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By Billy Meneses '22 and Dr. Susan Park
By Billy Meneses '22 and Dr. Susan Park
Imagine 100,000 years into the future and the remains of your fossilized body are being unearthed by a team of androids. Using laser-scanning lidar (light detection and ranging) technology they assemble a 3D reconstruction of the pile of rubble where a city once was, and out of which your index finger can be detected protruding from the corner. According to paleontologist Tim White of the University of California at Berkeley, the surest way for one of our hominin ancestors to have become an intact fossil was to “face plant” into a swampy area such that their bones were preserved instantaneously for posterity and were not subject to dismemberment by scavengers. One reason why ancient fossils are not so easy to find.
Luckily today, ancient human fossils dating to 100,000 years old are being discovered by archaeologists and paleontologists around the world, including Africa, Western Eurasia, Central Eurasia, Eastern Eurasia, The Americas and Oceania. Perhaps surprisingly, it is the ancient genomes—not the bones-- of individuals from way back when that are informing scientists of the migration patterns as well as family structures of ancient human populations. Ancient DNA (aDNA), while miniscule in physical size, has enormous capacity for holding information about individuals and their relatives. Furthermore, aDNA samples can be enriched from just one small fossil sample, such as a finger bone.
This past summer, a group of Hotchkiss students and faculty (including the two authors) took part in an ongoing Middle Bronze Age archaeological dig at the Tel Kabri site in northern Israel, only 13 kilometers from the southern border of Lebanon (Figure 1a-b). There archaeologists from the United States, Israel, and Germany have set up shop on a parcel of land flanked by avocado trees, peeling away layers of dirt to reveal a Canaanite palace that flourished around 1500 BCE, outfitted with its very own wine cellar. It is estimated the palace and its surroundings was home to roughly 6,000 inhabitants at the time of its occupancy.
Figure 1a. Volunteers setting up for the work day. By 5:30am daylight was in full effect.
Figure 1b. Hotchkiss student volunteers uncover a wall of the palace. (Suleyka Alonso ‘22 and Eden Oostenink ‘20 pictured in the center)
As volunteers on the dig site, we would wake up well before sunrise so that we could escape the harsh rays of the sun as much as possible. By the time we arrived at the dig site, the sun began rising, and so we immediately unloaded all of the materials, which were stored in a shipping container and we carried them down to the dig site entrance. Then we got to work, dusting or picking away at respective sections of dirt which, soon enough would reveal bits and pieces of pottery, bones, flint, and more (Figure 2a-b and Figure 3). The archaeologists kept an organized record of everything that we found and our progress each day, making sure that we were making the short time that the dig site was in commission for the season worthwhile. As the day came to a close, and the sun rose to its maximum potential, we cleaned the area, piling up the hoes and picks, and carrying the buckets of pottery over to the shipping container. Once we finished packing everything up, we locked the container and loaded the bus which would take us back to the kibbutz, our temporary place of residence.
In the afternoon, we all gathered around a stretch of grass to wash off all the pottery we had collected during the work day. We dug around buckets of warm water, fishing out the pieces of pottery at the bottom and scrubbing them clean. It was always an exciting moment when you grabbed a large piece out of the bucket and you could see how it rounded at the edges, possibly belonging to an ancient pot. Occasionally, some pieces of pottery revealed patterns that matched with other collected pieces, which would then allow the archaeologists to start amassing the fragments of an ancient object. On some evenings, the archaeologists organized lectures ranging from topics such as ancient flora and the earliest recorded use of the familiar baking ingredient, vanilla.
Figure 2a. An example of pottery found at Tel Kabri
Figure 2b. A skull of a medium-sized mammal, likely a goat or other small mammal.
Figure 3. Getting shade from the intense sun. (L-R, Simone Strauss, Maria Fernandez, and Billy Meneses)
One of the archaeologists, Philipp Stockhammer of the Max Planck Institute, gave an evening lecture about the relatively new scientific discipline of archaeogenetics, which aims to locate and examine ancient DNA from organisms of the past. Once the ancient DNA samples of humans are collected, there is a distinction made between ‘modern humans’ that are anatomically similar to humans today to as far as approximately 200,000 years ago, and ‘archaic hominins’ (such as Neanderthal) which pre-dated Homo sapiens1. Stockhammer’s lab published two landmark papers in 2019, both in the peer-reviewed journal Science. In a July publication they reported the genome-wide sequencing of ten Iron Age to Bronze Age individuals from the ancient city of Ashkelon2, located today along the Mediterranean coast of Israel (Figure 4). The people of that age were commonly known as the Philistines. In the Bible, young David battles and overcomes the giant Philistine, Goliath. Ancient DNA analysis of Goliath’s compatriots showed their lineage was derived from Levantine origins (a region that includes modern day Syria, Lebanon, Jordan, Israel, Palestine) and combined with European gene flow resulting from migrations arriving from the north. Remarkably, in yet another application of ancient DNA, Stockhammer and his colleagues published a study of 104 humans from the Late Neolithic to Middle Bronze Age covering a 700-year timespan3. All of the 104 individuals were analyzed for kinship to one another in order to generate family pedigrees, one spanning as many as four successive generations. In addition to ancient DNA, the scientists used strontium isotope tracking from tooth samples to conclude that females migrated more frequently than males, most likely so they could marry outside of their local tribe. These findings are just a few of the examples where ancient DNA is clarifying our understanding of ancient human societies.
Whole genome sequencing has been possible since the human genome project was launched in 1990. Since then, the Broad Institute of MIT has reported the successful sequencing of over 100,000 whole genomes4. That’s equivalent to 70 petabytes of data, which translates to 1.2 billion hours of streaming music files. However, among the 3.2 billion base pairs in every human genome, there is only 0.1% variation from one human to another. Nowadays, genome sequencing is in high demand. The personal genome sequencing company 23andme, founded in 2006 by Ann Wojcicki, has more than 10 million customers seeking knowledge about their genetic inheritance5. It’s worth noting that 23andme does not sequence a person’s entire genome, only the 0.02% where variations linked to traits and disease risk have been previously reported in the scientific literature6. And unlike ancient DNA, you don’t need someone’s finger to get a DNA sample. You just have to send a saliva sample.
Figure 4. Colored symbols indicating sites where ancient DNA was collected from a period spanning the Iron Age to Bronze Age. Location of Ashkelon in modern day Israel, and of Tel Kabri where Hotchkiss students took part in an ongoing archaeological dig. (adapted from Feldman, et al)
References
1. Slatkin, Montgomery and Fernando Racimo. “Ancient DNA and human history.” Proceedings of the National Academy of Science, vol. 113, no. 23, 2016, 6380-87.
2. Feldman, Michal, et al “Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.” Science Advances, vol. 5, no. 7, 2019, eaax0061.
3. Mittnik, Alissa, et al. “Kinship-based social inequality in Bronze Age Europe.” Science. Vol. 366, no. 6466, 731-734.
4. The Broad Institute website
https://www.broadinstitute.org/news/broad-institute-sequences-its-100000th-whole-human-genome-national-dna-day
5. 23andme company website
https://customercare.23andme.com/hc/en-us/articles/202904600-Difference-Between-DNA-Genotyping-Sequencing
6. The PBS Newshour website
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