The platypus, classified as a mammal because it produces milk and is covered in a coat of fur, also possesses features of reptiles, birds and their common ancestors, along with some curious attributes of its own. One of only two mammals that lays eggs, the platypus also sports a duck-like bill that holds a sophisticated electrosensory system used to forage for food underwater. Males possess hind leg spurs that can deliver pain-inducing venom to its foes competing for a mate or territory during the breeding season.

“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammalian genomes,” says Richard K. Wilson, Ph.D., director of the The Genome Center at Washington University and the paper’s senior author. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved throughout evolution.”

The platypus represents the earliest offshoot of the mammalian lineage some 166 million years ago from primitive ancestors that had features of both mammals and reptiles. “What is unique about the platypus is that it has retained a large overlap between two very different classifications, while later mammals lost the features of reptiles,” says Wes Warren, Ph.D., an assistant professor of genetics, who led the project.

Comparison of the platypus genome with the DNA of humans and other mammals, which diverged later, and the genomes of birds, whose ancestors branched off an estimated 315 million years ago, can help scientists fill gaps in their understanding of mammalian evolution. The comparison also will allow scientists to date the emergence of genes and traits specific to mammals.

The Nature paper analyzes the genome sequence of a female platypus named Glennie from New South Wales, Australia. The project was largely funded by the National Human Genome Research Institute, part of the National Institutes of Health, and includes scientists from the United States, Australia, England, Germany, Israel, Japan, New Zealand and Spain.

“At first glance, the platypus appears as if it was the result of an evolutionary accident,” says Francis S. Collins, M.D., Ph.D., director of NHGRI. “But as weird as this animal looks, its genome sequence is priceless for understanding how mammalian biological processes evolved.”

“While we’ve always been able to compare and consider all of these creatures on the basis of their physical characteristics, internal anatomy and behavior, it’s truly amazing to be able to compare their genetic blueprints and begin to get a close-up look at how evolution brings about change,” Wilson says.

As part of their analysis, the researchers compared the platypus genome with genomes of the human, mouse, dog, opossum and chicken. They found that the platypus shares 82 percent of its genes with these animals. The chicken genome was chosen because it represents a group of egg-laying animals, including extinct reptiles, which passed on much of their DNA to the platypus and other mammals over the course of evolution.

The researchers also found genes that support egg laying - a feature of reptiles - as well as lactation - a characteristic of all mammals. Interestingly, the platypus lack nipples, so its young nurse through the abdominal skin.

The researchers also attempted to determine which characteristics of the platypus were linked to reptiles at the DNA level. When they analyzed the genetic sequences responsible for venom production in the male platypus, they found it arose from duplications in a group of genes that evolved from ancestral reptile genomes. Amazingly, duplications in the same genes appear to have evolved independently in venomous reptiles.

The platypus swims with its eyes, ears and nostrils closed, relying on electrosensory receptors in its bill to detect faint electric fields emitted by underwater prey. Surprisingly, the researchers found the genome contains an expansion of genes that code for a particular type of odor receptor. “We were expecting very few of these odor receptor genes because the animals spend the majority of their life in the water,” Warren says.

Similar genes are found in animals that rely on a sense of smell, such as rodents and dogs, and the scientists suspect that their addition in the platypus allows the animals to detect odors while foraging underwater.

At roughly 2.2 billion base pairs, the platypus genome is about two-thirds the size of the human genome and contains about 18,500 genes, similar to other vertebrates. The animal has 52 chromosomes, including an unusual number of sex chromosomes: 10. The platypus X chromosome bears resemblance to the sex chromosome of a bird, known as Z.

Sequencing and assembling the platypus genome proved far more daunting than sequencing any other mammalian genome to date. About 50 percent of the genome is composed of repetitive elements of DNA, which makes it a challenge to assemble properly.

The platypus genome sequence, along with those for other organisms, such as the mouse, dog, cow, and many other animals can be accessed at GenBank (www.ncbi.nih.gov/Genbank) at NIH’s National Center for Biotechnology Information.

[Caroline Arbanas @ Washington University School of Medicine]

Scene: The 2008 RALPH Awards, held at a highly secret location somewhere in the Northern Hemisphere. via Reno Gazette-Journal

Professor Downing found that constructed ponds and lakes on farmland in the United States bury carbon at a much higher rate than expected; as much as 20-50 times the rate at which trees trap carbon. In addition, ponds were found to take up carbon at a higher rate than larger lakes.

“Aquatic ecosystems play a disproportionately large role in the global carbon budget,” Downing said. “Despite being overlooked in the past, it’s small bodies of water that are important because they take up carbon at a high rate and there are more of them than previously thought. The combined effect is that farm ponds could be burying as much carbon as the world’s oceans, each year.”

Ponds capture carbon in two main ways:

The research estimated there are 304 million natural lakes and ponds in the world, covering an area of 4.2 million square kilometers, twice the area previously thought. As many as 90 percent of these water bodies are one hectare (two acres) or less in area.

Downing’s research team published its most recent findings in the Feb. 15 issue of the journal Global Biogeochemical Cycles in a paper titled, “Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century.” The team included members from Europe, the United States and Canada. The work was sponsored by the National Center for Ecological Analysis and Synthesis and the Iowa Department of Natural Resources.

Downing has presented invited seminars on this research to the International Society of Limnology, the American Society of Limnology and Oceanography, and at several major research institutions in North America and Europe. Most recently, he was invited to discuss his research by the Pond Conservation, a charity in the United Kingdom dedicated to creating and protecting ponds and the wildlife they support. He will spoke today at University College London. An upcoming presentation is scheduled for the annual meeting of the European Pond Conservation Network in Valencia, Spain.

Jeremy Biggs, Pond Conservation director of policy and research, said the research has exciting implications. “It may be that ponds will be the modern equivalent of the swamps that formed coal in the past. But before we all rush into making ponds to trap carbon we need to do some basic research here in the UK. If the rate of carbon uptake in ponds in Europe is the same as that found in the USA study, we may well have discovered an important new natural way of trapping carbon,” he said.

Downing’s ongoing research, partnering with the United States Geological Survey, and his contributions to the Iowa Lakes Survey will investigate the role of small Iowa lakes in the absorption of atmospheric carbon dioxide and other important gases such as methane.

[John Downing @ Iowa State University]

The new study is led by Lothar Stramma from the Leibniz Institute of Marine Sciences (IFM-GEOMAR) in Kiel, Germany, and is co-authored by Janet Sprintall, a physical oceanographer at Scripps Oceanography and others. The researchers found through analysis of a database of ocean oxygen measurements that levels in tropical oceans at a depth of 300 to 700 meters (985 to 2,300 feet) have declined during the past 50 years. The ecological impacts of this increase could have substantial biological and economical consequences.

“We found the largest reduction in a depth of 300 to 700 meters (985 to 2,300 feet) in the tropical northeast Atlantic, whereas the changes in the eastern Indian Ocean were much less pronounced,” said Stramma. “Whether or not these observed changes in oxygen can be attributed to global warming alone is still unresolved. The reduction in oxygen may also be caused by natural processes on shorter time scales.”

Sprintall said the oxygen-poor areas have the potential to move into coastal areas via currents that flow from the mid-depth tropical oceans, where the oxygen changes were observed, and along the west coast of continents.

“The width of the low-oxygen zone is expanding deeper but also shoaling toward the ocean surface,” said Sprintall, a specialist in observing changes of fluxes in ocean properties such as heat distribution.

Sprintall contributed data to the study gathered during recent cruises undertaken as part of the Climate Variability and Predictability (CLIVAR) program, a long-running study operated by the World Climate Research Programme that seeks to understand climate through ocean-atmosphere interactions.

The study, “Expanding Oxygen-Minimum Zones in the Tropical Oceans,” appears in the May 2 edition of the journal Science. The research team includes Stramma, Sprintall, NOAA scientist Gregory Johnson, and Volker Mohrholz from the Institute for Baltic Sea Research in Warnem??nde, Germany.

The team selected ocean regions for which they could obtain the greatest amount of data to document the decline in oxygen. Some of the more recent data came from oxygen sensors which have been added to about 150 of the profiling floats used in Argo, a worldwide network of sensors that track basic ocean conditions such as temperature and salinity. There are more than 3,000 Argo floats operating in the world’s oceans, and Sprintall said the quality of the data gathered by the Argo floats suggests that more units in the network should be outfitted with oxygen sensors.

Lisa Levin, a biological oceanographer at Scripps Oceanography who studies oxygen-minimum zones that intercept the seafloor, said an expansion of oxygen-minimum zones in the oceans could lead to diminished biodiversity and to the expanded distributions of organisms that have adapted to live in hypoxic, or oxygen-poor waters.

“I think it’s uncharted territory,” said Levin, who was not affiliated with the study. “Thicker oxygen minimum zones could affect nutrient cycling, predator-prey relationships and plankton migrations. Where the expanding oxygen-minimum zones impinge on continental margins, we could see huge ecosystem changes.”

[Rob Monroe and Mario Aguilera @ UC San Diego]