Sunday, December 28, 2008

Neanderthal Timeline

The Neanderthal (Homo neanderthalensis) or Neandertal was a species of the Homo genus that inhabited Europe and parts of western Asia. The first proto-Neanderthal traits appear in Europe as early as 350,000 years ago. By 130,000 years ago, full blown Neanderthal characteristics had appeared and by 50,000 years ago, Neanderthals disappeared from Asia, although they did not reach extinction in Europe until 33,000 to 24,000 years ago, perhaps 15,000 years after Homo sapiens had migrated into Europe.

Thursday, December 25, 2008

LUCA:Last Universal Common Ancestor

In trying to find the elements necessary for the origin of life, another question of importance is "what was the last universal original ancestor of life?"

A 3.8-billion-year-old organism was not the creature usually imagined. In LUCA, the prevailing belief is that it was a heat-loving or hyperthermophilic organism; like those odd organisms living in the hot vents along the continental ridges deep in the oceans today, above 90 degrees Celsius .
However, the new data suggests that LUCA was actually sensitive to warmer temperatures and lived in a climate below 50 degrees.

The research compared genetic information from modern organisms to characterize the ancient ancestor of all life on earth. Researchers identified common genetic traits between animals, plant, bacteria, and used them to create a tree of life with branches representing separate species. These all stemmed from the same trunk – LUCA, the genetic makeup that we then further characterized.

The RNA Connection to the Origin of Life
What this means is that in the origin of life question an important step has taken place towards reconciling conflicting ideas about LUCA. In particular, they are much more compatible with the theory of an early RNA world, where early life on Earth was composed of ribonucleic acid (RNA), rather than deoxyribonucleic acid (DNA).

RNA is particularly sensitive to heat and is unlikely to be stable in the hot temperatures of the early Earth. But the data indicate that LUCA found a cooler micro-climate to develop, which helps resolve this paradox and shows that environmental micro domains played a critical role in the development of life on Earth.

Tuesday, December 23, 2008

RNA and the Origin of Life

What were the conditions necessary for the formation of life? Some scientists believe that RNA was responsible for the development. RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn't have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other).

The RNA mechanism to overcome this thermodynamic barrier has been studied by incubating short RNA fragments in water of different temperatures and pH. Under an acidic environment and temperature lower than 70 degrees Celsius, the RNA pieces ranging from 10-24 in length could naturally fuse into larger fragments. This was generally accomplished within 14 hours.

The operation involved the RNA fragments which came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size in which case the larger the better until an optimal efficiency is reached around 100 and then it drops again.

The researchers note that this spontaneous fusing, or ligation, would a simple way for RNA to overcome initial barriers to growth and reach a biologically important size; at around 100 bases long, RNA molecules can begin to fold into functional, 3D shapes.

Saturday, December 20, 2008

RadioActive Dating - Potassium-Argon

Potassium-Argon dating

The element potassium (symbol K) has three nuclides, K39, K40, and K41. Only K40 is radioactive; the other two are stable. K40 can decay in two different ways: it can break down into either calcium or argon. The ratio of calcium formed to argon formed is fixed and known. Therefore the amount of argon formed provides a direct measurement of the amount of potassium-40 present in the specimen when it was originally formed.

Because argon is an inert gas, it is not possible that it might have been in the mineral when it was first formed from molten magma. Any argon present in a mineral containing potassium-40 must have been formed as the result of radioactive decay. F, the fraction of K40 remaining, is equal to the amount of potassium-40 in the sample, divided by the sum of potassium-40 in the sample plus the calculated amount of potassium required to produce the amount of argon found. The age can then be calculated from equation (1).

In spite of the fact that it is a gas, the argon is trapped in the mineral and can't escape. (Creationists claim that argon escape renders age determinations invalid. However, any escaping argon gas would lead to a determined age younger, not older, than actual. The creationist "argon escape" theory does not support their young earth model.)

The argon age determination of the mineral can be confirmed by measuring the loss of potassium. In old rocks, there will be less potassium present than was required to form the mineral, because some of it has been transmuted to argon. The decrease in the amount of potassium required to form the original mineral has consistently confirmed the age as determined by the amount of argon formed.

Thursday, December 18, 2008

Human Migration From Asia To Americas

Finding A new set of ideas on migration to North America have been proposed. One idea is a hypothesis that seems to map the peopling process during the pioneering phase and well beyond, and another is that at the same time there was much more genetic diversity in the founder population than was previously believed.
The Conventional View
Questions about human migration from Asia to the Americas have perplexed anthropologists for decades, but as scenarios about the peopling of the New World come and go, the big questions have remained. One questions is do the ancestors of Native Americans derive from only a small number of “founders” who trekked to the Americas via the Bering land bridge? Also, how did their migration to the New World proceed? And was climate change involved; did the climate have anything to do with their migration? And finally what took them so long?

Changing the Conventional View
A phylogeographic analysis of a new mitochondrial genome dataset allows scientists to draw several conclusions.
30,000 years ago - clades
First, the ancestral population on its way to the Americas paused in Beringia long enough for specific mutations to accumulate. These mutations separate the New World founder lineages from their Asian sister-clades. (A clade is a group of mitochondrial DNAs (mtDNAs ) that share a recent common ancestor. Sister-clades would include two groups of mtDNAs that each share a recent common ancestor and the common ancestor for each clade is closely related.)

Another way to express this is the ancestors of Native Americans who first left Siberia for greener pastures perhaps as much as 30,000 years ago, came to a standstill on Beringia – a landmass that existed during the last glacial maximum that extended from Northeastern Siberia to Western Alaska, including the Bering land bridge – and they were isolated there long enough – as much as 15,000 years – to maturate and differentiate themselves genetically from their Asian sisters.
Lineages are distributed quickly not gradually
Founding lineages or haplotypes are uniformly distributed across North and South America instead of exhibiting a nested structure from north to south. So after the Beringian standstill, the initial North to South migration occured in a swift pioneering process, not a gradual diffusion.

Bi-directional Migrations to North America then Back to Beringia
The DNA data also suggest a lot more going back and forth than was previously suspected of populations during the past 30,000 years in Northeast Asia and North America. The dataset analysis shows that after the initial peopling of Beringia, there were a series of back migrations to Northeast Asia as well as forward migrations to the Americas from Beringia. There was a bi-directional gene flow between Siberia and the North American Arctic.

Using Mitochondrial datasets from populations in the Americas and East Asia
The investigation of the pioneering phase in the Americas, a research team, a group of geneticists from around the world, pooled their genomic datasets and then analyzed 623 complete mitochondrial DNAs (mtDNAs) from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia.
What Mitochondrial DNA data reflects
Mitochondrial DNA, that is, DNA found in organelles, rather than in the cell nucleus, is considered to be of separate evolutionary origin, and is inherited from only one parent – the female. The dataset sequence was used to direct genotyping from 20 American and 26 Asian populations.

The Discovery 3 New Sub-Clades
The team identified three new sub-clades that incorporate nearly all of Native American haplogroup C mtDNAs – all of them widely distributed in the New World, but absent in Asia; and they defined two additional founder groups, which differ by several mutations from the Asian-derived ancestral clades.

Disconnect in migration dates
Did the migration occur quickly or slowly? Migration may have occured 30,000 years ago, but the earliest archeological evidence is that it occurred only 15,000 years ago.
The point of departure places Homo sapiens at the Yana Rhinoceros Horn Site in Siberia as early as 30,000 years before the present, but the earliest archaeological site at the southern end of South America is dated to only 15,000 years ago.

Two possible scenarios
First the ancestors of Native Americans peopled Beringia before the Last Glacial Maximum, but remained locally isolated – likely because of ecological barriers – until entering the Americas 15,000 years before the present (the Beringian incubation model, BIM).
The second is that the ancestors of Native Americans did not reach Beringia until just before 15,000 years before the present, and then moved continuously on into the Americas, being recently derived from a larger parent Asian population (direct colonization model, DCM).

The conclusion of the study
The team set out to test the two hypotheses: one, that Native Americans’ ancestors moved directly from Northeast Asia to the Americas; the other, that Native American ancestors were isolated from other Northeast Asian populations for a significant period of time before moving rapidly into the Americas all the way down to Tierra del Fuego.

The data supports the second hypothesis: The ancestors of Native Americans peopled Beringia before the Last Glacial Maximum, but remained locally isolated until entering the Americas at 15,000 years before the present. So they moved into the Americas quickly.

Saturday, December 13, 2008

Genome Sequence of Neanderthal Man

Were Neanderthals and Humans connected at some time in the past? This question is still up for debate, but recently the complete mitochondrial genome of a 38,000-year-old Neanderthal has been sequenced.

At the Max-Planck Institute for Evolutionary Anthropology in Germany scientists have reconstructed the genome sequence. They sequenced the Neanderthal mitochondria—powerhouses of the cell with their own DNA including 13 protein-coding genes—nearly 35 times over. This coverage allowed them to sort out those differences between the Neanderthal and human genomes resulting from damage to the degraded DNA extracted from ancient bone versus true evolutionary changes.

This new sequence and its analysis confirms that the mitochondria of Neanderthals falls outside the variation found in humans today and it provides no evidence of integration between the two lineages although it remains a possibility. It also shows that the last common ancestor of Neanderthals and humans lived about 660,000 years ago, give or take 140,000 years.

The new sequence revealed that the Neanderthals have fewer evolutionary changes overall, but a greater number that alter the amino acid building blocks of proteins. This means that the Neanderthals had a smaller population size than humans do, which makes natural selection less effective in removing mutations.

That notion is consistent with arguments made by other scientists based upon the geological record. Anthropologists argue there were a few thousand Neanderthals that roamed over Europe 40,000 years ago. That smaller population might have been the result of the smaller size of Europe compared to Africa. Another geological issue was that the Neanderthals also would have had to deal with repeated glaciations.

Tuesday, December 2, 2008

Single Main Migration Across Bering Strait

Did a relatively small number of people from Siberia who trekked across a Bering Strait land bridge some 12,000 years ago give rise to the native peoples of North and South America?

Researcher working with an international team of geneticists and anthropologists, have produced new genetic evidence that's likely to hearten proponents of the land bridge theory. The study, is one of the most comprehensive analyses so far among efforts to use genetic data to shed light on the topic.

The researchers examined genetic variation at 678 key locations or markers in the DNA of present-day members of 29 Native American populations across North, Central and South America. They also analyzed data from two Siberian groups. The analysis shows:

  • genetic diversity, as well as genetic similarity to the Siberian groups, decreases the farther a native population is from the Bering Strait -- adding to existing archaeological and genetic evidence that the ancestors of native North and South Americans came by the northwest route.

  • a unique genetic variant is widespread in Native Americans across both American continents -- suggesting that the first humans in the Americas came in a single migration or multiple waves from a single source, not in waves of migrations from different sources. The variant, which is not part of a gene and has no biological function, has not been found in genetic studies of people elsewhere in the world except eastern Siberia.

The researchers say the variant likely occurred shortly prior to migration to the Americas, or immediately afterwards.

The Genetic Markers for North American Populations originate in East Asia
There is reasonably clear genetic evidence that the most likely candidate for the source of Native American populations is somewhere in east Asia, the research concludes. If there were a large number of migrations, and most of the source groups didn't have the variant, then you would not see the widespread presence of the mutation in the Americas.

Studies with Genetic Markers

Researchers studied the same set of 678 genetic markers used in the new study in 50 populations around the world, to learn which populations are genetically similar and what migration patterns might explain the similarities. For North and South America, the current research breaks new ground by looking at a large number of native populations using a large number of markers.

The pattern the research uncovered -- that as the founding populations moved south from the Bering Strait, genetic diversity declined -- is what one would expect when migration is relatively recent. There has not been time yet for mutations that typically occur over longer periods to diversify the gene pool.

The study also found that:

  • The study's findings hint at supporting evidence for scientists who believe early inhabitants followed the coasts to spread south into South America, rather than moving in waves across the interior.

  • Assuming a migration route along the coast provides a slightly better fit with the pattern that are seen in genetic diversity.

  • Populations in the Andes and Central America showed genetic similarities.

  • Populations from western South America showed more genetic variation than populations from eastern South America.

  • Among closely related populations, the ones more similar linguistically were also more similar genetically.