"Where do we come from?" This has been one of the fundamental questions asked by humans for thousands of years. Is it philosophical? Religious? Anthropological? Depending on your view point it determines how you look for the answer. From an anthropolical viewpoint physical anthropologists have been looking for answers by studying morphological characteristics of bones or skeletons that have been uncovered, such as skull shape, of the fossilised remains of our human and proto-human ancestors.
Molecular Anthropology - New study
Molecular anthropologists have been comparing the DNA of living humans of diverse origins to build evolutionary trees. Because mutations occur in our DNA at a regular rate and will often be passed along to our children these differences or polymorphisms, as they are termed, show that on a genotypical level make us all unique and analysis of these differences will show how closely we are related. But using these techniques, however, have led to opposing views on how modern humans evolved from our archaic ancestors.
Two competing theories
The two main hypotheses agree that Homo erectus evolved in Africa and spread to the rest of the world around 1 - 2 million years ago; it is regarding our more recent history where they disagree.
1) Multi-regional evolution
This theory suggests that modern humans evolved from archaic forms, such as Neanderthal and Homo erectus. They originated concurrently in different regions of the world supported by physical evidence, such as the continuation of morphological characteristics between archaic and modern humans. But this is the minority view.
2) Out of Africa view
This view holds that modern humans evolved in Africa before colonizing the world. The recent African origin view holds that modern humans evolved once in Africa between 100 - 200 thousand years ago. Subsequently modern humans colonised the rest of the world without genetic mixing with archaic forms supported by the majority of genetic evidence. This is now the majority view.
Which theory is right?
One way to answer this is by looking at mitochondrial DNA. While DNA is present inside the nucleus of every cell of our body it is the DNA of the cell's mitochondria that has been most commonly used to construct evolutionary trees.
What is Mitochondrial DNA?
This is DNA found outside of the cell nucleus. They are inherited only from the mother, which allows tracing of a direct genetic line. They also have their own genome of about 16,500 bp. Each contains 13 protein coding genes, 22 tRNAs and 2 rRNAs. Fewer samples is required vecause they are present in large numbers in each cell. And they have a higher rate of substitution that is mutations where one nucleotide is replaced with another than nuclear DNA making it easier to resolve differences between closely related individuals. They don't recombine. Mitochnondrial DNA doesn't recombine with other Mitochondrial DNA. The process of recombination which occurs in nuclear DNA mixes sections of DNA from the mother and the father creating a strained genetic history.
So Mitochondrial DNA tells us what?
The out of Africa theory has support from Mitochondrial DNA. But these conclusions have been criticised for a lack of statistical support. This is due to the fact that a small section of the Mitochondrial DNA called the D-loop, about 7% of the genome has been used for the studies. Statistically, the out of Africa theory is not well founded. Here is why. Three main problems with data from the D-loop section have been identified:
back mutation - sites that have already undergone substitution are returned to their original state
parallel substitution - mutations occur at the same site in independent lineages
rate heterogeneity - there is a large difference in the rate at which some sites undergo mutation when compared to other sites in the same region; data shows evidence of 'hot spots' for mutation.
But there has been a study that has fixed some of these problems. First the mitochondrial genome is one of the first genomes to be sequenced in its entirety. However it was not until recently that technological advances allowed large sequences to be obtained easily and a study of any appreciable size using whole genomes was undertaken. There were some clear advantages.
First the D-loop was evolving at a much higher rate. And this greater length of the complete genome allowed for the analysis of twice as many informative polymorphic sites (sites that show the same polymorphism in at least two sequences). Second the numbers of back- and parallel mutations found outside of the D-loop were practically zero. So this had no effect. And finally the rate of evolution of the rest of the genome was even between different genes and also between the different gene complexes; it was also even between different sites
Conclusions
The phylogenetic tree reconstructed with this latest dataset of complete mitochondrial genomes provides support to the 'recent African origin' theory. Chronologically speaking by determining the substitution rate of the genomic sequences, it is possible to derive dates for points on the tree and build a chronology of events in the evolution and migration of our species.
The most important date, in relation to the competing evolutionary theories, is the time when all the sequences coalesce into one -- the 'mitochondrial Eve.' That date about 171,500 years ago fits very well with that proposed in the recent African origin hypothesis.
On the other hand, in order to accept multi-regionality, a much older date would have had to be used; this would represent the common ancestor of Homo erectus and not Homo sapiens.
Showing posts with label phylogenetic tree. Show all posts
Showing posts with label phylogenetic tree. Show all posts
Tuesday, July 17, 2007
Monday, July 16, 2007
Accuracy of Fossils and Dating Methods
Fossils provide a record of the history of life. Any attempt to make a claim about evolution always comes back at some point to the geologic time scale. But if you are going to be looking at time scales that are that old how do you get the dates? Where are the dates coming from and how is the measurement occurring? How does the fossil record work with the geologic time scale. The answer is that you use radioactive carbon dating to get the dates. But this is only the most current method. But other methods have also been used to date the fossil record.
The Fossils Sequence Record
It was the study of rock layers in England near the beginning of the 19th century that lead to the study of paleontology and from there to the study of fossils. Early geologists, at the end of the 18th and early 19th century noticed how fossils appeared in certain sequences: some fossil assemblages were always found below other assemblages, not above. This meant that the ones below were older than the ones on top.
It took a canal surveyor circa 1800, William Smith in England, who noticed that he could map out great tracts of rocks on the basis of their contained fossils. The sequences he saw in one part of the country could be matched precisely with the sequences in another. This lead to the recognition of one of the principles of geology, i.e., stratigraphy, older rocks lie below younger rocks and that fossils occur in a particular, predictable order.
The next step was for geologists began to build up the stratigraphic column. And this gave us the familiar list of divisions in the geologic time scale -- Jurassic, Cretaceous, Tertiary, and so on. Most importantly, it was recognized that each time-unit was characterized by the appearance of particular fossils. The scheme worked all round the world, without fail.
The next observation occurred when geologists noted how fossils became more complex through time. At the oldest, or deepest layer of rock there was no record of fossils, but then they noticed that simple sea creatures were found at the next higher level, then more complex ones like fishes at the next higher level and so on. Next came life on land, then reptiles, then mammals, and finally humans. One fact was soon clear, no dinosaur record could be found to coincide with a human fossil record.
So it was apparent that there was some kind of 'progress' going on. It was all clear when in 1859 Charles Darwin published his "On the Origin of Species". The 'progress' shown by the fossils was a documentation of the grand pattern of evolution through long spans of time. The accuracy of the fossil record using the stratigraphy method has been well documented. The order of appearance in a sequence is well documented, but that is not all.
Phylogeny, mathematics, and other methods used to date fossils.
Biologists now have at their disposal a variety of independent means to look at the history of life. Besides the order of fossils in the rocks, another method is the use phylogenetic trees.
Phylogenetic trees are used to show how all the species of particular groups of plants or animals relate to each other. They are drawn up mathematically, using lists of morphological (external form) or molecular (gene sequence) characters.
What is noteworthy is that modern phylogenetic trees derive no input from stratigraphy, scientific comparisons between tree shape and stratigraphy can be used to confirm the fossil record. The majority of test cases show good agreement, so the fossil record accordingly relates the same story as the molecules enclosed in living organisms.
Techniques used for Absolute Dating
All of this gets us to one of the most important physical techniques, radioactive Dating. Carbon dating in geology may be relative or absolute. One does relative dating by observing fossils sequences using the stratigraphical method. One records which fossil is younger and which is older. The discovery of a different means, one for which absolute dating is possible occurred in the early 20th century. The methods are based on radioactive decay.
Certain naturally occurring elements are radioactive, and they break down or decay at well-known predictable rates. Chemists can measure the half-life of these elements, which is the time it takes for half of the radioactive parent element to break down into the stable daughter element. Then by comparing the two proportions of parent to daughter elements in the rock sample, and knowing the half-life, the absolute age can be calculated.
Carbon Dating
Carbon-14 dating is the best-known absolute dating technique. This is the one preferred by archaeologists prefer to use. But there is a problem, the half-life of carbon-14 is only 5730 years, so the method cannot be used for materials older than about 70,000 years. (After 70,000 the element is stable, it doesn't decay any longer.)
A second technique involves the use of isotopes. An isotope is an atom having the same number of protons in its nucleus as other varieties of the element but has a different number of neutrons. Radiometric dating using one of the following isotope series, such as rubidium/strontium, thorium/lead, potassium/argon, argon/argon, or uranium/lead can be used. All have a very long half-life, ranging from 700 million years to 48.6 billion years. Subtle differences in the relative proportions of the two isotopes can give good dates for rocks of any age.
The Fossils Sequence Record
It was the study of rock layers in England near the beginning of the 19th century that lead to the study of paleontology and from there to the study of fossils. Early geologists, at the end of the 18th and early 19th century noticed how fossils appeared in certain sequences: some fossil assemblages were always found below other assemblages, not above. This meant that the ones below were older than the ones on top.
It took a canal surveyor circa 1800, William Smith in England, who noticed that he could map out great tracts of rocks on the basis of their contained fossils. The sequences he saw in one part of the country could be matched precisely with the sequences in another. This lead to the recognition of one of the principles of geology, i.e., stratigraphy, older rocks lie below younger rocks and that fossils occur in a particular, predictable order.
The next step was for geologists began to build up the stratigraphic column. And this gave us the familiar list of divisions in the geologic time scale -- Jurassic, Cretaceous, Tertiary, and so on. Most importantly, it was recognized that each time-unit was characterized by the appearance of particular fossils. The scheme worked all round the world, without fail.
The next observation occurred when geologists noted how fossils became more complex through time. At the oldest, or deepest layer of rock there was no record of fossils, but then they noticed that simple sea creatures were found at the next higher level, then more complex ones like fishes at the next higher level and so on. Next came life on land, then reptiles, then mammals, and finally humans. One fact was soon clear, no dinosaur record could be found to coincide with a human fossil record.
So it was apparent that there was some kind of 'progress' going on. It was all clear when in 1859 Charles Darwin published his "On the Origin of Species". The 'progress' shown by the fossils was a documentation of the grand pattern of evolution through long spans of time. The accuracy of the fossil record using the stratigraphy method has been well documented. The order of appearance in a sequence is well documented, but that is not all.
Phylogeny, mathematics, and other methods used to date fossils.
Biologists now have at their disposal a variety of independent means to look at the history of life. Besides the order of fossils in the rocks, another method is the use phylogenetic trees.
Phylogenetic trees are used to show how all the species of particular groups of plants or animals relate to each other. They are drawn up mathematically, using lists of morphological (external form) or molecular (gene sequence) characters.
What is noteworthy is that modern phylogenetic trees derive no input from stratigraphy, scientific comparisons between tree shape and stratigraphy can be used to confirm the fossil record. The majority of test cases show good agreement, so the fossil record accordingly relates the same story as the molecules enclosed in living organisms.
Techniques used for Absolute Dating
All of this gets us to one of the most important physical techniques, radioactive Dating. Carbon dating in geology may be relative or absolute. One does relative dating by observing fossils sequences using the stratigraphical method. One records which fossil is younger and which is older. The discovery of a different means, one for which absolute dating is possible occurred in the early 20th century. The methods are based on radioactive decay.
Certain naturally occurring elements are radioactive, and they break down or decay at well-known predictable rates. Chemists can measure the half-life of these elements, which is the time it takes for half of the radioactive parent element to break down into the stable daughter element. Then by comparing the two proportions of parent to daughter elements in the rock sample, and knowing the half-life, the absolute age can be calculated.
Carbon Dating
Carbon-14 dating is the best-known absolute dating technique. This is the one preferred by archaeologists prefer to use. But there is a problem, the half-life of carbon-14 is only 5730 years, so the method cannot be used for materials older than about 70,000 years. (After 70,000 the element is stable, it doesn't decay any longer.)
A second technique involves the use of isotopes. An isotope is an atom having the same number of protons in its nucleus as other varieties of the element but has a different number of neutrons. Radiometric dating using one of the following isotope series, such as rubidium/strontium, thorium/lead, potassium/argon, argon/argon, or uranium/lead can be used. All have a very long half-life, ranging from 700 million years to 48.6 billion years. Subtle differences in the relative proportions of the two isotopes can give good dates for rocks of any age.
Different Isotopes can be used for cross-referencing dates
When radiometric dating was first used around 1920, it showed that the Earth was hundreds of millions, or billions, of years old. Since then, geologists have made many tens of thousands of radiometric age determinations, using the different isotope pairs and scientists have refined the earlier estimates. This is important, for the accuracy of a fossil is not dependent on one finding; other checks are possible.
Now a day's there is only a 1% chance of error occurring with the current dating technology. In fact new geologic time scales are published every few years, providing the latest dates for major time lines. One important result is that some older dates may change by a few million years up and down, but the younger dates are very stable.
A good example occurs with the work on the boundary mark known for about 50 years now as the Cretaceous-Tertiary boundary. This boundary marks the end of the dinosaur's period, which was 65 million years ago. Repeated retests, using more sophisticated techniques and equipment have not shifted that date. It continues to be accurate to within a few thousand years. With modern, extremely precise methods the error bars are often only 1% or so.
Conclusion: The strict rules of the scientific method ensure the accuracy of fossil dating.
Conclusion
The fossil record is fundamental to an understanding of evolution. The first technique used was stratigraphy, looking at the sequence of fossils as the appeared in geologic formations. Other methods were also developed, Phylogenetic trees of species, mathematical models, carbon dating and radioactive isotope dating were also developed. These different techniques do not contradict one another, but in fact support the timeline that has been identified. Fossils do tell the evolutionary story of live on earth.
When radiometric dating was first used around 1920, it showed that the Earth was hundreds of millions, or billions, of years old. Since then, geologists have made many tens of thousands of radiometric age determinations, using the different isotope pairs and scientists have refined the earlier estimates. This is important, for the accuracy of a fossil is not dependent on one finding; other checks are possible.
Now a day's there is only a 1% chance of error occurring with the current dating technology. In fact new geologic time scales are published every few years, providing the latest dates for major time lines. One important result is that some older dates may change by a few million years up and down, but the younger dates are very stable.
A good example occurs with the work on the boundary mark known for about 50 years now as the Cretaceous-Tertiary boundary. This boundary marks the end of the dinosaur's period, which was 65 million years ago. Repeated retests, using more sophisticated techniques and equipment have not shifted that date. It continues to be accurate to within a few thousand years. With modern, extremely precise methods the error bars are often only 1% or so.
Conclusion: The strict rules of the scientific method ensure the accuracy of fossil dating.
Conclusion
The fossil record is fundamental to an understanding of evolution. The first technique used was stratigraphy, looking at the sequence of fossils as the appeared in geologic formations. Other methods were also developed, Phylogenetic trees of species, mathematical models, carbon dating and radioactive isotope dating were also developed. These different techniques do not contradict one another, but in fact support the timeline that has been identified. Fossils do tell the evolutionary story of live on earth.
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