Fossil DNA - Genetics



Ancient DNA is DNA isolated from ancient specimens. It can be also loosely described as any DNA recovered from biological samples that have not been preserved specifically for later DNA analyses. Examples include the analysis of DNA recovered from archaeological and historical skeletal material, mummified tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost cores, Holocene plankton in marine and lake sediments, and so on. Unlike modern genetic analyses, ancient DNA studies are characterized by low quality DNA.

This places limits on what analyses can achieve. Furthermore, due to degradation of the DNA molecules, a process which correlates loosely with factors such as time, temperature, and presence of free water, upper limits exist beyond which no DNA is deemed likely to survive. Allentoft et al (2012) tried to calculate this limit by studying the decay of mitochondrial and nuclear DNA in Moa bones. The DNA degrades in an exponential decay process. According to their model, mitochondrial DNA is degraded to 1 base pair after 6,830,000 years at -5°C. Nuclear DNA degrades at least twice as fast as mtDNA. As such, early studies that reported recovery of much older DNA, for example from Cretaceous dinosaur remains, may have stemmed from contamination of the sample. Read more ...




In the News ...


DNA Study Reveals Genetic History of Europe   Sci-News - April 24, 2014
An international team of scientists has used ancient DNA recovered from human remains dating from up to 5,500 BC to reconstruct the first detailed genetic history of modern Europe. The research reveals a dramatic series of events including major migrations from both Western Europe and Eurasia, and signs of an unexplained genetic turnover about 4,000-5,000 years ago. The team used DNA extracted from bone and teeth samples from prehistoric human skeletons to sequence a group of maternal genetic lineages that are now carried by up to 45 per cent of Europeans. They established that the genetic foundations for modern Europe were only established in the Mid-Neolithic, after this major genetic transition around 4,000 years ago. This genetic diversity was then modified further by a series of incoming and expanding cultures from Iberia and Eastern Europe through the Late Neolithic




'Living fossil' coelacanth genome sequenced   BBC - April 17, 2013

The genetic secrets of a "living fossil" have been revealed by scientists. Researchers sequenced the genome of the coelacanth: a deep-sea fish that closely resembles its ancestors, which lived at least 300 million years ago. The study found that some of the animal's genes evolved very slowly, giving it its primitive appearance. The work also shed light on how the fish was related to the first land-based animals. The coelacanth has four large, fleshy fins, which some scientists believe could have been the predecessors of limbs.




Fossilized human feces found in Oregon cave   Global Post - July 16, 2012

New fossilized DNA found in Oregon is proving that humans lived in cave dwellings as early as 14,300 years ago, the Associated Press reported. The DNA was extracted from coprolites, otherwise known as fossilized feces. Along with the coprolites, stone points were discovered in the same cave. The points found in the cave differ from those used by the Clovis people, once thought to be the first North Americas, suggesting that this tribe lived at the same time, or possibly before, the Clovis people.




The figure shows the evolution of gene families in ancient genomes across the Tree of Life. The sizes of the little pie charts scale with the number of evolutionary events in lineages, slices indicate event types: gene birth (red), duplication (blue), horizontal gene transfer (green), and loss (yellow). The Archean Expansion period (3.33 to 2.85 billion years ago) is highlighted in green.

Scientists decipher 3 billion-year-old genomic fossils   PhysOrg - December 19, 2010

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 paleontologists 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 - probably the most catastrophic event in the history of cellular life, but we don't have any biological record of it.

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.





GENETICS





PALEONTOLOGY INDEX


ANCIENT AND LOST CIVILIZATIONS


PHYSICAL SCIENCES INDEX


ALPHABETICAL INDEX OF ALL FILES


CRYSTALINKS HOME PAGE


PSYCHIC READING WITH ELLIE


2012 THE ALCHEMY OF TIME