protozoan ancestor has long been recognized as a pivotal transition in the history of life.

“The question is, who were the ancestors of animals and what genetic tools did they pass down to the original animals,” says Sean B. Carroll, a UW–Madison professor of genetics and the senior author of the PNAS study. “This is a difficult question to answer because the events are completely invisible in the fossil record.”

Choanoflagellates represent an order of transparent, single-celled microbes that propel themselves with whiplike appendages. They exist in many forms today and, like animals, their lineage stretches back hundreds of millions of years ago to the mix of microscopic life that first evolved on Earth.

“Choanoflagellates thrive today and are the closest non-animal organisms to animals. They are to animals what chimps are to humans, and by studying some of their genetic characteristics, we can begin to make some strong inferences” about how animals evolved, Carroll says.

In recent years, biologists have come to understand that nature, in her use of genes, is thrifty. Instead of inventing new genes to accomplish new tasks, animals tend to redeploy existing genes in new ways. For example, genes used to make the very pedestrian wings of fruit flies are also those that butterflies use in different ways to make their far more colorful and shapely wings. Understanding this phenomenon has enabled scientists to track evolutionary relationships between animals by looking for common genetic themes.

Undertaking a similar exploration in choanoflagellates, Carroll and his colleague, Nicole King, also of the Howard Hughes Medical Institute at UW–Madison, discovered a signaling gene in a choanoflagellate that, until now, was known only in animals.

“To build a multicellular organism compatible with a multicellular lifestyle, is something that is very difficult,” explains Carroll. “It takes a lot of genetic machinery to do that, and you have to ask the question, did it all arise when animals came along, or was some of it in place earlier?”

The current study, he says, strongly suggests that the key genes animals use today were indeed already available on the eve of animal evolution.

“We’re starting to get a glimpse of the genetic tool kit we have in common. In choanoflagellates, we’ve found genes that heretofore were believed to exist only in animals. It’s a confirmation of the idea that the genes come first, before their exploitation by organisms.”

The gene-based signaling pathway found in extant choanoflagellates, Carroll says, resembles a similar pathway found in organisms as diverse as sponges and humans.

“Choanoflagellates express genes involved in animal development that are not found in other single-celled organisms, and that may be linked to the origin of animals. In other words, it looks like, walks like, and smells like genes that we are familiar with but that, apparently, evolved at the base of the node where animals split off the tree.”

The identification of a common ancestor to all animals is important, according to Carroll, because it helps fill in the big picture of the evolution and diversity of life on Earth. It helps us understand, he says, how animals came to be and how nature creatively uses the same molecular tools to sculpt life in different ways.