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New approach to investigate the relationships between Denisovan and human populations

Arnellos, Dimitrios (2019) BINP41 20172
Degree Projects in Bioinformatics
Popular Abstract
The relationship between ancient hominins and modern humans, from a new perspective

Many questions followed the discovery and identification of the Neanderthal from the fossil record in 1856 as to its place in the hominin tree and its relationship with modern humans. Was it a direct ancestor? A remote cousin? Or did it mix with humans? Once reliable nuclear DNA data became available in 2010, the verdict was that indeed, modern humans and Neanderthals mixed at some point in the past. In 2010, a new ancient hominin was found in Denisova Cave in Southern Siberia whose DNA was also sequenced and showed that it was closely related to the Neanderthals. DNA analyses have suggested that the ancestors of modern-day Melanesians, people from Papua... (More)
The relationship between ancient hominins and modern humans, from a new perspective

Many questions followed the discovery and identification of the Neanderthal from the fossil record in 1856 as to its place in the hominin tree and its relationship with modern humans. Was it a direct ancestor? A remote cousin? Or did it mix with humans? Once reliable nuclear DNA data became available in 2010, the verdict was that indeed, modern humans and Neanderthals mixed at some point in the past. In 2010, a new ancient hominin was found in Denisova Cave in Southern Siberia whose DNA was also sequenced and showed that it was closely related to the Neanderthals. DNA analyses have suggested that the ancestors of modern-day Melanesians, people from Papua New Guinea and some islands in the Pacific, have mixed with the Denisovan hominin.

Since the techniques of extracting ancient DNA from fossils are still in their infancy, there is much emphasis on the statistical methods used to analyse the data and how to improve them to increase their accuracy and power. Contrary to published reports, our preliminary analyses suggested that DNA segments in modern Africans have Denisovan ancestry. These findings motivated us to adopt a new powerful method to investigate these data further. This method detects stretches of DNA that are Identical by Descent (IBD) inherited directly from a common ancestor, between two individuals.

We used the algorithm Refined IBD as it is implemented in the BEAGLE software, since it exhibited the best performance. This algorithm was not used before to infer relatedness between genetically distant individuals as modern humans and the ancient hominins, due to the many difficulties in carrying out such a comparison. We identified four biases and addressed them one at a time. We demonstrate that IBD performed robustly against three out of four of these biases. Our results agreed with our previous preliminary results and confirmed that Africans are more closely related to the Denisovan than non-Africans. However, the fourth bias still needs to be investigated to greater detail to show that the results are indeed correct.

Under the assumption that modern Africans are more closely related to the Denisovan than non-Africans we also argue that the data could indicate that this result is not due to direct mixing of the ancestors of modern Africans with Denisovans, but rather with a close relative to the Denisovans and the Neanderthals.With additional testing, these results will be validated. The interbreeding event within Africans would be confirmed and detecting IBD as a method to infer distant relationships would be established.

Master’s Degree Project in Bioinformatics 30 credits 2017
Animal and Plant Sciences Department, University of Sheffield

Advisor: Eran Elhaik
University of Sheffield (Less)
Please use this url to cite or link to this publication:
author
Arnellos, Dimitrios
supervisor
organization
course
BINP41 20172
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8995934
date added to LUP
2019-09-30 10:57:31
date last changed
2019-09-30 10:57:31
@misc{8995934,
  author       = {{Arnellos, Dimitrios}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{New approach to investigate the relationships between Denisovan and human populations}},
  year         = {{2019}},
}