Saturday, January 1, 2011

SCIENTISTS DECIPHER 3 BILLION-YEAR-OLD GENOMIC FOSSILS

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About 580 million years ago, life on Earth began a rapid period of change called the Cambrian Explosion, a period defined by the birth of new life forms over many millions of years that ultimately helped bring about the modern diversity of animals. Fossils help palaeontologists chronicle the evolution of life since then, but drawing a picture of life during the 3 billion years that preceded the Cambrian Period is challenging, because the soft-bodied Precambrian cells rarely left fossil imprints. However, those early life forms did leave behind one abundant microscopic fossil: DNA.

Because all living organisms inherit their genomes from ancestral genomes, computational biologists at MIT reasoned that they could use modern-day genomes to reconstruct the evolution of ancient microbes. They combined information from the ever-growing genome library with their own mathematical model that takes into account the ways that genes evolve: new gene families can be born and inherited; genes can be swapped or horizontally transferred between organisms; genes can be duplicated in the same genome; and genes can be lost.

The scientists traced thousands of genes from 100 modern genomes back to those genes' first appearance on Earth to create a genomic fossil telling not only when genes came into being but also which ancient microbes possessed those genes. The work suggests that the collective genome of all life underwent an expansion between 3.3 and 2.8 billion years ago, during which time 27 percent of all presently existing gene families came into being.

Eric Alm, a professor in the Department of Civil and Environmental Engineering and the Department of Biological Engineering, and Lawrence David, who recently received his Ph.D. from MIT and is now a Junior Fellow in the Harvard Society of Fellows, have named this period the Archean Expansion.

Because so many of the new genes they identified are related to oxygen, Alm and David first thought that the emergence of oxygen might be responsible for the Archean Expansion. Oxygen did not exist in the Earth's atmosphere until about 2.5 billion years ago when it began to accumulate, likely killing off vast numbers of anerobic life forms in the Great Oxidation Event.

"The Great Oxidation Event was probably the most catastrophic event in the history of cellular life, but we don't have any biological record of it," says Alm.

Closer inspection, however, showed that oxygen-utilizing genes didn't appear until the tail end of the Archean Expansion 2.8 billion years ago, which is more consistent with the date geochemists assign to the Great Oxidation Event.

Instead, Alm and David believe they've detected the birth of modern electron transport, the biochemical process responsible for shuttling electrons within cellular membranes. Electron transport is used to breathe oxygen and by plants and some microbes during photosynthesis when they harvest energy directly from the sun. A form of photosynthesis called oxygenic photosynthesis is believed to be responsible for generating the oxygen associated with the Great Oxidation Event, and is responsible for the oxygen we breathe today.

The evolution of electron transport during the Archean Expansion would have enabled several key stages in the history of life, including photosynthesis and respiration, both of which could lead to much larger amounts of energy being harvested and stored in the biosphere.

"Our results can't say if the development of electron transport directly caused the Archean Expansion," says David. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems."

David and Alm also went on to investigate how microbial genomes evolved after the Archean Expansion by looking at the metals and molecules associated with the genes and how those changed in abundance over time. They found an increasing percentage of genes using oxygen, and enzymes associated with copper and molybdenum, which is consistent with the geological record of evolution.

"What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of living organisms," says Alm. "And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail."

(Photo: Lawrence David)

MIT

RODENTS WERE DIVERSE AND ABUNDANT IN PREHISTORIC AFRICA WHEN OUR HUMAN ANCESTORS EVOLVED

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Rodents get a bad rap as vermin and pests because they seem to thrive everywhere. They have been one of the most common mammals in Africa for the past 50 million years.

From deserts to rainforests, rodents flourished in prehistoric Africa, making them a stable and plentiful source of food, says paleontologist Alisa J. Winkler, an expert on rodent and rabbit fossils. Now rodent fossils are proving their usefulness to scientists as they help shed light on human evolution.

Rodents can corroborate evidence from geology and plant and animal fossils about the ancient environments of our human ancestors and other prehistoric mammals, says Winkler, a research professor at Southern Methodist University.

"Rodents are often known in abundance, and there are many different kinds from a number of famous hominid and hominoid localities," says Winkler. "Many paleoanthropologists are very interested in the faunal and ecological context in which our own species evolved."

Rodents — rats, mice, squirrels, porcupines, gerbils and others — are the largest order of living mammals, constituting 42 percent of the total mammalian diversity worldwide. That's according to data drawn from the research literature in an analysis by Winkler and her paleontology colleagues Christiane Denys, of the Museum National d'Histoire Naturelle in Paris, and D. Margaret Avery of the Iziko South African Museum in Cape Town.

Their review documents more than 130 formally named genera in "Fossil Rodents of Africa," the first comprehensive summary and distribution analysis of Africa's fossil rodents since 1978.

The analysis is a chapter in the new 1008-page scientific reference book "Cenozoic Mammals of Africa" (University of California Press, 2010), the first comprehensive scientific review of Africa's fossil mammals in more than three decades. The book comprises 48 chapters by 64 experts, summarizing and interpreting the published fossil research to date of Africa's mammals, tectonics, geography, climate and flora of the past 65 million years.

Rodents have been around much longer than humans or human ancestors in Africa, with the earliest from northern Africa dating from about 50 million years ago. Today scientists are aware of 14 families of rodents in Africa.

Winkler cites locales where fossils of the sharp-toothed, gnawing creatures have been found relevant to our human ancestors:

* Ethiopia's Middle Awash, where some fossils date to when the chimpanzee and human lines split 4 million to 7 million years ago and where the famous "Ardi" primate was discovered;
* Tanzania's Olduvai Gorge, dubbed the "Cradle of Mankind";
* The Tugen Hills and Lake Turkana sites of Kenya, where important human ancestor fossils have been discovered;
* In younger southern African cave faunas dating to the Stone Age.

Their fossils also have been found in other older Eastern Africa sites, where apes and humans have been linked to the monkey lineage.

"At many of these sites, identification of Africa's rodents provides important collaborating information on the ecology of the locales and on environmental change through time," the authors write.

Rodent diversity likely underestimated; more fossils than scientists
The diversity of ancient Africa's rodents most likely has been underestimated, say the authors. Just how much isn't known, though, because the quantity of rodent fossils being discovered far exceeds the handful of scientists who specialize in identifying and studying the specimens.

That diversity continues to expand. The last exhaustive analysis of Africa's rodents was carried out by R. Lavocat in 1978. At that time scientists recorded 54 genera, 76 fewer than those documented by Winkler, Denys and Avery in their analysis.

Winkler and her colleagues summarize the distribution and ecology of existing rodent families, as well as the systematics, biochronology and paleobiogeography of rodent families in Africa's fossil record. The diversity they document reflects "the wide variety of habitats present on the continent" and paints a picture of Africa's paleoecology.

Given the huge rodent diversity in modern Africa, "it is likely that such an extensive fauna was also present in the past," the scientists write.

An example of that relationship is the scaly-tailed flying squirrel, an exclusively African group of forest-dwelling rodents that are not related to true squirrels. They are well known from about 18 million to 20 million years ago in eastern Africa, Winkler says, suggesting the presence of closed habitats, such as forests. That corroborates other evidence of forests from fossil animals, plants and geology, she says.

"Although there are even older scaly-tailed flying squirrels known from the currently arid regions of northern Africa," says Winkler, "they do not appear to have been gliders, as are most current forms, and the question of when members of the group first developed gliding locomotion still remains."

(Photo: SMU)

SMU

BEING GOOD MOMS COULDNT SAVE THE WOOLLY MAMMOTH

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New research from The University of Western Ontario leads investigators to believe that woolly mammoths living north of the Arctic Circle during the Pleistocene Epoch (approx. 150,000 to 40,000 years ago) began weaning infants up to three years later than modern day African elephants due to prolonged hours of darkness.

This adapted nursing pattern could have contributed to the prehistoric elephant’s eventual extinction. The findings were published recently in the journal, Palaeogeography, Palaeoclimatology, Palaeoecology.

By studying the chemical composition of adult and infant mammoth teeth, Jessica Metcalfe, an Earth Sciences PhD student working with professor Fred Longstaffe, was able to determine woolly mammoths that once inhabited Old Crow, Yukon didn’t begin eating plants and other solid foods before the age of two (and perhaps as late as three) and considers predatory mammals like saber-toothed cats and a lack of sufficient vegetation to be the secondary reasons for delayed weaning.

“In modern Africa, lions can hunt baby elephants but not adults. They can’t kill adults. But they can kill babies and by and large, they tend to be successful when they hunt at night because they have adapted night vision,” explains Metcalfe, who examined fossil specimens alongside Grant Zazula of the Yukon Paleontology Program. “In Old Crow, where you have long, long hours of darkness, the infants are going to be more vulnerable, so the mothers nursed longer to keep them close.”

Metcalfe says delayed weaning by Old Crow mammoths may have further significance for understanding mammoth life histories and extinction.

“Today, a leading cause of infant elephant deaths in Myanmar is insufficient maternal milk production,” offers Metcalfe. “Woolly mammoths may have been more vulnerable to the effects of climate change and human hunting than modern elephants not only because of their harsher environment, but also because of the metabolic demands of lactation and prolonged nursing, especially during the longer winter months.”

Metcalfe concludes that knowing more about the past, can only help researchers understand more about the present and the future.

“Mammoths lived all over the world for thousands of years, even millions of years, and then became extinct about 10,000 years ago, which was around the time the climate started warming the last time,” says Metcalfe. “Understanding their ecology, their adaptations and their behaviour not only gives us insight into why they became extinct but also, potentially, gives us a better understanding of modern day mammals and how they might respond to the current warming of the planet.”

The University of Western Ontario

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