Where does our hat come from: The largest family tree in the world has been created

If someone told you that you have roots in Africa or in the Land of Fire, how would you react? A new, huge pedigree for all mankind attempts to summarize the way in which all people living today relate both to each other and to the ancients ancestors us. And to break various myths that are based on intolerant and racist perceptions that are perpetuated as other unscientific institutions

To build this family tree or genealogy, researchers sifted thousands of genome sequences collected from both modern and ancient humans, as well as ancient human relatives, according to a new study published in the journal Science.

These genomes originated from 215 populations scattered around the world. Using a computer algorithm, the team uncovered distinct patterns of genetic variation within these sequences, noting where they matched and where they differed. Based on these patterns, the researchers drew theoretical lines of origin between the genomes and got an idea of ​​which gene variants, or allelic genes, were most likely brought by the common ancestors of these humans.

Where did the ancestors of those associated and where did they move?

In addition to mapping these genealogical relationships, the team approached where in the world the common ancestors of the related individuals lived. They assessed these sites based on the age of the sample genomes and the location where each genome was sampled.

“The way we estimated where our ancestors lived is, in fact, very early,” said first author Anthony Wilder Wohns, who was a doctoral student at Oxford University’s Big Data Institute during the study. Despite their limitations, the data still record important events in human evolutionary history. For example, we certainly see overwhelming evidence of the “Outside of Africa” ​​event, ie its initial spread Homo Sapiens from East Africa to Eurasia and beyond, “said Wohns, who is now a postdoctoral fellow at MIT and Harvard’s Broad Institute.

The method used by the researchers “works well to improve known ancestral positions and, as sampling improves, has the potential to detect currently unknown human movements,” wrote Aida Andrés, an associate professor in the Department of Genetics, Evolution and Environment. of University College London’s Institute of Genetics (UCL), and Jasmin Rees, PhD candidate at the UCL Institute of Genetics, in a commentary also published in the journal Science on Thursday. Thus, in the future, when more data are available, such analyzes could potentially reveal chapters of human history that are currently unknown to us.

Building the human family tree

To build a unified genealogy of humanity, the researchers first collected genomic data from various large, publicly available datasets, such as the 1000 Genome Diversity Program, the Human Genome Diversity Program, and the Simons Diversity Program. From these datasets, they collected about 3,600 high-quality genome sequences from modern humans. “High quality” genome sequences are those with very few gaps or errors, which are largely assembled in the right order, according to a 2018 report in the journal Nature Biotechnology.

High-quality genomes from ancient humans were harder to find, as DNA from ancient specimens tends to be severely degraded, Wohns said. However, looking at already published research, the team was able to find eight high-quality genomes of ancient humans to include in their tree. These included three Neanderthal genes, one of which is believed to be over 100,000 years old, one Denisova genome between 74,000 and 82,000 years old, and four genomes from a nuclear family that lived in the Altai Mountains of Russia about 4,600 years ago. (The Neanderthal and the Denisovans are extinct relatives of Homo sapiens).

In addition to these high-quality ancient genomes, the team identified more than 3,500 additional, lower-quality genomes with significant degradation, ranging in age from a few hundred to several thousand years, Wohns said. These degraded genomes were not included in the main tree generation assay, but the team sifted the fragments to see which isolated alleles could be found in the samples. These fragmentary data helped the researchers confirm when different alleles first appeared in the genealogical record, since the samples from which the genomes came were dated by carbon.

The ancient genomes provide a “unique snapshot of genetic diversity in the past” that could help reveal when and where a genetic variant first appeared and how it then spread, Andrés and Rees told Live Science in a joint statement. . “While this study does not incorporate low-quality ancient genomes into tree construction, their use to inform the age of variants within the tree remains strong for these media and promises many exciting developments in the future.”

Wohns and his colleagues used this data to re-examine whether the lineages described in their family tree made sense in terms of time – and, in most cases, did. “It is very reassuring to see that 90 more than 90% of the time, we are consistent with samples that archaeologists can date with radiocarbon,” Wohns said. “But there are, you know, 5% or 10% of these genetic variants where we see inconsistent estimates,” he said, as to when they first appeared, according to conflicting results from the archaeological record and estimates made by their tree-building algorithm. In those cases, the team adjusted its tree to reflect time that could be confirmed by radio dating, he said.

Geographical analysis and constraints

Although based on just a few thousand genome samples, the group’s final family tree “actually captures several things about the genealogy of all of humanity,” Wohns said. Using the tree as a scaffolding, the team then carried out its geographical analysis to see when and where the theoretical ancestors of the sampled populations probably lived. From this, not only did they find clear evidence of migration from Africa, but they also uncovered possible evidence of interactions between Homo sapiens and now extinct humanoids such as the Denisovans, he said.

For example, their results showed that the ancestors of modern humans could be found in Papua New Guinea some 280,000 years ago, hundreds of thousands of years before the first known evidence of modern humans inhabiting the area. “This does not necessarily mean that Homo Sapiens really took over the area so long ago,” but it does suggest that there is a genetic variant that is found only in this area and shows that there is a really deep origin where it is not found elsewhere, “he said. .

Part of this unique origin may come from the reproduction of modern humans with Denisovans, as also suggested in a 2019 report in Cell magazine, which found genomic evidence that modern humans crossed with multiple Denisovans.

“The genealogical trees created in this study will undoubtedly prove useful to those who study human evolution,” but the methods and data used to construct these trees “do not come without their limitations,” wrote Andrés and Rees in their comment.

One limitation is that most genomic sequences have taken place in Eurasian populations, so although the new study incorporated thousands of modern genomes, the data may not fully capture global genetic diversity. “The further integration of underrepresented populations will continue to address this constraint,” they said.

“There is a lot of uncertainty in these estimates,” Wohns said of the team’s recent results. “If we did not have the genome of everyone who ever lived, and where and when they lived, that is the only way to get the truth.” The team reconstructed human history as closely as possible based on the data at its disposal, but with more genome samples and more sophisticated software, the tree could certainly be improved, he said.

“The nice thing about the methods we created is that they could work with millions of potential samples,” Wohns said. Wohns said he is now working on developing new machine learning algorithms to improve the team’s assessments of where and when our ancestors lived. In a separate project, he plans to use the same method of creating trees to better understand the genetic basis of human disease. Its goal is to do this by locating the origin of disease-related alleles and then reconstructing how and when these gene variants spread to different populations.

The same tree-planting method could also be used to trace the evolutionary history of other organisms, such as bees or cattle, and even infectious agents, such as viruses, he added.

“The power and analysis of tree logging methods promise to help clarify the evolutionary history of humans and other species,” Andrés and Rees wrote in their commentary. “It is possible that the most powerful ways of drawing conclusions about evolutionary history in the future will be firmly rooted in these methods.”