YSM Issue 96.2

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FEATURE Palaeogenomics BY MATTHEW BLAIR ART BY MALIA KUO VACATIONING IN SPAIN HOW ANCIENT HUMANS ESCAPED THE ICE AGE Genetic testing platforms like 23andMe and Ancestry.com have been in the spotlight for many years now. These testing programs have grown immensely popular, with some people finding long-lost relatives or discovering that a historical figure is somewhere in their family tree. But for those living over forty thousand years ago, unfortunately, no such genetic testing was available. Those early humans lived without ever knowing their full genetic history. Some early humans perhaps wholly missed the opportunity to gloat that they were related—somewhere in their bloodline—to the first Homo sapiens to discover fire. Now, however, He Yu of Peking University in Beijing, China and her team of researchers have constructed a genetic narrative for these early humans. Their study is the most comprehensive examination of certain hunter-gatherer groups living in Europe around the Ice Age. It reveals important information about the mixing between different groups and their migratory patterns. This study shines a light on the genetic differences and similarities of different hunter-gatherer groups and focuses especially on how these groups survived the Last Glacial Maximum (LGM), which was the most intense period during the last Ice Age. The group’s study examined where hunter-gatherer groups migrated in order to evade the massive glaciers and blisteringly cold temperatures moving across the globe during the LGM, which lasted from twenty-five thousand to nineteen thousand years ago. The LGM is particularly interesting to study because researchers believe it created a large migration of hunter-gatherer groups. Prior studies have found that the LGM pushed hunter-gatherer groups to move into southern latitudes, specifically the Iberian peninsula and southern France, with some studies also suggesting that hunter-gatherers could have moved into the Italian peninsula, the Balkans, and the southeastern European Plain. It is impossible to determine where groups may have moved during the LGM without having a snapshot of their locations and genetic makeups before and after this period. As such, the study spans from thirty-five thousand to five thousand years ago, covering before, during, and after the LGM. “This paper focuses on where people traveled to find refuge and, after the LGM, expanded again to form the later population structure,” Yu said. Using mostly bones, teeth, and other materials that could contain genetic information, Yu and her research team created new genomic information for hunter-gatherer groups that are now extinct. It is easy to send in your saliva sample to a genetic testing company site, but researchers had to meticulously comb through paleogenomic data to construct a very large and complex family tree. In this paper, 356 ancient hunter-gatherer genomes were analyzed, 116 of which were newly reported by researchers across the globe in fourteen countries throughout western and central Eurasia. Once the researchers confirmed that these samples contained genetically viable information, they began the process of genetic testing. The first, most crucial, step in this process is to extract the DNA and sequence the genome. Often, however, sequencing the genome is the simplest part. “When we get the data, we have a lot to do with it. We first examine their genetic differentiation, trying to see what samples look more similar and which are more dissimilar. Specifically, we focus on the alleles and other genetic information that could be shared between some individuals and not others,” Yu said. Alleles are the genetic information that could potentially be shared between individuals—the genetic information that could contribute to physical traits like blue eyes or brown hair. This process of analyzing these alleles and other genetic information involves a great deal of high-level statistical analysis and other methods of biological comparison. This data analysis allows researchers to test specific hypotheses about the movement and mixing of hunter-gatherer groups. There are many different ideas about where a group could have gone and which other hunter-gatherers they 30 Yale Scientific Magazine May 2023 www.yalescientific.org
Palaeogenomics FEATURE might have e n c o u n t e r e d along the way, but this method of data collection and analysis can quantitatively prove or disprove these conclusions. The researchers also considered a multitude of other factors, including the radiocarbon dates of the materials, so that they can pinpoint the age of the samples and discover other archaeological information. Simply, radiocarbon dating is the process by which researchers analyze the amount of radioactive carbon-14 left in a sample in order to measure its age. Further, cultural information about specific hunter-gather groups, such as knowledge about their mortuary practices or the types of weaponry they commonly used, allowed the researchers to make increasingly sound conclusions about the movements of certain hunter-gatherer groups and their possible relations to other groups. With this research, Yu and her team of researchers have established a genomic study of remarkable depth and breadth. By drawing on multitudes of biological and historical information, they created a firmly-rooted “family tree” for huntergatherer groups. When working with a data set that is so ancient, many challenges can arise. The majority of the time, the samples used usually come from bones or teeth. These physical samples last through the ages which makes them strong candidates for DNA extraction. In especially old samples, however, the DNA degenerates and is poorly preserved. “The samples that are reported, of course, are not the only samples that we have processed. There were various samples that did not produce enough DNA and some which had none at all, failing during the DNA extraction process,” Yu said. Even when a sample does produce enough DNA, that data must be observed with a critical eye. As these samples have often been studied by multiple parties and transported across the globe, the risk for contamination is high. “For many samples, we also had a hard time trying to detect and confirm if they are contaminated or not. Further, if samples were found to be contaminated, we then had to go through the process of separating the DNA of that specimen from its contaminants so that we could get real information,” Yu said. This study showed that huntergatherer groups flocked to western and southwestern Europe to escape the Ice Age. “It was always assumed that the Iberian Peninsula was a refuge during the Ice Age, but this is the first time we genetically confirmed that there is really a human population—with the same genetic ancestry found earlier in other regions of Europe—living in that area,” Yu said. This is a powerful confirmation that paints a clearer picture of the survival, migration, and mixing of hunter-gatherer groups. But researchers still have questions, especially about the importance of another region as a refuge during the Ice Age: the Italian Peninsula. In this region, there were massive genomic changes before and after the Ice Age, so researchers cannot make a succinct conclusion on whether or not it was a refuge based on DNA evidence alone. These regions saw a huge genomic turnover, with distinct genetic populations before and after the LGM. “Genetic information could help us to answer or confirm some points, but it alone cannot confirm them all. It is important in these sorts of studies to combine information from different sources and evidence from different disciplines,” Yu said. History itself is expansive, and trying to capture the movement of many different groups over tens of thousands of years is an exceedingly difficult task, but researchers like Yu and her team are embarking on this journey through time to reveal important information about how our earliest ancestors survived and how all of us are here today. As we move forward and learn more about our personal genomic histories through popular testing platforms, we can appreciate the work they are doing to capture the genomic ancestry of humans across the world. ■ www.yalescientific.org May 2023 Yale Scientific Magazine 31
Page 1 and 2: Yale Scientific THE NATION’S OLDE
Page 3 and 4: CONTENTS More articles online at ww
Page 5 and 6: The Editor-in-Chief Speaks THROUGH
Page 7 and 8: Physiology / Astronomy NEWS A NEW A
Page 9 and 10: Computer Science FOCUS TEACHING MAC
Page 11 and 12: Environmental Science FOCUS THE CAR
Page 13 and 14: Geochemistry FOCUS carbon dioxide d
Page 15 and 16: Medicine FOCUS PHOTOGRAPH COURTESY
Page 17 and 18: Dermatology FOCUS Bumps, whiteheads
Page 19 and 20: Ecology FOCUS ANIMALS AGAINST RISIN
Page 21 and 22: Ecology FOCUS to sediment depositio
Page 23 and 24: Public Health FOCUS In a paper publ
Page 25 and 26: Environmental Engineering FEATURE S
Page 27 and 28: FEATURE Materials Engineering Astro
Page 29: Bioelectronics FEATURE stability, a
Page 33 and 34: Immunology FEATURE viruses, unlike
Page 35 and 36: ALUMNI PROFILE AMYMARIE BARTHOLOMEW
Page 37 and 38: THE DARKNESS MANIFESTO You’ve pro
Page 39 and 40: Wrought into a cycle, carbon schlep

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