A new and formidable family tree for all of humanity attempts to summarize how all humans alive today relate to each other and to our ancient ancestors.
To build a family tree, or genealogy, researchers sifted through thousands of genome Sequences collected from both modern and ancient humans, as well as ancient relatives of humans, according to a new study published Thursday (February 24) in the journal. to know. These genomes came from 215 groups scattered around the world. Using a computer algorithm, the team revealed distinct patterns of hereditary Difference within these sequences, highlighting where they coincided and where they differed. Based on these patterns, the researchers drew theoretical lines of descent between the genomes and came up with an idea of which genetic variants, or alleles, were likely carried by these people’s common ancestors.
In addition to mapping these genealogical relationships, the team approximated where in the world the common ancestors of the sequenced individuals lived. They estimated these locations based on the ages of the genomes sampled and the location at which each genome was sampled.
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“The way we estimated where ancestors lived, in particular, is very preliminary,” said first author Anthony Wilder Wons, who was a doctoral student at the University of Oxford’s Big Data Institute at the time of the study. Despite its limitations, the data still captures key events in humans evolutionary Date. For example, “We definitely see compelling evidence of Happening outside Africa“meaning the initial dispersal of sane man From East Africa to Eurasia and beyond, said Wons, now a postdoctoral researcher at the Broad Institute at MIT and Harvard University.
The method the researchers used “works well to improve known ancestral sites and, as sampling improves, has the potential to identify currently unknown human movements,” said Aida Andress, associate professor in the Department of Genetics, Evolution and Environment at University College London. (UCL) Institute of Genetics, and Jasmine Rais, a doctoral student at the UCL Institute of Genetics, wrote in comment, which was also published in Science on Thursday. Therefore, in the future, when more data becomes available, such analyzes can likely reveal chapters of human history that are currently unknown to us.
Building a human family tree
To build a unified lineage for humanity, the researchers first collected genetic data from several large, publicly available datasets, including the 1000 Genomes Project, the Human Genome Diversity Project, and the Simmons Genome Diversity Project. From these data sets, they collected about 3,600 high-quality genome sequences from modern humans. “High-quality” genome sequences are those with very few gaps or errors, and which are largely assembled in the correct order, according to a 2018 report in the journal. nature biotechnology.
Since then, it has been difficult to obtain high-quality genomes from ancient humans DNA Wohns said older specimens tend to deteriorate severely. However, in researching through previously published papers, the team was able to find eight high-quality ancient hominin genomes to include in their tree. These included three Neanderthals The genome, one thinks to be over 100,000 years old; Denisovan genome Approximately 74,000 to 82,000 years ago; And four genomes are from a nuclear family that lived in the Altai Mountains in Russia about 4,600 years ago. (Neanderthals and Denisovans became extinct relatives sane man.)
In addition to these high-quality ancient genomes, the team identified more than 3,500 additional low-quality genomes with significant degradation, ranging in age from a few hundred to several thousand years, Wons said.
These degraded genomes did not enter into the main tree-building analysis, but the team searched the fragments to see which isolated alleles could be identified in the samples. This fragmented data helped the researchers ensure that the different alleles first appeared in the genealogical record, given that the samples from which the genomes came were radiocarbon dated.
Ancient genomes offer a “unique snapshot of genetic diversity in the past,” which can help reveal when and where the genetic variant first appeared, and how it subsequently spread, Andres and Reese told Live Science in a joint statement. “While this study does not incorporate ancient, low-quality genomes into the construction of the tree, its use to inform the age of variants within the tree remains powerful for these means, and promises many exciting developments in the future.”
Wohns and colleagues used this data to double-check whether the pedigree lines depicted in their family tree were rational and timely — and in most cases, they did.
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“It is very reassuring to see…more than 90% of the time, we agree with the samples that Archaeologists “Radiocarbon dating can be done,” Wohns said. But there is, you know, 5[%] or 10% of those genetic variants where we see conflicting estimates “in terms of their first appearance, according to conflicting results from the archaeological record and estimates made by their tree-building algorithm,” he pointed out. In these cases, the team modified the tree to reflect the timing at which Confirm it by radiocarbon dating, he said.
Although it is based on a few thousand genome samples, the team’s final family tree “actually captures a lot of lineages for all of humanity,” Wons said. Using the tree as a scaffold, the team then conducted their geographic analysis, to see when and where their isotopic ancestors were likely to live in the sample. From this, they not only found clear evidence of migration out of Africa, but also discovered potential evidence for interactions between sane man and hominins that are now extinct, such as the Denisovans, he said.
For example, their results indicated that the ancestors of modern humans could be found in Papua New Guinea about 280,000 years ago, hundreds of thousands of years before the first known evidence of modern human habitation in the region. This does not necessarily indicate that H. sane It’s actually occupied the area for a long time, “but it probably suggests that there’s some genetic variation that’s only found in that area, and suggests that there’s a really deep ancestry that isn’t found anywhere else,” he said.
Some of this unique lineage may stem from modern humans interbreeding with Denisovans, as also suggested in a 2019 report in the journal. cellwhich found genetic evidence of modern humans interbreeding with multiple Denisovans.
“The trees generated in this study will undoubtedly prove useful to those who study human evolution,” Andres and Reese write in their commentary, but the methods and data used to construct said trees “are not without their limitations.” One limitation is that most of the genetic sequencing has been done in Eurasian communities, so although the new study included thousands of recent genomes, the data may not fully capture global genetic diversity, they told Live Science in an email. “Further integration of the underrepresented population will continue to address this limitation,” they said.
“There is a lot of uncertainty in these estimates,” Wons said of the team’s latest findings. “Unless we have the genomes of everyone who has ever lived, where and when they lived, that’s the only way we can get the truth out.” The team reconstructed human history as closely as possible with the available data, but with more genome samples and more sophisticated software, the tree can certainly be improved upon.
Related: Pictures: Searching for extinct humans in ancient cave mud
“The nice thing about the methods we’ve created is that they will work with millions of potential samples,” Wohns said. “So, as we have more data, we’ll get better estimates.”
Wohns said he is now developing new machine-learning algorithms to improve the team’s estimates of where and when our ancestors lived. In a separate project, he plans to use the same tree-building method to better understand the genetic basis of human disease. It aims to do this by determining the point of origin of disease-associated alleles and then reconstructing how and when these genetic variants spread across different populations.
The same tree-building method can also be used to trace the evolutionary history of other organisms, such as honey bee Or livestock, and even infectious agents, such as Viruseshe added.
“The strength and accuracy of tree-logging methods promise to help clarify the evolutionary history of humans and other species,” Andres and Rees wrote in their commentary. “Probably the most powerful way to infer the evolutionary history going forward is to ground it firmly in these methods.”
Editor’s Note: This article was updated at 10AM on February 25, 2022, with additional comments from Aida Andres and Jasmine Reis. The original article was published at 7 AM ET on the same day.
Originally published on Live Science.
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