TY - BOOK

T1 - Ancient and Modern Population Genomics of the Peopling of the Americas

AU - Moreno Mayar, José Victor

PY - 2017

Y1 - 2017

N2 - Genome-wide studies, particularly from ancient samples, have substantially expanded our understandingof human evolutionary history. However, ancient DNA (aDNA) research has remaineda challenging field, due to post-mortem DNA damage and contamination. While these are unavoidable,technological and methodological improvements have made it possible to assess theirpotential effect on the data and results. We have implemented and extensively tested a statisticalmethod for estimating contamination from high-throughput sequencing data based on haploidchromosomes (Chapter 2). We found our method to produce reliable results even for datasets withlimited depth of coverage (0.5X) and high error rates. This feature is particularly well suited foraDNA studies where it is unlikely to produce higher-coverage genomes. Moreover, we have developeda tool that allows for ancestry assessment of low-coverage data using multidimensionalscaling (Appendix A). These and similar methods have been applied in a number of studies thathave contributed to generating a more detailed description of human dispersals across the globe.It is now accepted that anatomically modern humans expanded out of Africa and colonized mostof the Old World by 30 kya. Subsequently, they crossed Beringia, the land bridge connectingNortheast Asia and Alaska, after the Last Glacial Maximum. However, archaeology, anthropology,linguistics and even genetics have not reached a consensus on key aspects such as the number ofmigration waves, their origin and their time and routes of entrance. We sequenced the first highcoveragehuman genome (USR1) from Terminal Pleistocene Alaska; the most likely entryway intothe New World (Chapter 3). The USR1 genome revealed a basal Native American population thatlikely diverged in Beringia from Native Americans, which later differentiated beyond the glacial icesheets. Our findings support a single founding source population for all Native Americans. Theseinclude human remains that have been hypothesized to be members of a separate migration fromthe Old World, such as the Kennewick Man for which we confirmed his Native American origin(Appendix B). Moreover, the USR1 genome allowed us to re-assess the source of two secondarymigrations that likely gave rise to Na-Dene-speaking and Inuit populations. We conclude that bothderive their Native American ancestry from a similar source; however, they carry ancestry fromtwo different Asian migrations. Finally, we explore a more recent, trans-Pacific contact betweenPolynesians and Native Americans (Chapter 4). We analyzed genotype data from modern-dayRapanui and found that they carry Native American ancestry, which derives from an admixtureevent that antedates the presence of Europeans in the region. These findings provide new insightsinto the initial peopling of the Americas as well as secondary contacts with an unprecedentedresolution, which could only be achieved by generating genome-wide data.

AB - Genome-wide studies, particularly from ancient samples, have substantially expanded our understandingof human evolutionary history. However, ancient DNA (aDNA) research has remaineda challenging field, due to post-mortem DNA damage and contamination. While these are unavoidable,technological and methodological improvements have made it possible to assess theirpotential effect on the data and results. We have implemented and extensively tested a statisticalmethod for estimating contamination from high-throughput sequencing data based on haploidchromosomes (Chapter 2). We found our method to produce reliable results even for datasets withlimited depth of coverage (0.5X) and high error rates. This feature is particularly well suited foraDNA studies where it is unlikely to produce higher-coverage genomes. Moreover, we have developeda tool that allows for ancestry assessment of low-coverage data using multidimensionalscaling (Appendix A). These and similar methods have been applied in a number of studies thathave contributed to generating a more detailed description of human dispersals across the globe.It is now accepted that anatomically modern humans expanded out of Africa and colonized mostof the Old World by 30 kya. Subsequently, they crossed Beringia, the land bridge connectingNortheast Asia and Alaska, after the Last Glacial Maximum. However, archaeology, anthropology,linguistics and even genetics have not reached a consensus on key aspects such as the number ofmigration waves, their origin and their time and routes of entrance. We sequenced the first highcoveragehuman genome (USR1) from Terminal Pleistocene Alaska; the most likely entryway intothe New World (Chapter 3). The USR1 genome revealed a basal Native American population thatlikely diverged in Beringia from Native Americans, which later differentiated beyond the glacial icesheets. Our findings support a single founding source population for all Native Americans. Theseinclude human remains that have been hypothesized to be members of a separate migration fromthe Old World, such as the Kennewick Man for which we confirmed his Native American origin(Appendix B). Moreover, the USR1 genome allowed us to re-assess the source of two secondarymigrations that likely gave rise to Na-Dene-speaking and Inuit populations. We conclude that bothderive their Native American ancestry from a similar source; however, they carry ancestry fromtwo different Asian migrations. Finally, we explore a more recent, trans-Pacific contact betweenPolynesians and Native Americans (Chapter 4). We analyzed genotype data from modern-dayRapanui and found that they carry Native American ancestry, which derives from an admixtureevent that antedates the presence of Europeans in the region. These findings provide new insightsinto the initial peopling of the Americas as well as secondary contacts with an unprecedentedresolution, which could only be achieved by generating genome-wide data.

UR - https://soeg.kb.dk/permalink/45KBDK_KGL/1pioq0f/alma99122078216305763

M3 - Ph.D. thesis

BT - Ancient and Modern Population Genomics of the Peopling of the Americas

PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen

ER -