Over the past decade, the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences researcher FU Qiaomei has used ancient DNA technology to reveal the history of ancient human populations, specifically those in East Asia.
Revealing the Genomic Sequence of Archaic Humans
Skulls were displayed as part of the Neanderthal exhibition at the Musee de l'Homme in Paris on March 26, 2018. / AFP PHOTO / STEPHANE DE SAKUTIN
To unravel the history of human DNA, researchers reconstructed the genome of two extinct groups of archaic humans -Denisovans and Neanderthals. Researchers also mapped the history of global population migration and their interactions. The team uncovered the genetic structure of the oldest East Asian people, which revealed adaptive genetic changes during the East Asian Ice Age, and traced the formation of population patterns in Northern and Southern China and the origin of Austronesian people in southern China reports EurekAlert.
In the study published in the journal Cell, titled "Evolving ancient DNA techniques and the future of human history," the team reviews the history of ancient DNA technological development, discusses technical bottlenecks researchers face, suggests solutions, and assesses the future of the technology.
A key technological development discussed by researchers is high-throughout sequencing, a technique for rapidly sequencing large amounts of DNA. Theoretically, it can sequence all DNA molecules per sample.
Before the technique became commonplace, the field of aDNA relied on polymerase chain reaction techniques for sequence-specific DNA fragments. Researchers only extracted a limited amount of DNA information with the mentioned technology and faced challenges distinguishing genuine aDNA from contaminants.
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Advancements in aDNA Sequencing
Complementing the numerous advances in sequencing, aDNA researchers developed improved methods of DNA library construction to reflect the characteristics of aDNA better. One of these methods, partial uracil-DNA glycosylase treatments, and single-stranded DNA library constructions are two of the most vital.
Partial UDG treatment preserves part of the DNA damage signal at the fragment tips of DNA while also removing most aDNA damage throughout the molecule. This method improved the accuracy of sequencing aDNA results while preserving the gestures of aDNA required for validation.
Meanwhile, single-stranded DNA library construction enables the direct sequencing of denatures and damaged DNA fragments lost in typical DNA library construction techniques.
However, advances in library construction have limited efficacy since aDNA samples typically contain large amounts of environmental DNA. as a result, useful endogenous ancient DNA sequences often account for only less than 1% of the resulting sequence.
In an effort to tackle the problem, researchers applied DNA capture technology to the field of aDNA by creating DNA and RNA probes with similar sequences to their targets. After researchers added the probes to extracted samples, the target aDNA binds to the probes and is "fished out" from the massive amount of environmental DNA.
This technology is currently being widely used in aDNA human genome research. As of now, more than two-thirds of aDNA data come from data captured using the "1240k" probe set.
Not only does DNA capture technology improve the efficiency of sequencing aDNA, but it also allows the recovery of usable data from gathered samples that otherwise would be too degraded for further analysis.
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