Ancient DNA and teeth show: Romans brought mules with them

The Romans were the first to bring mules to Central Europe. Before they took mules northward across the Alps in the first century, horses were the only riding animals used by the peoples there. This was revealed by genetic analyses conducted by a research group from the ArchaeoBioCenter at LMU, the State Collection for Paleoanatomy Munich, and the University of Vienna.

 

Until the end of the Iron Age in the first century before Christ, the peoples in Celtic settlements in the northern Alpine foothills exclusively bred horses. Highly prized by the Celts as “animals for the elite,” horses were chiefly used for military operations. When Romans pushed into the regions north of the Alps shortly before the birth of Christ and settled there, they took mules with them from the Mediterranean area. Mules were esteemed by the military as pack and work animals. Romans valued the horse-donkey hybrids particularly for their strength, endurance, and sure-footedness in mountainous terrain. In addition, mules can survive on less valuable feed and are more resistant to diseases than horses and donkeys.

 

Before now, the beginning of the economic and military significance of mules for the peoples in settlement regions north of the Alps was fraught with uncertainties. Even for experts, it is tricky to distinguish the archeological remains of Equidae – that is to say, horses, donkeys, and their hybrids, mules and hinnies – from each other. Most skeleton parts of animals from this family are just too similar. A team of researchers from the Chair of Paleoanatomy, Domestication Research, and the History of Veterinary Medicine at LMU, the University of Vienna, and the State Collection for Paleoanatomy Munich has now investigated ancient DNA from more than 400 equids from one Celtic and seven Roman settlements in the northern provinces of the Roman Empire – today’s southern Germany, eastern Switzerland, and Austria.

 

The researchers compared the genetic analyses with the results of traditional methods of species identification – analysis of the morphology, shape, and size of mandibular teeth and particular bones. Remains of mules were found only in the Roman settlements. Furthermore, the investigations revealed that mules can be identified not only from their ancient DNA, but also through the characteristics of their premolar teeth in particular.

 

“However, the secure identification of the horse-donkey hybrids is contingent upon access to comprehensive reference collections of equid skeletons, so that researchers can compare them against archeological finds,” explains Joris Peters, Director of the State Collection for Paleoanatomy Munich and Chair of Paleoanatomy at LMU. “DNA is not always sufficiently well preserved in archeological material to be able to identify animals with certainty. Building up comprehensive natural history collections is therefore also essential for research into past cultures.”

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JOURNAL

Journal of Archaeological Science

DOI

10.1016/j.jas.2022.105624 

Dogs are more genetically similar to ancient wolves in Asia than those in Europe, suggesting a domestication somewhere in the east

n international group of geneticists and archaeologists, led by the Francis Crick Institute, have found that the ancestry of dogs can be traced to at least two populations of ancient wolves. The work moves us a step closer to uncovering the mystery of where dogs underwent domestication, one of the biggest unanswered questions about human prehistory. 

Dogs are known to have originated from the gray wolf, with this domestication occurring during the Ice Age, at least 15,000 years ago. But where this happened, and if it occurred in one single location or in multiple places, is still unknown.

Previous studies using the archaeological record and comparing the DNA of dogs and modern wolves have not found the answer.

In their study, published in Nature today (29 June), the researchers turned to ancient wolf genomes to further understanding of where the first dogs evolved from wolves. They analysed 72 ancient wolf genomes, spanning the last 100,000 years, from Europe, Siberia and North America.

The remains came from previously excavated ancient wolves, with archaeologists from 38 institutions in 16 different countries contributing to the study. The remains included a full, perfectly preserved head from a Siberian wolf that lived 32,000 years ago. Nine different ancient DNA labs then collaborated on generating DNA sequence data from the wolves.

By analysing the genomes, the researchers found that both early and modern dogs are more genetically similar to ancient wolves in Asia than those in Europe, suggesting a domestication somewhere in the east.

However, they also found evidence that two separate populations of wolves contributed DNA to dogs. Early dogs from north-eastern Europe, Siberia and the Americas appear to have a single, shared origin from the eastern source. But early dogs from the Middle East, Africa and southern Europe appear to have some ancestry from another source related to wolves in the Middle East, in addition to the eastern source.

One possible explanation for this dual ancestry is that wolves underwent domestication more than once, with the different populations then mixing together. Another possibility is that domestication happened only once, and that the dual ancestry is due to these early dogs then mixing with wild wolves. It is not currently possible to determine which of these two scenarios occurred. 

Anders Bergström, co-first author and post-doctoral researcher in the Ancient Genomics lab at the Crick, says: “Through this project we have greatly increased the number of sequenced ancient wolf genomes, allowing us to create a detailed picture of wolf ancestry over time, including around the time of dog origins.”

“By trying to place the dog piece into this picture, we found that dogs derive ancestry from at least two separate wolf populations – an eastern source that contributed to all dogs and a separate more westerly source, that contributed to some dogs.”

The team are continuing the hunt for a close ancient wolf ancestor of dogs, which could reveal more precisely where domestication most likely took place. They are now focusing on genomes from other locations not included in this study, including more southerly regions.

As the 72 ancient wolf genomes spanned around 30,000 generations, it was possible to look back and build a timeline of how wolf DNA has changed, tracing natural selection in action.

For example, they observed that over a period of around 10,000 years, one gene variant went from being very rare to being present in every wolf, and is still present in all wolves and dogs today. The variant affects a gene, IFT88, which is involved in the development of bones in the skull and jaw. It is possible that the spread of this variant could have been driven by a change in the types of prey available during the Ice Age, giving an advantage to wolves with a certain head shape, but the gene could also have other unknown functions in wolves.

Pontus Skoglund, senior author and group leader of the Ancient Genomics lab at the Crick, says: “This is the first time scientists have directly tracked natural selection in a large animal over a time-scale of 100,000 years, seeing evolution play out in real time rather than trying to reconstruct it from DNA today.”

“We found several cases where mutations spread to the whole wolf species, which was possible because the species was highly connected over large distances. This connectivity is perhaps a reason why wolves managed to survive the Ice Age while many other large carnivores vanished.”

"Similar whole-genome time series from the Ice Age, in humans or other animals, could provide new information about how evolution happens."

Underwater jars reveal Roman period winemaking practices

 

IMAGE: FROM THE AMPHORAE TO UNDERSTANDING THE CONTENT; THIS MULTI-ANALYTICAL ANALYSIS RELIED ON ARCHAEOBOTANY AND MOLECULAR IDENTIFICATION. view more 

CREDIT: LOUISE CHASSOUANT, CC-BY 4.0 (HTTPS://CREATIVECOMMONS.ORG/LICENSES/BY/4.0/)

Winemaking practices in coastal Italy during the Roman period involved using native grapes for making wine in jars waterproofed with imported tar pitch, according to a study published June 29, 2022 in the open-access journal PLOS ONE by Louise Chassouant of Avignon University and colleagues.

The authors examined three Roman period amphorae – wine jars – from a seabed deposit near the modern harbor of San Felice Circeo, Italy, about 90 km southeast of Rome. A combination of chemical markers, plant tissue residue, and pollen provided evidence of grape derivatives and pine within the jars. The evidence suggests the amphorae were used in both red and white winemaking processes, while the pine was used to create tar for waterproofing the jars and perhaps also flavoring the wine, as has been observed at similar archaeological sites.

The grapevine pollen matches wild species from the area, suggesting these winemakers were using local plants, although it remains unclear whether these were domesticated at the time. The pine tar, on the other hand, is non-local, and was likely imported from Calabria or Sicily based on other historical sources.

The authors emphasize the benefit of this multidisciplinary approach to characterize cultural practices from archaeological artefacts. In this case, the identification of plant remains, chemical analysis, historical and archaeological records, amphorae design, and previous findings all contributed to the conclusions of this analysis, providing an example of methodology for interpreting a history beyond the artefacts which would not be possible using a single technique.

The authors add: “If there was a message to be retained from the reading of this article, it would be related to the multidisciplinary methodology to be applied. Indeed, by using different approaches to unravel the content and nature of the coating layer of Roman amphorae, we have pushed the conclusion further in the understanding of ancient practices than it would have been with a single approach.”

The freely available article in PLOS ONE: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0267129

Pests back in the middle Neolithic period – Farmers developed effective strategies to counteract them

 

IMAGE: LOWER JAW AND FRONT LIMB BONES OF WOOD MICE (APODEMUS CF. SYLVATICUS) AND BLACKTHORN FRUIT WITH GNAWING TRACES BY MICE. view more 

CREDIT: RAÜL SOTERAS, AGRICHANGE PROJECT

As early as the Neolithic period, pests posed a threat to agricultural yields, as shown by the remains of mice and insects found in prehistoric wells by a Basel-led archaeological research team. However, there are also indications that people knew how to defend against these pests – for example, by switching to less vulnerable kinds of grain.

Around 8,000 years ago, people began creating more permanent settlements in Europe and practicing agriculture. While many research projects have focused on the agricultural practices of that time, they have generally left aside the effect of pests. Particularly for the western Mediterranean region of Europe, there has been almost no record of the occurrence of harmful insects and rodents until now.,.

A study by the research group led by Professor Ferran Antolín at the University of Basel has now shown that people in southern Europe had to deal with pests such as wood mice and grain weevils even back in the middle Neolithic period – and also developed effective strategies to counteract them. The study was conducted as part of the AgriChange project, financed by the Swiss National Science Foundation. ETH Zurich and the German Archaeological Institute were also involved.

Preserved in dirt

For their study, Dr. Simone Häberle and Dr. Marguerita Schäfer examined the sediment layers of three prehistoric wells, looking for the remains of insects and small rodents. The wells are part of a Neolithic settlement Les Bagnoles (southern France) that has been dated to around 4300–3700 BCE. The waste material collected in the wells has been exceptionally well preserved thanks to the permanent wet conditions and the resulting lack of oxygen.

Unexpectedly, the archaeozoologists found the bones of more than forty wood mice in one of the wells. These were probably part of a larger population attracted by the waste and the food stored in the settlement – the farmers may have disposed of the mice they found stealing their supplies in the abandoned well. “The wood mouse therefore probably established itself in human settlements before it was ousted by the house mouse in the Bronze Age,” says Häberle. “This shows that people were already changing the natural ecosystems even back then, and that their settlements were an attractive habitat for certain wild animals.”

The samples also contained the remains of many insects – such as the grain weevil, which is only a few millimeters long and still infests grain stores today, in addition to other potentially harmful seed and ground beetles. “It’s very rare that the remains of both small mammals and insects can be examined in one place,” says Schäfer. “That makes our observations all the more relevant and suggests interesting possibilities for future research into prehistoric pests.”

Resilience against pests

The results also allow inferences to be drawn about how Neolithic farmers approached the threat of pests. “Around 4000 BCE, people in various places around the western Mediterranean switched from naked wheat, which is vulnerable to storage pests, to glume wheat,” says Antolín. “After that, evidence of grain weevils in Les Bagnoles seems to decrease.” This could indicate that the farmers developed a certain level of resilience against pests through this switch to glume wheat.

“These more resistant grains such as einkorn and emmer only account for a small part of our cultivated land today. More attention should definitely be paid to them when considering the future resilience of agriculture,” says Antolín, adding that this is a useful lesson from the past.

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JOURNAL

Animals

DOI

10.3390/ani12121511 

Famous Sterkfontein Caves deposit 1 million years older than previously thought

 

New dates for Australopithecus-bearing Sterkfontein Cave deposit places South African hominin fossils at the center of global paleo researchPrint

 

IMAGE: FOUR DIFFERENT AUSTRALOPITHECUS CRANIA THAT WERE FOUND IN THE STERKFONTEIN CAVES, SOUTH AFRICA. THE STERKFONTEIN CAVE FILL CONTAINING THIS AND OTHER AUSTRALOPITHECUS FOSSILS WAS DATED TO 3.4 TO 3.6 MILLION YEARS AGO, FAR OLDER THAN PREVIOUSLY THOUGHT. THE NEW DATE OVERTURNS THE LONG-HELD CONCEPT THAT SOUTH AFRICAN AUSTRALOPITHECUS IS A YOUNGER OFFSHOOT OF EAST AFRICAN AUSTRALOPITHECUS AFARENSIS. view more 

CREDIT: JASON HEATON AND RONALD CLARKE, IN COOPERATION WITH THE DITSONG MUSEUM OF NATURAL HISTORY.

Fossils found at the Sterkfontein Caves in South Africa reveal nearly four million years of hominin and environmental evolution. Since research began at the site in 1936 with the discovery, by Robert Broom, of the first adult hominin of the genus Australopithecus, it has become famous for the hundreds of Australopithecus fossils yielded from excavations of ancient cave infills, including iconic specimens such as the cranium known as Mrs. Ples and the Little Foot skeleton. 

The majority of Sterkfontein’s wealth of Australopithecus fossils has been excavated from an ancient cave infill called ‘Member 4’ – the richest deposit of Australopithecus fossils in the world. Over the last 56 years of Wits-led research at Sterkfontein, the age of Member 4 at Sterkfontein have remained contested, with age estimates ranging from as young as about 2 million years ago, younger than the appearance of our genus Homo, back to  about 3 million years.

New research presented in a paper published in the journal PNAS re-evaluates the age of Australopithecus from Member 4 at Sterkfontein together with the Jacovec Cavern, which contains a few additional hominin fossils in a deeper chamber in the cave.  

“The new ages range from 3.4-3.6 million years for Member 4, indicating that the Sterkfontein hominins were contemporaries of other early Australopithecus species, like Australopithecus afarensis, in east Africa,” says Professor Dominic Stratford, director of research at the caves, and one of the authors on the paper. 

The new ages are based on the radioactive decay of the rare isotopes aluminum-26 and beryllium-10 in the mineral quartz.  “These radioactive isotopes, known as cosmogenic nuclides, are produced by high-energy cosmic ray reactions near the ground surface, and their radioactive decay dates when the rocks were buried in the cave when they fell in the entrance together with the fossils,” says Professor Darryl Granger of Purdue University in the United States and lead author on the paper.

Previous dating of Member 4 has been based on dating calcite flowstone deposits found within the cave fill, but careful observations show that the flowstone is actually younger than the cave fill and so it underestimates the age of the fossils.  

“This re-assessment of the age of Sterkfontein Member 4 Australopithecus fossils has important implications for the role of South Africa on the hominin evolution stage. Younger hominins, including Paranthropus and our genus Homoappear between about 2.8 and 2 million years ago. Based on previously suggested dates, the South African Australopithecus species were too young to be their ancestors, so it has been considered more likely that Homo and Paranthropus evolved in East Africa,” says Stratford.

The new dates show that Australopithecus existed at Sterkfontein almost a million years prior to the appearance of Paranthropus and Homo, providing more time for them to evolve here, in the Cradle of Humankind, and placing the hominins from this site front and center in the history early human evolution. 

“This important new dating work pushes the age of some of the most interesting fossils in human evolution research, and one of South Africa’s most iconic fossils, Mrs Ples, back a million years to a time when, in east Africa, we find other iconic early hominins like Lucy,” says Stratford.

“The redating of the Australopithecus-bearing infills at the Sterkfontein Caves will undoubtably re-ignite the debate over the diverse characteristics of Australopithecus at Sterkfontein, and whether there could have been South African ancestors to later hominins,” says Granger.

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JOURNAL

Proceedings of the National Academy of Sciences

Fossils in the ‘Cradle of Humankind’ may be more than a million years older than previously thought

 

— The earth doesn’t give up its secrets easily – not even in the “Cradle of Humankind” in South Africa, where a wealth of fossils relating to human evolution have been found.

For decades, scientists have studied these fossils of early human ancestors and their long-lost relatives. Now, a dating method developed by a Purdue University geologist just pushed the age of some of these fossils found at the site of Sterkfontein Caves back more than a million years. This would make them older than Dinkinesh, also called Lucy, the world’s most famous Australopithecus fossil.

The “Cradle of Humankind” is a UNESCO World Heritage Site in South Africa that comprises a variety of fossil-bearing cave deposits, including at Sterkfontein Caves. Sterkfontein was made famous by the discovery of the first adult Australopithecus, an ancient hominin, in 1936. Hominins includes humans and our ancestral relatives, but not the other great apes. Since then, hundreds of Australopithecus fossils have been found there, including the well-known Mrs. Ples, and the nearly complete skeleton known as Little Foot. Paleoanthropologists and other scientists have studied Sterkfontein and other cave sites in the Cradle of Humankind for decades to shed light on human and environmental evolution over the past 4 million years.

Darryl Granger, a professor of earth, atmospheric, and planetary sciences in Purdue University’s College of Science, is one of those scientists, working as part of an international team. Granger specializes in dating geologic deposits, including those in caves. As a doctoral student, he devised a method for dating buried cave sediments that is now used by researchers all over the world. His previous work at Sterkfontein dated the Little Foot skeleton to about 3.7 million years old, but scientists are still debating the age of other fossils at the site.

In a study published in the Proceedings of the National Academy of Sciences, Granger and a team of scientists including researchers from the University of the Witwatersrand in Johannesburg, South Africa and the University Toulouse Jean Jaurès in France, have discovered that not only Little Foot, but all of the Australopithecus-bearing cave sediments date from about 3.4 to 3.7 million years old, rather than 2-2.5 million years old as scientists previously theorized. That age places these fossils toward the beginning of the Australopithecus era, rather than near the end. Dinkinesh, who hails from Ethiopia, is 3.2 million years old, and her species, Australopithecus africanus, hails back to about 3.9 million years old.

Sterkfontein is a deep and complex cave system that preserves a long history of hominin occupation of the area. Understanding the dates of the fossils here can be tricky, as rocks and bones tumbled to the bottom of a deep hole in the ground, and there are few ways to date cave sediments. 

In East Africa, where many hominin fossils have been found, the Great Rift Valley volcanoes lay down layers of ash that can be dated. Researchers use those layers to estimate how old a fossil is. In South Africa – especially in a cave – the scientists don’t have that luxury. They typically use other animal fossils found around the bones to estimate their age or calcite flowstone deposited in the cave. But bones can shift in the cave, and young flowstone can be deposited in old sediment, making those methods potentially incorrect. A more accurate method is to date the actual rocks in which the fossils were found. The concrete-like matrix that embeds the fossil, called breccia, is the material Granger and his team analyze.

“Sterkfontein has more Australopithecus fossils than anywhere else in the world,” Granger said. “But it’s hard to get a good date on them. People have looked at the animal fossils found near them and compared the ages of cave features like flowstones and gotten a range of different dates. What our data does is resolve these controversies. It shows that these fossils are old – much older than we originally thought.”

Granger and the team used accelerator mass spectrometry to measure radioactive nuclides in the rocks, as well as geologic mapping and an intimate understanding of how cave sediments accumulate to determine the age of the Australopithecus-bearing sediments at Sterkfontein,

Granger and the research group at the Purdue Rare Isotope Measurement Laboratory (PRIME Lab) study so-called cosmogenic nuclides and what they can reveal about the history of fossils, geological features and rock. Cosmogenic nuclides are extremely rare isotopes produced by cosmic rays —high-energy particles that constantly bombard the earth. These incoming cosmic rays have enough energy to cause nuclear reactions inside rocks at the ground surface, creating new, radioactive isotopes within the mineral crystals. An example is aluminum-26: aluminum that is missing a neutron and slowly decays to turn into magnesium over a period of millions of years. Since aluminum-26 is formed when a rock is exposed at the surface, but not after it has been deeply buried in a cave, PRIME lab researchers can date cave sediments (and the fossils within them) by measuring levels of aluminum-26 in tandem with another cosmogenic nuclide, beryllium-10.

In addition to the new dates at Sterkfontein based on cosmogenic nuclides, the research team made careful maps of the cave deposits and showed how animal fossils of different ages would have been mixed together during excavations in the 1930s and 1940s, leading to decades of confusion with the previous ages. “What I hope is that this convinces people that this dating method gives reliable results,” Granger said. “Using this method, we can more accurately place ancient humans and their relatives in the correct time periods, in Africa, and elsewhere across the world.”

The age of the fossils matters because it influences scientists’ understanding of the living landscape of the time.  How and where humans evolved, how they fit into the ecosystem, and who their closest relatives are and were, are pressing and complex questions. Putting the fossils at Sterkfontein into their proper context is one step towards solving the entire puzzle.

Population bottlenecks that reduced genetic diversity were common throughout human history

 

Analysis shows that more than half of historical groups experienced founder events

 

IMAGE: FROM CONTEMPORARY AND ANCIENT DNA, UC BERKELEY RESEARCHERS ESTIMATED WHEN POPULATION BOTTLENECKS OCCURRED FOR SEVERAL HUNDRED GROUPS AROUND THE WORLD AND THROUGHOUT RECENT HUMAN HISTORY. THE COLORS INDICATE THE NUMBER OF GENERATIONS THE BOTTLENECK OR FOUNDER EVENT PRECEDED THE INDIVIDUALS WHOSE DNA WAS SEQUENCED. view more 

CREDIT: RÉMI TOURNEBIZE, UC BERKELEY

Human populations have waxed and waned over the millennia, with some cultures exploding and migrating to new areas or new continents, others dropping to such low numbers that their genetic diversity plummeted. In some small populations, inbreeding causes once rare genetic diseases to become common, despite their deleterious effects.

A new analysis of more than 4,000 ancient and contemporary human genomes shows how common such “founder events” were in our history. A founder event is when a small number of ancestral individuals gives rise to a large fraction of the population, often because war, famine or disease drastically reduced the population, but also because of geographic isolation — on islands, for example — or cultural practices, as among Ashkenazi Jews or the Amish.

More than half of the 460 groups represented by these individuals had experienced a population bottleneck somewhere in their past that decreased their genetic diversity and likely increased the incidence of recessive hereditary diseases.

The analysis by population geneticists at the University of California, Berkeley, is the first comprehensive look at founder events across a broad swath of human populations over the past 10,000 years or so of human history and pinpoints when these events occurred.

According to the authors, the findings will be useful not only to archeologists and historians tracking the movement and mixing of populations around the world, but also to scientists and doctors studying human genetic variation. The genetic diseases of inbred populations have helped scientists find many disease-causing mutations in the human genome and discover the causes of numerous genetic and inherited diseases.

“Genomic data is really powerful because it not only tells us about where we come from, it tells us about our history at various different time scales, and you can look at how closely related different individuals are to each other,” said senior author Priya Moorjani, an assistant professor of molecular and cell biology at UC Berkeley. “But also, it tells us about bits of DNA that are functionally important and can cause diseases. So, they become quite important to study from a biomedical perspective.”

Many of the populations represented by individuals in the sample were or are much more inbred than ethnic Ashkenazi Jews, who some scientists have estimated once dwindled to a population of less than a couple of thousand individuals about 1,000 years ago. The Onge, a group in the Andaman Islands of the Indian Ocean, underwent a population bottleneck 10 times more extreme than that of Ashkenazi Jews, and today it numbers only about 100 individuals.

The researchers found that many Native American populations and groups from Oceania and South Asia also suffered severe population bottlenecks. Some coincide with known historical events — for instance, the residents of Rapa Nui (Easter Island) underwent a founder event about 260 years ago, coincident with the migration of Europeans to the island.

Others correlate well with the known movement of peoples into an area and with changing cultural artifacts and practices. For example, Anatolian farmers and Eurasian steppe pastoralists moved into Europe between about 4,000 and 10,000 years ago, and the groups intermingled with existing European hunter-gatherers.

“The first surprise was that over half the groups we surveyed had evidence for founder events,” Moorjani said. “So, it's not just Ashkenazi Jews or Finns that have a unique history, but many populations living today have had strong founder events — in fact, stronger founder events than these two groups, like several contemporary South Asian groups, hunter-gatherers or populations living on islands. And many of these groups would be really important for prioritizing functional studies. We have learned so much about genetic variation from groups like Ashkenazi Jews and Finns that the potential for discovery is really high if we can expand these studies to other worldwide populations.”

Moorjani, former UC Berkeley undergraduate Gillian Chu and first author Rémi Tournebize, now a postdoctoral fellow at the Instituto Gulbenkian de Ciência in Oeiras, Portugal, published their findings today (June 23) in the journal PLOS Genetics.

Working with incomplete ancient DNA

The analysis was made possible by a genomics analysis program called ASCEND (Allele Sharing Correlation for the Estimation of Non-equilibrium Demography), which was created by Tournebize and Moorjani specifically to analyze partial genome sequences — in particular, ancient DNA. This DNA is generally sequenced from bones or teeth that are hundreds to thousands of years old and represent not only our Homo sapiens ancestors, but other human groups, like Neanderthals and Denisovans.

Such DNA is typically damaged so that only a portion of the individual’s genome can be sequenced. But since human genomes contain about 3 billion base pairs of DNA, even a mere 100,000 base pairs can provide information about that person’s heritage, Moorjani said. Many genome analysis programs today work only with nearly complete genome sequences, primarily from contemporaneous peoples.

“While ancient DNA is really powerful, one of the challenges is that it has much lower quality compared to data from living people, because once an individual dies, the DNA starts degrading, and it's very hard to recover very high quality data compared to present-day individuals,” Moorjani said. “But the majority of the demographic inference methods are built thinking that you can get large numbers of samples from populations and high-quality data across the genome. Our methods were developed to leverage this low-coverage, highly degraded DNA to really understand our evolutionary history.”

ASCEND measures the sharing of DNA between individuals within and across populations. When a population undergoes a founder event, its size dwindles to a few individuals. The offspring of these founder individuals, in turn, share long blocks in their genome that are inherited “identical by descent” from these few ancestors. As time passes, these blocks will become smaller due to crossover events that occur during meiosis, when chromosomes duplicate and mix before segregating to egg and sperm cells. The rate of crossovers is well characterized and provides a kind of molecular clock. The ASCEND program compares how large the shared blocks are within individuals in a population to infer when the individuals might have shared a common ancestor, i.e., when a founder event occurred in the population’s history. A large-scale, pair-wise statistical comparison of genomic DNA allows an estimation of when and how intense the bottleneck was.

The genome data came from the Allen Ancient DNA Resource, a database created by David Reich and collaborators at Harvard University, with whom Moorjani earned her Ph.D. The public database currently includes available present-day and ancient genomes from more than 14,000 individuals and more than a million common mutations or variants — single nucleotide polymorphisms, or SNPs — within those DNA sequences. At the time Moorjani started her study, the database held fewer ancient and modern genomes. She and Tournebize focused on the genomes of 2,310 present-day individuals from 184 groups, then expanded their study to look at an additional 1,947 individuals representing 164 worldwide ancient populations.

“Applying this method, we uncovered founder events that had not been identified previously, for instance, in populations from ancient Morocco or Siberia,” Tournebize said. “As a French guy, I was really surprised to discover a founder event in Basque people, dated around the 1st century BCE and possibly related to Roman colonization of this region. We'll need more genetic data, especially from ancient samples, and collaboration with social scientists to understand the detailed historical events that might be associated with this bottleneck.”

To test the ASCEND program in other species, Moorjani and Tournebize turned to dogs. The genome sequences of about 40 modern dog breeds are available, so the researchers ran them through the program to determine how long ago founder events occurred in breeds ranging from African village dogs — the least inbred — to breeds like boxers, dobermans and rottweilers, the most inbred. Consistent with the establishment of many dog breeds during Victorian times, they confirmed extreme founder events in most breeds within the last 25 generations, that is, 75 to 125 years.

“Dogs are so interesting that it was exciting to expand the analysis to another species, but it was really sad to see how strong the founder events are,” she said. “Most dogs these days have so many more problems than village dogs. Their rates of cancers and congenital diseases are pretty high. And that's largely because of these very severe founder events in their history during breed formation.”

Population mixing

In another recent paper, Moorjani and her colleagues described a different genomics analysis program that analyzes a single individual’s genome, whether complete or partial, and estimates the amount of admixture of other populations over time. The researchers used this program, called DATES (Distribution of Ancestry Tracts of Evolutionary Signals), to analyze about 1,100 ancient genomes and reconstruct major gene flow events in Europe since about 10,000 BCE.

One surprising finding was that the genomes of Anatolian farmers, who lived in what is today Turkey, show admixture of genes from Iranian Neolithic farmers long before the advent of agriculture in Anatolia. This suggests that farming did not originate in Anatolia, as many archeologists have suggested.

“We had samples of Anatolian hunter-gatherers who don't have Iranian ancestry and samples of Anatolian early farmers who have Iranian ancestry, but we didn't know when this mixture occurred,” she said. “In our case, we were able to actually figure out the key time point when this group formed, which predates agriculture in the region. And based on that, we are able to tell that farming must have spread through cultural diffusion, rather than having originated in Anatolia.”

Another discovery was the timing for the formation of Bronze Age steppe pastoralists. These groups made a large impact, both genetically and demographically, in Eurasia during the Bronze Age and, according to some studies, are responsible for the spread of Indo-European languages. Archeological studies suggest these groups inhabited regions of the steppe in present day Russia and Ukraine from 3,300 to 2,600 BCE. Using the genetic dating method, the researchers found these groups were genetically formed between 4,400 and 4,000 BCE, predating previous findings by over a half a millennium.

“Our study emphasizes the power of dating population mixtures and formation, rather than just using temporal sampling and tracking the presence or absence of a particular ancestry in ancient samples, which is highly dependent on sampling choice and density,” said UC Berkeley postdoctoral fellow Manjusha Chintalapati, first author of the paper.

Moorjani plans to use ASCEND and DATES to take a closer look at many ancient populations, in particular those in India, that have strong founder events that suggest the possibility of many unrecognized recessive diseases that could help to reduce disease burden in the group and shed light on the basic functions of human genes.

“In our analysis, we find that 64% of South Asian populations have very strong founder events, so we are trying to do targeted sample collection in these groups to characterize some of the deleterious variants due to the founder events,” she said.

DATES, for example, suggests that each isolated population in South Asia has admixtures of local indigenous hunter-gatherers, Near Eastern farmers and Steppe pastoralists or herders, but in different proportions that remained the same for many hundreds of generations. Strikingly, most European populations also derive ancestry from similar three groups, though the groups have continued to freely mix with each other after the initial mixture.

“It's really exciting to do this work at Berkeley, where Allan Wilson's lab came up with the idea of a molecular clock, and to continue on his path to use genomic data for learning about the timing of different evolutionary events,” Moorjani said, referring to the late biochemist and pioneer of molecular evolution, who died in 1991.

The two studies were funded by the Burroughs Wellcome Fund, a Sloan Research Fellowship and the National Institutes of Health (R35GM142978).

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JOURNAL

PLoS Genetics

DOI

10.1371/journal.pgen.1010243