There is currently a lot of debate and controversy over the Neanderthal genome as it is a relatively new topic that is being investigated. We are well aware that the Neanderthal is the most closely related ancestor to the present day humans that are around today. However there is still a large scale debate over how closely related we are in terms of genetics. (Hublin and Pääbo et al). The first insight into the Neanderthal genome occured in 1997, where mitochondrial DNA was extracted from a Neanderthal found in 1856. Since then there has been another 15 attempts to sequence other Neanderthal specimens. Through careful analysis of the data it has shown that their mitochondrial DNA falls outside of ours. Therefore meaning they have not provided any contribution into our current genome. (Krings et al). These clear and distinct differences between the two mitochondrial genomes have enabled us to clearly distinguish between the Neanderthal DNA and current humans. This has proved to be a vital key when establishing authenticity of the DNA, and has minimised cross contamination of the Neanderthal and current human DNA.
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There has been a huge increase in debate and interest as we now know that the modern day human and the distant Neanderthal may have lived around the same time, as close as 30,000 years ago. (Smith et al ). In the Richard E Green et al paper it states there are 206 nucleotide base differences between modern human and Neanderthal mitochondrial DNA out of the 16,568 that are know. This was one of the first papers that led to a great deal of speculation over contamination issues. This was because the paper stated that the last common ancestor was around 660,000 years ago. However there are genes believed to be in the region of around 1-4 million years old. Therefore evidence leading towards contamination between modern human and Neanderthal cross contamination. (Garrigan and Hammer ) the modern day humans and Neanderthals are believed to be remarkably similar and only around 0.5% difference between them. They both contain around 3.2 billion base pairs in their genome.
In 2006, 454 life sciences and the max Planck institute for evolutionary anthropology set out to sequence the Neanderthal genome. 454 life sciences used a new sequencing strategy to develop millions of short sequences that are able to distinguish the differences between the current human and Neanderthal genome. However this strategy leads to the destruction of the sample and repeats are not possible. However in the Noonan analysis they used another technique called metagenomics by inserting the DNA into a bacterial vector. This creates a living library of DNA sequences that can be used repeatedly if needed, and is used to correct errors. First of all they extracted bone from the femur of a 38,000 year old Neanderthal and many other specimens from Germany, Russia and Spain were analysed. They used very little bone, around 0.3 grams to extract the DNA. Richard Green and Noonan et al both published their results. The two different teams recovered very similar results. They came to the conclusion that the most recent ancestor lived around 700,000 years ago, and the separation of the human and Neanderthal to be around 370,000 years ago. There was a lot of controversy and belief there may have been admixture incorporated into the Neanderthal genome. It was not up until several years later in the beginning of 2009 that svante paablo published he had sequenced around 63% of the Neanderthals genome.
With the development of new high-throughput DNA sequencing analysis, this has enabled a large step towards constructing the Neanderthal genome (Richard E Green et al). Currently there are many problems with proving how authentic the Neanderthal DNA really is. First of all there is very little definitive Neanderthal DNA used in the analysis to start with. This is because there may also be a very high level of microbial DNA incorporated into the specimen, due to bacterial incorporation and decomposition of the bones. Another is how contaminated the Neanderthal DNA may be in terms of current human DNA, depending upon how the specimen has been handled. If the DNA extraction is not carried out very carefully this may lead to cross contamination of present day humans with Neanderthal DNA, leading to inaccurate genome results. In 2007 there was a review of the Green and Noonan paper by Wall and Kim. They found many inconsistencies within the data and believed this may have been due to contamination with human DNA. After careful re-evaluation, the Neanderthal split time was estimated at around 35,000 years for Green and 325,000 years for Noonan. (Wall and Kim et al).
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PCR is an excellent and essential piece of equipment to distinguish the DNA; however it is very hard to distinguish between the two DNA types of the modern human and Neanderthal as they are very similar. (Johannes Krause et al). PCR has played a key role in allowing a small DNA fragment to be copied many times over, enabling very small pieces of Neanderthal DNA to be amplified. However this can lead to amplification of current day human contaminated DNA.
Male contamination can also be detected found from indication of the Y chromosome in a female specimen. This is because if the Neanderthal specimen is female then there should be no Y chromosomes present whatsoever. The result is a very good indicator of the contamination levels. This has been an important tool as the bulk of the Neanderthal specimens have been female. (Richard E. Green et al). There has also been a tool to determine female cross contamination. If the specimen is male then it will be heterozygous X, if it is not then this shows female contamination. However this is less reliable and likely to provide inaccurate results, as Neanderthal DNA has a high possibility of sequencing errors in the DNA. Another strategy is to carry out the experiment several times over to detect any contaminated DNA on the same specimen. This may increases accuracy but may not always be possible as this can prove to be very costly and time consuming and may not always be possible. Thanks to the Mitochondrial Genome of the Neanderthals being sequenced this leads to a library of fixed differences between current day man and Neanderthals. This has enabled a more accurate and reliable DNA source indicator. (Richard E Green et al). There are now a strict set of rules and procedures that are carried out to ensure minimal cross contamination takes place. These include laboratory procedures such as, Neanderthal specimens and their extracted DNA have to be kept well away from other experiments and away from UV radiation and bleaching. The DNA extracting scientists often operate in a clean room, where purified air is delivered and they wear sterile clothes and face masks. Finally the experiments may be replicated to ensure the highest reliability if time and money is not a problem. This generally have lead to a great improvement in reliability. (Richard E Green et al).
Experiments have been carried out to see how contaminated specimens were under clean room conditions. The results shown from one report claim It was less than 1% contaminated for the two DNA extractions from the same 38,000 yr old Neanderthal from the Vindija cave (Serre et al, 2004). However there are still problems after the specimen moves from the green room to another, such as when producing mitochondrial libraries of the Neanderthals DNA. This may in turn still leave the mitochondrial DNA susceptible to cross contamination with modern day humans at a later stage. (Wall and Kim, 2007).
Noonan and Green could not conclude from their analysis if there has been any hybridization between the modern day human and Neanderthal. However they claim that there is little chance of it every occurring to a significant level. There appears to be evidence that post mortem DNA damage may lead to the de-amination of Cytosine to Uracil, leading to a high mutation rate (Hofreiter M et al). There seems to be a high mutation rate recorded in the Noonan data when compared to the Green data, indicating that post mortem DNA damage is not the case in the Green et all study.
One of the latest studies to be carried out to help determine our ancestry links between us and Neanderthals was the Saqqaq genome project. This was from a 4000 year old Neanderthal hair sample found in a well preserved permafrost region. (Drmanac,R. et al). The SNP analysis carried out showed less than 0.8% contamination, and further analysis showed it fitted in with haplotypes from north-east Asia. (Bentley, D. R. et al).With adequate handling and careful DNA extraction techniques, this enabled the sample to be almost completely contamination free.
Other insights into the Neanderthals genome have uncovered some other very interesting findings. For example the discovery of the changes within the FOXP2 gene that is used in conjunction with speech development. Neanderthals have been shown to also carry the exact same FOXP2 protein involved with speech. There still needs to be a lot of experimental analysis in vivo and vitro over how these genes came about and the divergence times. There is also many other experiments currently taking place. Such as, there is good evidence to believe Neanderthals were unable to digest lactose in milk in adulthood. (Johannes Krause et al)
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There are currently two main theories likely to explain the extinction of the Neanderthals. The climate change hypothesis, stating that the repeated and rapid changes in temperature during the glacial period between 60,000 to 30,000 years ago. Also the competition hypothesis, believing modern day humans who came about into Europe at around 45,000 years ago simply out competed the Neanderthals. The multiregional model suggests that modern day humans came about from different regions of the world but still allowed for a certain level of gene flow between them to maintain the species, with a common ancestor believed to be over a million years ago. The recent replacement model indicates in contrast a single population expanded out of Africa and replaced ancestral populations around 200,000 years ago. (Todd R. Disotell). A recent Neanderthal child was found in Portugal and believed to provide evidence that modern day humans and Neanderthals may have hybridized. (Duarte et al). This specimen appeared to have the same facial features of modern day humans, but a distinctly different body type of the Neanderthal. However this was dismissed on grounds that it was almost impossible to accurately depict and reconstruct a Neanderthal infant face.
The Neanderthal genome data collected as far clearly falls outside of modern day humans. The best estimate is that we shared our last common ancestor somewhere in the region of around half a million years ago. Therefore, the strongest supporting hypothesis is that our ancestors are derived from a single population around Africa. They remained relatively static there for many thousands of years and only moved out to other regions relatively recently within the last 100,000 years. This in turn due to competition, replaced other primitive humans including the Neanderthals all across the globe.
One of the most important tools when determining if there was any hybridization between modern day humans and Neanderthals is to study the shared polymorphisms between the two species. This process needs the analysis of many Neanderthal specimens, currently there are over 400 Neanderthals found to date. Once the complete Neanderthal genome has been completed to 100% or as close to that as possible, more data will be available. From this a set of specific, fixed differences between the two species can be observed as markers. This will be a good indicator of how reliable the data from the DNA will be in terms of contamination from current human DNA. This is now possible for the mitochondrial DNA, and hopefully sometime soon in the future will be available for the whole genome above the 63% level. The sequencing of the entire Neanderthal genome is a very highly skilled and technical leap forward for genetics, also adding to our understanding of our ancestry. However there are still currently problems with contamination issues and also high sequencing error rates. Therefore at this time it is hard to come to any solid conclusions from the analysis of the data. (Wall JD et al). With increases in technology and sequencing methods, less contamination due to specialised clean rooms, and with the expanding masses of information on the Neanderthal genome, it will not be long until firm answers and conclusions can be drawn.