May 22, 2008
UW lab plays supporting role in platypus genome study
The platypus seems to have been engineered with spare parts from a duck, lizard and beaver. This egg-laying mammal has intrigued evolutionary biologists and geneticists enough that a large international, multi-institutional study was launched to map its genome. More than 100 scientists assisted in the work.
The platypus genome and its function are significant because the animal is on a critical branch in the evolutionary tree, according to Evan Eichler, a UW and Howard Hughes Medical Institute geneticist whose lab was one of many worldwide that assisted with the genome analysis.
Animals like the platypus are thought to be one of the first outcroppings from birds and reptiles that emerged from 160 million to 200 million years ago. This outgroup was named monotremes in reference to the one common opening for their urinary, genital, and digestive tracts.
Only two main branches of monotremes exist today: four different terrestrial spiny anteater species and the platypus. They live only in Australia, Tasmania and New Guinea. The platypus, with its water-resistant fur, leathery bill, and webbed feet, is semi-aquatic. Males have venomous hind claws.
Another evolutionary split led to marsupials, which incubate their young in a pouch, and to placentals, which grow a temporary organ that nourishes a baby inside the uterus.
The numbers of monotremes and marsupials have decreased, Eichler said, as placentals out competed them and became the most abundant mammals. Opossums are the only marsupials left in America. Otherwise, Australia is the last holdout for marsupials, most famously the kangaroo, wallaby and the endangered Tasmanian devil. Unlike marsupials, monotremes did not leave a rich fossil record.
Even though its young hatch from eggs and retain some reptilian qualities, the platypus is a bona fide mammal, Eichler pointed out, because it has modified sweat glands that produce milk for its offspring.
The platypus genome study results published last week in Nature show that platypus DNA has conserved an astounding array of bird, reptile, and primitive mammal characteristics.
The study head was Wes Warren, assistant professor of genetics at Washington University in St. Louis, where much of the work was done. The DNA samples, taken from a female named Glennie, were sent from an Australian wildlife preserve. DNA from the platypus provided a rare opportunity to follow, in a single species, the evolution of traits of several classes in the animal kingdom.
Warren’s Washington University lab piped data from the platypus genome sequence to the UW computers of Ze “Ginger” Cheng and Lin Chen, both computational biologists in the Eichler lab. Each did a separate genome-wide analysis to look for duplicated regions.
Duplicated regions of a genome, Eichler explained, are the hotspots of evolutionary change. They are where mutations occur to produce new gene functions that are, on occasion, beneficial for adaptation. Their actual role in evolution is still unclear. In people, structural rearrangement of chromosomes happens most often in duplicated regions of the genome. This restructuring has been associated with certain human illnesses and disease susceptibility. However, Eichler added, most of the duplicated areas have not been analyzed in detail and are difficult to track in new genomes.
Other animal genomes are studied to figure out what is unusual in the human genome that distinguishes people from other primates like chimpanzees, and what in the human genome is similar to other animal genomes.
