New Generation Sequencing Technologies: Population Genetics

New Generation Sequencing Technologies Population GeneticsNew generation sequencing technologies have the potential to quickly accelerate population patrimonials research, allowing scientists to comprehensively under nominate complex evolutionary histories, as well as functional and ecological biodiversity (Shokralla, et al., 2012 Shendure Hanlee, 2008). Prior to 1977, duration payoff involved the handling of toxic chemicals and radio-active isotopes, restricting sequencing to persons of high expertise and speciality (Hunkapiller, 1991 Swerdlow, et al., 1990 Sanger, et al., 1977). In 1977, Fred Sanger and Alan R. Coulson published two methodological papers describing a new variety show of deoxyribonucleic acid sequencing engineering science, which would lead to the method (capillary-based, semi-automated Sanger biochemistry) used almost exclusively in the field, for the next 30 years (Shendure Hanlee, 2008). Sanger sequencing transformed biology. It became a tool for deciphe ring complete genes and, later, faultless genomes. Due to the unprecedented extent at which Sanger technology grew, factory-like enterprises, cal direct sequencing centres, were established, housing hundreds of DNA sequencing instruments, operated by cohorts of personnel (Schuster, 2008 Hunkapilla, et al., 1991).Despite the dominance of Sanger sequencing in laboratories, for a number of decades, the technology had and continues to be hampered by inherent limitations in throughput, scalability, speed and resolution (Shendure Hanlee, 2008). To overcome these barriers, an entirely new technology was required, one that democratised the field, putting the technology of comprehensive genetic analysis into the hands of individual investigators, not only major genome research centres (Shendure Hanlee, 2008). The need for new technologies was pushed for by the facilitators of the Human Genome Project (HGP) (Ventor, et al., 2001). The excitement and successful termination of the HGP, by t wo competing research bodies, lead to collective hunger for more advanced, economical sequencing technologies. Next-generation sequencing (NGS), also known as massively parallel sequencing, was such(prenominal) a technology and has ignited a revolution in genomic science, similar to that seen when Sanger technology was presented in 1977, honing in on the era of post-genomic research (Schuster, 2008).The revolutionary nature of NGS technologies eldest became apparent in 2005, in two interrupt publications, 454 Life Sciences (Marguiles, et al., 2005) and the Multiplex Polony Sequencing Protocol (Shendure, et al., 2005). The methodology of both research groups resulted in vast reductions in the requisite reaction volume, while dramatically extending the number of sequencing reactions (Schuster, 2008). Despite such advances, in sequencing technology, NGS had a slow uptake in the scientific community, with a number of scientists having reservations. match to Schuster (2008), scientis ts accustomed to Sanger sequencing, as well as the initial scepticism echoed by funding bodies, resulted in a fear that large financial investments into Sanger-sequencing technologies would not pose returns, due to the technologies becoming obsolete. Other concerns were also raised, regarding the sequencing fidelity, read length, infrastructure cost and the handling of the large data volumes produced by NGS (Zhang, et al., 2011). It was the process of combining ongoing Sanger sequencing projects with NGS technologies that promoted its acceptance, into the scientific community. Once the enormous potential of the technology had been realised, along with new and upcoming biology projects that required sequencing outside of what the modern Sanger technology could feasibly produce, the concerns raised by NGSs early sceptics started to be overlooked. A combination of both first and second generation technologies are now used in sequencing facilities and projects around the world, the im plications of which, for the fields of evolutionary biology and population genetics is vast.Researchers now have the ability to observe small changes in ecological community structure that may occur undermentioned anthropogenic or natural environmental fluctuations (Hajibabaei, et al., 2011 Leininger, et al., 2006 Hunkapiller, et al., 1991). Such implications of NGS technologies has led to the generation of whole-genome sequence data, for thousands of individuals (Akey Shriver, 2011 Harismendy, et al., 2009). The availability of such data is leading to a better perceptiveness of evolutionary processes, such as descriptions of sex-biased dispersal and mutation rate biases (e.g., Wilson Sayres, M. A., et al., 2011). Furthermore, the ability to sequence the genomes of species, that have been long extinct, is no longer nonsensical, provided the samples from which DNA is to be extracted is unflustered viable (Green, et al., 2010 Reich, et al., 2010). The hope that such projects may h elp population geneticists better understand the process of extinction, whether anthropomorphically or naturally induced, may help those endangered species whose current possibility of extinction, in the near future, is high (Akey Shriver, 2011 Miller, et al., 2011). However, despite such ambitious aspirations of population geneticists, one large area of research that remains surprisingly unanswered, within the literature, is the definition of a population or the population concept (Waples Gaggiotti, 2006).Given the importance of such a concept, one might expect to find a commonly used definition, one that is applicable to wild species, to determine how umpteen populations exist within a delineated geographic area and the relationships amongst them (Waples Gaggiotti, 2006). However, one does not exist, rather there is evidence that what makes a population is based on the research question. NGS technologies are providing population geneticists with the opportunity to flesh out a precise definition of a population, on the molecular level. For example, Waples Gaggiotti (2006) ask How different must molecular units be before individuals can be considered a part of separate populations? Different criteria can be established and assigned to individuals, in order to determine the answer. The interplay of different evolutionary forces (selection, migration, drift) will favour different species, with different forces world more obvious, at the molecular level, than others. The ability to pose a research question, pertaining to the individuals, within a particular habitat, is now possible due to the ability to sequence numerous samples with NGS technologies.The implications, in population genetics, for a new generation of sequencing technologies, are a greater focus on testing expectations. Such expectations, simultaneously, result in excitement and daunt to those undertaking evolutionary and population genetic research, at present. Excitement exists because fun damental questions, pertaining to the patterns of genetic variation, within and between species, can now be analysed, with new generation sequencing technologies, such as NGS. Although NGS technology may still be in its infancy, the powerful possibility of analysing massive data sets is within tump over of the individual and large-scale sequencing facilities alike, at a highly reduced cost. However, the methodological tools and theoretical models needed to interpret such large data sets are evenly daunting to both new, and experienced, evolutionary and population geneticists. Despite such present and future challenges, population genetics research is looking promising, thanks to advances in NGS toleration and computation.ReferencesAkey, J. M. Shriver, M. D. (2011). A grand challenge in evolutionary population genetics new paradigms for exploring the past and charting the future in the post-genomic era. Frontiers in Genetics 2, 1-2.Green R. E., Krause J., Briggs A. W., Maricic T. , Stenzel U., Kircher M., Patterson N., Pbo S. (2010). A draft sequence of the Neanderthal genome. Science 328, 710722.Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G. A. C. 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The Spartans took their stand against the massive army of Iranians in a three day battle which resulted in the Persians taking the win simply may have precise well led to the Greeks winning the Greco-Persian War. A culmination of strong tactical science and bravery contributed to the Spartans making a stand much longer and stronger than some(prenominal)body could have ever predicted. The Persian king Xerxes led his massive army through the sign mountain pass known as Thermopylae expecting no considerable fight on the part of the Spartans. The Persians bid to conquer Greece was significantly halted because of the Spartan resistance, which was led by Leonidas,followed by a small army of Spartans, amounting to no more than 300. But no matter the size of Spartas fleet, Sparta if not the strongest, was one of the strongest armed forces powers in antique Greece. And despite them being vastly outnumbered by the Persians at Thermopylae, they did indeed prove their military strength and sophistication which resulted in their near thrash of the Persian army.Greek destination was and still is up to today a heavy influence on the modern refinings of the Western world. It is because of this heavy influence of Greek culture in the western world, the knowledge of their history proves crucial to many aspects of our understanding of our own cultures. This heavy influence on the development of the western world could very easily be the reason that the Battle of Thermopylae and other battles surrounding it, have become of such importance and high level of study. The valiant stand of the Spartans at Thermopylae lead to the Greeks defeat of the Persians in the Greco-Persian war and enabled the further development of a culture from which the western world gains many of its principles and ideas. If the Spartans had not decelerate the Persians at Thermopylae there may have been a very different ending to the Greco-Persian war. This being an important observation because the Greco-Persian war played such a crucial reference in the history of Greece, a defeat could have resulted in a very different future for the western civilization.The culture of Greece was one that strived for perfection in every sense of the word, but there was a dark side to the culture that so many have full-grown to praise. This dark side can be seen in the Spartans intervention of the Helots, who were in essence a Greek culture in their own, the Messenias, but early on became enslaved by the power Spartans who were in desperate need to acquire more land to deal with the burden of overpopulation. The Spartans held true and easily demonstrated as what is seen as Greeces inability to incorporate. The poor treatment of the Helots lead them to begin a 30 year drive, in which the Spartans took twenty years to take control of the situation. tending of more events like this, is what turned Sparta into the war state that it became. The attempt to suppress the Helots, by the Spartans, in many ways assisted the Spartans in their attempt to defeat the Persians. No longer willing to undergo a s imilar revolt, the Spartans devoted a considerable amount of time and energy making certain to prohibit all such events. It was because of these efforts that major components of Spartan culture, as we know it today, were all enforced. This can be easily seen in the devotion to physical perfection and war-ridden techniques. And equally as important as their attempt to suppress the Helots was the contribution of the Helots in constructing their armor and warring tools. So despite the overwhelmingly poor treatment of the Helots, they played a crucial role in preparing the Spartans for the challenges to come and in the heat of battle. Even though they may have played an indirect role the affect that had on both the culture and the Battle of Thermopylae itself was indeed direct.The Greeks had a large influence on the development of western world in many respects. Whether it is an influence on science or art, to anyone who has studied Greece in the days of its glory the influences be ea sily pinpointed. These influences continue into the art of war. As antecedently stated, war was a constant in Greece so much so that it became imbedded in its very culture. Consequently the way in which war was conducted in ancient Greece has become a portrait of the way in which it should be conducted, and set a standard around the Western world for years to come. Despite war being one of the most immoral, barbaric, and most appalling of all human creations, the Greeks did the impossible, by successfully portraying war as something of beauty, patriotism, freedom and self-sacrifice. Therein lays a reason the significance of the Battle at Thermopylae. That one battle not only captured the spirit of the Greeks, more specifically the Spartans, in three days but became a turning point of the art of war. But the Battle of Thermopylae more importantly defended the very future of the modern world.It was Spartan culture, which in many ways, influenced the Spartans ability to stand against t he Persians as long as they did. To overlook the role of Spartan culture in relation to their stand at Thermopylae would be to overlook one of the most influential aspects of the battle. Spartan culture was one of great complexity having many intricate characteristics, which adapted to the situations that they held witness to. Spartans were people of innate patriotic pride and military prowess, who sought perfection in every form. But equal to their patriotism was their oppressive tactics towards their captives. Spartans werent people who believed in the concept of freedom. The Spartans for several centuries, while in Laconia and Messenia, exercised a ruthless enslavement of other native Greeks, whose land they conquered. Sparta was a military aristocracy, who wasnt a military state for the sake of being a military state. In many respects Spartas army, parallel to not other, was created and maintained for the sole purpose of suppressing the Helots. In theory it was because of Spart as inability to incorporate that lead to their standing army.Spartas military achievements are, no doubt, the most impressive of all their possible accomplishments. By the core of the sixth century Sparta was already considered the strongest military force in Greece. Despite the brute strength the of the Spartan army, the Spartan were still worried that a revolt from their underclass (the Helots)would cripple their advancement as a society.The Helot underclass were always threatening to rise up in significant numbers against their masters. So, at the beginning of each new civil year Spartas chief elected officials, the board of five ephors (overseers, supervisors), formally declared war on them. If any Helots did choose to rebel, they might then be killed with impunity.The awareness of a possible revolt kept the Spartans military forces extremely strong. This tension between the Spartans and Helots, strongly inclined(p) the military forces for both the expected and unexpected, a b eneficial trait which played to their advantage at the Battle of Thermopylae. Another trait that played to their advantage was the educational system of Sparta. The agoge was instated into Spartan culture to both develop the physical and mental maturity of all Spartan boys and was a requirement for all Spartan males.