̽��ֱ�� of Cambridge - Toomas Kivisild

First Peoples: two ancient ancestries ‘reconverged’ with settling of South America

fpjl2 — Thu, 31 May 2018 18:01:52 +0000

Recent research has suggested that the first people to enter the Americas split into two ancestral branches, the northern and southern, and that the “southern branch” gave rise to all populations in Central and South America.

Now, a study shows for the first time that, deep in their genetic history, the majority – if not all – of the Indigenous peoples of the southern continent retain at least some DNA from the “northern branch”: the direct ancestors of many Native communities living today in the Canadian east.

̽��ֱ��latest findings, published today in the journal Science, reveal that, while these two populations may have remained separate for millennia – long enough for distinct genetic ancestries to emerge – they came back together before or during the expansion of people into South America.

̽��ֱ��new analyses of 91 ancient genomes from sites in California and Canada also provide further evidence that the first peoples separated into two populations between 18,000 and 15,000 years ago. This would have been during or after migrating across the now-submerged land bridge from Siberia along the coast.

Ancient genomes from sites in Southwest Ontario show that, after the split, Indigenous ancestors representing the northern branch migrated eastwards to the great lakes region. This population may have followed the retreating glacial edges as the Ice Age began to thaw, say researchers.

̽��ֱ��study also adds to evidence that the prehistoric people associated with Clovis culture – named for 13,000-year-old stone tools found near Clovis, New Mexico, and once believed to be ancestral to all Native Americans – originated from ancient peoples representing the southern branch.

This southern population likely continued down the Pacific coast, inhabiting islands along the way. Ancient DNA from the Californian Channel Islands shows that initial populations were closely related to the Clovis people.

Yet contemporary Central and South American genomes reveal a “reconvergence” of these two branches deep in time. ̽��ֱ��scientific team, led by the universities of Cambridge, UK, and Illinois Urbana-Champaign, US, say there must have been one or a number of “admixture” events between the two populations around 13,000 years ago.

They say that the blending of lineages occurred either in North America prior to expansion south, or as people migrated ever deeper into the southern continent, most likely following the western coast down.

“It was previously thought that South Americans, and indeed most Native Americans, derived from one ancestry related to the Clovis people,” said Dr Toomas Kivisild, co-senior author of the study from Cambridge’s Department of Archaeology.

“We now find that all native populations in North, Central and South America also draw genetic ancestry from a northern branch most closely related to Indigenous peoples of eastern Canada. This cannot be explained by activity in the last few thousand years. It is something altogether more ancient,” he said.

Dr Ripan S. Malhi, co-senior author from Illinois Urbana-Champaign, said: “Working in partnership with Indigenous communities, we can now learn more about the intricacies of ancestral histories in the Americas through advances in paleogenomic technologies. We are starting to see that previous models of ancient populations were unrealistically simple.”

Present day Central and South American populations analysed in the study were found to have a genetic contribution from the northern branch ranging between 42% to as high as 71% of the genome.

Surprisingly, the highest proportion of northern branch genetics in South America was found way down in southern Chile, in the same area as the Monte Verde archeological site – one of the oldest known human settlements in the Americas (over 14,500 years old).

“It’s certainly an intriguing finding, although currently circumstantial – we don’t have ancient DNA to corroborate how early this northern ancestral branch arrived,” said Dr Christiana Scheib, first author of the study, who conducted the work while at the ̽��ֱ�� of Cambridge.

“It could be evidence for a vanguard population from the northern branch deep in the southern continent that became isolated for a long time – preserving a genetic continuity.

“Prior to 13,000 years ago, expansion into the tip of South America would have been difficult due to massive ice sheets blocking the way. However, the area in Chile where the Monte Verde site is located was not covered in ice at this time,” she said.

“In populations living today across both continents we see much higher genetic proportions of the southern, Clovis-related branch. Perhaps they had some technology or cultural practice that allowed for faster expansion. This may have pushed the northern branch to the edges of the landmass, as well as leading to admixture encounters.”

While consultation efforts varied in this study from community-based partnerships to more limited engagement, the researchers argue that more must be done to include Indigenous communities in ancient DNA studies in the Americas.

̽��ֱ��researchers say that genomic analysis of ancient people can have adverse consequences for linked Indigenous communities. Engagement work can help avoid unintended harm to the community and ensure that Indigenous peoples have a voice in research.

“ ̽��ֱ��lab-based science should only be a part of the research. We need to work with Indigenous communities in a more holistic way,” added Schieb, who has recently joined the ̽��ֱ�� of Tartu’s Institute of Genomics, where Kivisild also holds an affiliation.

“From the analysis of a single tooth, paleogenomics research can now offer information on ancient diet and disease as well as migration. By developing partnerships that incorporate ideas from Native communities, we can potentially generate results that are of direct interest and use to the Indigenous peoples involved,” she said.

New research using ancient DNA finds that a population split after people first arrived in North America was maintained for millennia before mixing again before or during the expansion of humans into the southern continent.

̽��ֱ��lab-based science should only be a part of the research. We need to work with Indigenous communities in a more holistic way

Dr Christiana Scheib

Scheib/Kivisild/Mahli

Two of the four possible combinations of ancient admixture highlighted by the researchers.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

Yes

Genetic study suggests present-day Lebanese descend from biblical Canaanites

fpjl2 — Thu, 27 Jul 2017 16:02:17 +0000

Scientist have sequenced the entire genomes of 4,000-year-old Canaanite individuals who inhabited the Near East region during the Bronze Age, and compared these to other ancient and present-day populations. ̽��ֱ��results, published in the American Journal of Human Genetics, suggest that present-day Lebanese are direct descendants of the ancient Canaanites.

̽��ֱ��Near East is often described as the cradle of civilisation. ̽��ֱ��Bronze Age Canaanites, later known as the Phoenicians, introduced many aspects of society that we know today - they created the first alphabet, established colonies throughout the Mediterranean and were mentioned several times in the Bible.

However, historical records of the Canaanites are limited. They were mentioned in ancient Greek and Egyptian texts, and the Bible which reports widespread destruction of Canaanite settlements and annihilation of the communities. Experts have long debated who the Canaanites were genetically, what happened to them, who their ancestors were and if they had any descendants today.

In the first study of its kind, an international team of scientists have uncovered the genetics of the Canaanite people and a firm link with people living in Lebanon today. ̽��ֱ��team discovered that more than 90 per cent of present-day Lebanese ancestry is likely to be from the Canaanites, with an additional small proportion of ancestry coming from a different Eurasian population.

̽��ֱ��team, including researchers from Cambridge ̽��ֱ��’s Department of Archaeology and Anthropology, and led by the Wellcome Trust Sanger Institute, estimate that new Eurasian people mixed with the Canaanite population about 2,200 to 3,800 years ago at a time when there were many conquests of the region from outside.

̽��ֱ��analysis of ancient DNA also revealed that the Canaanites themselves were a mixture of local people who settled in farming villages during the Neolithic period and eastern migrants who arrived in the area around 5,000 years ago.

"Ancient DNA is becoming an indispensable tool for understanding population movements of the past. This study in particular provides previously inaccessible information about a group of people known only by surviving written accounts and interpretations of archaeological findings,” said Dr. C L Scheib, one of two Cambridge co-authors, along with Dr Toomas Kivisild.

“ ̽��ֱ��fact that we can retrieve whole genomes from conditions not considered ideal for DNA preservation also shows how far the field has advanced technically," she said.

In the study, researchers sequenced whole genomes of five Canaanite individuals who lived 4,000 years ago in a city known as Sidon in present-day Lebanon. Scientists also sequenced the genomes of 99 present-day Lebanese and analysed the genetic relationship between the ancient Canaanites and modern Lebanese.

Dr Marc Haber, first author from the Sanger Institute, said: “It was a pleasant surprise to be able to extract and analyse DNA from 4,000-year-old human remains found in a hot environment, which is not known for preserving DNA well. We overcame this challenge by taking samples from the petrous bone in the skull, which is a very tough bone with a high density of ancient DNA.”

Dr Claude Doumet-Serhal, co-author and Director of the Sidon excavation site in Lebanon, said: “For the first time we have genetic evidence for substantial continuity in the region, from the Bronze Age Canaanite population through to the present day. These results agree with the continuity seen by archaeologists.

“Collaborations between archaeologists and geneticists greatly enrich both fields of study and can answer questions about ancestry in ways that experts in neither field can answer alone.”

Adapted from a Wellcome Trust press release.

Researchers analysed DNA extracted from 4,000-year-old human remains to reveal that more than 90% of Lebanese ancestry is from ancient Canaanite populations.

̽��ֱ��fact that we can retrieve whole genomes from conditions not considered ideal for DNA preservation also shows how far the field has advanced technically

C.L Scheib

Wellcome Genome Campus Public Engagement

Cambridge co-author C.L Scheib conducting ancient bone analysis at the Wellcome Genome Campus.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Yes

Ancient ‘trace’ in Papuan genomes suggests previously unknown expansion out of Africa

fpjl2 — Wed, 21 Sep 2016 17:02:39 +0000

A new study of human genomic diversity suggests there may have in fact been two successful dispersals out of Africa, and that a “trace” of the earlier of these two expansion events has lingered in the genetics of modern Papuans.

Three major genetic studies are published today in the same issue of Nature. All three agree that, for the most part, the genomes of contemporary non-African populations show signs of only one expansion of modern humans out of Africa: an event that took place sometime after 75,000 years ago.

Two of the studies conclude that, if there were indeed earlier expansions of modern humans out of Africa, they have left little or no genetic trace. ̽��ֱ��third, however, may have found that ‘trace’.

This study, led by Drs Luca Pagani and Toomas Kivisild from the ̽��ֱ�� of Cambridge’s Department of Archaeology and Anthropology, has found a “genetic signature” in present-day Papuans that suggests at least 2% of their genome originates from an even earlier, and otherwise extinct, dispersal of humans out of Africa.

Papuans and Philippine Negritos are populations that inhabit Papua New Guinea and some of the surrounding islands in Southeast Asia and Oceania. In the genomes of these populations, the researchers discovered more of the African ‘haplotypes’ – groups of genes linked closely enough to be inherited from a single source – than in any other present-day population.

Extensive analysis on the extra 2% of African haplotypes narrowed down the split between African (Yoruban) and Papuan lineages to around 120,000 years ago – a remarkable 45,000 years prior to the very earliest that the main African expansion could have occurred.

̽��ֱ��study analysed genomic diversity in 125 human populations at an unprecedented level of detail, based on 379 high resolution whole genome sequences from across the world generated by an international collaboration led by the Cambridge team and colleagues from the Estonian Biocentre.

Lead researcher Luca Pagani said: “Papuans share for most part same evolutionary history as all other non-Africans, but our research shows they may also contain some remnants of a chapter that is also yet to be described.

“While our research is in almost complete agreement with all other groups with regard to a single out-of-Africa event, this scenario cannot fully account for some genetic peculiarities in the Papuan genomes we analysed.”

Pagani says the sea which separates the ‘ecozones’ of Asia and Australasia may have played a part: “ ̽��ֱ��Wallace line is a channel of deep sea that was never dry during the ice ages. This constant barrier may have contributed to isolating and hence preserving the traces of the otherwise extinct lineage in Papuan populations.”

Toomas Kivisild said: “We believe that at least one additional human expansion out of Africa took place before the major one described in our research and others. These people diverged from the rest of Africans about 120,000 years ago, colonising some land outside of Africa. ̽��ֱ��2% of the Papuan genome is the only remaining trace of this otherwise extinct lineage.”

̽��ֱ��Estonian Biocentre’s Dr Mait Metspalu said: “This endeavour was uniquely made possible by the anonymous sample donors and the collaboration effort of nearly one hundred researchers from 74 different research groups from all over the world.”

Metspalu’s colleague Richard Villems added: “Overall this work provides an invaluable contribution to the understanding of our evolutionary past and to the challenges that humans faced when settling down in ever-changing environments.”

Researchers say the deluge of freely available data will serve as future starting point to further studies on the genetic history of modern and ancient human populations.

Several major studies, published today, concur that virtually all current global human populations stem from a single wave of expansion out of Africa. Yet one has found 2% of the genome in Papuan populations points to an earlier, separate dispersal event – and an extinct lineage that made it to the islands of Southeast Asia and Oceania.

Papuans share for most part same evolutionary history as all other non-Africans, but our research shows they may also contain some remnants of a chapter that is also yet to be described.

Luca Pagani

♪ ~

Dani tribesman on his way to his village in the Baliem Valley, Papua.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Yes

Licence type:

Attribution

Decline in the number of males involved in reproduction during the period of global growth

fpjl2 — Tue, 17 Mar 2015 17:55:11 +0000

In a study published recently in Genome Research, scientists from ̽��ֱ�� of Cambridge, Estonian Biocentre, ̽��ֱ�� of Tartu, Arizona State ̽��ֱ�� and 64 other institutions around the world discovered that accumulation of material culture during the middle and late stages of Neolithic, four to eight thousand years ago, is associated with a dramatic decline in genetic diversity in male lineages whereas female genetic diversity was on the rise.

It has been widely recognized that a major bottleneck, or decrease in genetic diversity, occurred approximately 50 thousand years ago when a subset of humans left Africa to colonize the rest of the world. Signatures of this bottleneck can be seen in most genes of non-African populations regardless of whether they are inherited from both parents or, as confirmed in this work, only along the father’s or mother’s genetic lines.

“Most surprisingly to us, we detected another, male-specific, bottleneck during the period of global growth. ̽��ֱ��signal for this bottleneck dates to a time period when humans in different parts of the world had already for thousands of years been sedentary farmers,” said senior author Toomas Kivisild from the ̽��ֱ�� of Cambridge’s Division of Biological Anthropology.

View an infographic of the research story here.

Melissa Wilson-Sayers, one of the lead authors from the School of Life Sciences at Arizona State ̽��ֱ��, added: “Instead of ‘survival of the fittest’ in biological sense, the accumulation of wealth and power may have increased the reproductive success of a limited number of socially ‘fit’ males and their sons.”

̽��ֱ��researchers said studying genetic history is important for understanding underlying levels of genetic variation. Having a high level of genetic diversity is beneficial to humans for several reasons. First, when the genes of individuals in a population vary greatly, the group has a greater chance of thriving and surviving — particularly against disease. It may also reduce the likelihood of passing along unfavorable genetic traits, which can weaken a species over time.

According to Monika Karmin, co-author from ̽��ֱ�� of Tartu, their findings further stress the differences in human male and female genetic histories which also may have implications related to human health.

“ ̽��ֱ��striking difference in the number of reproductive males and females in that time window certainly affected the diversity of genes on the male genetic line,” said Karmin. “We know that some populations are predisposed to certain types of genetic disorders. Researchers worldwide are trying to figure out what the underlying genetic structure is, so now also the fact that the male part of human lineages has gone trough a severe bottleneck has to be considered.”

“When a doctor tries to provide a diagnosis when you are sick, you’ll be asked about your environment, what’s going on, and your genetic history based on your family’s health. If we want to understand human health on a global scale, we need to know our global genetic history; that is what we are studying here,” added Wilson-Sayers.

̽��ֱ��researchers believe this will be relevant for informing patterns of genetic diversity across whole human populations, including informing about susceptibility to diseases, independently in different populations.

Adapted from an Arizona State ̽��ֱ�� press release.

Wealth and power may have played a stronger role than “survival of the fittest”.

Most surprisingly to us, we detected another, male-specific, bottleneck during the period of global growth

Toomas Kivisild

Arizona State ̽��ֱ��

Details from infographic produced by Arizona State ̽��ֱ��

̽��ֱ��text in this work is licensed under a Creative Commons Licence. If you use this content on your site please link back to this page. For image rights, please see the credits associated with each individual image.

Yes

Indians and Europeans share a milky past

ns480 — Fri, 09 Sep 2011 10:09:02 +0000

̽��ֱ��Cambridge team, in association with fellow researchers at CCMB Hyderabad, UCL, ̽��ֱ�� of Tartu, Harvard and ̽��ֱ�� of Chennai, were studying genetic changes that allow some 32 per cent of the world’s population to be lactase persistent – able to digest lactose, the sugar in milk. To their surprise they found the same mutation, with the same origin, at high frequency in Europe and India.

̽��ֱ��team’s study may also help scientists’ understanding of evolutionary processes such as biological adaptation and how culture and economic developments affect human biology. Its authors say the study has shown that with a little kick from natural selection, genes can spread far, wide and fast.

Lactase persistence is common in Europe, the Middle East and some parts of Africa and India – areas where domesticated cattle are widespread - but either rare or absent in most other parts of the world.

When someone who is not lactase persistent drinks milk they will often suffer symptoms such as abdominal pain, bloating, nausea and diarrhoea – otherwise known as lactose intolerance.

While all babies produce the gut enzyme lactase, essential for the digestion of lactose in milk, the production of the enzyme is usually shut down some time before adulthood.

Although once thought of as normal, lactase persistence was found in the 1960s to be an unusual trait in humans and seems to be completely absent from other mammals whose lactase production diminishes significantly after being weaned and is never resumed.

̽��ֱ��focus of the Cambridge-led study was India – the world’s largest producers and consumers of milk. ̽��ֱ��team looked at nearly 2,300 DNA samples from across the Indian subcontinent from all major language groups and geographic regions – the first study of its kind.

Previous studies had shown that lactase persistence had evolved at least four times in the last 10,000 years, independently in Europe, the Middle East and Africa. However, little was known about its genetic causes in India, until now.

Cambridge’s Dr Irene Gallego Romero, the lead author, said: “India was an unknown quantity. But since lactase persistence had evolved independently in the Middle East and Africa, and because cattle had been domesticated independently in India around seven or eight thousand years ago, we were expecting to see uniquely Indian genetic causes.”

̽��ֱ��vast majority of lactase persistent Europeans carry a mutation -13910T, that has been shown to have been strongly favoured by natural selection among people with supplies of milk to hand. It seems to have originated somewhere in Europe around 7,500 years ago. ̽��ֱ��mutation seems to be absent from samples of early central European farmer’s skeletons who lived around the time that domestic cattle, sheep and goats arrived there.

“To our surprise we found that the -13910T mutation was also common in India – especially in those populations with a tradition of milk drinking,” said Dr Toomas Kivisild of Cambridge ̽��ֱ��, senior author of the study.

“Not only that, but by looking at nearby genetic regions we could show that the Indian -13910T has the same origin as that found in Europeans; that it could lead back to the same few people who may have migrated between Europe and India.

However, that raises the question of why there are few instances of lactase tolerance in between.

Professor Mark Thomas of UCL, a co-author, said: “Genetic data doesn’t support some sort of large migration of people from Europe to India in the last 10,000 years. What’s more likely is that just a few migrants carried this mutation to India, and then it spread quickly.”

̽��ֱ��study also revealed large differences in the distribution of -13910T in India with many southern and eastern populations – especially those who do not practice pastoralism – having near zero frequencies.

̽��ֱ��study team speculate that the spread of the lactase persistent gene variant was highly dependent on the mobility of cattle keepers and the extent to which they reproduced with people who did not keep cattle.

In India, reproductive isolation between castes, tribes and religions can be strong. ̽��ֱ��study group suggest such isolation may have also been common historically when lactase persistence was spreading.

This work was supported by the UK-India Education Research Initiative (grant number RG47772), the European Commission Seventh Framework Programme Internal Training Networks (LeCHE, grant number 215362-2), the European Union Seventh Framework Programme Ecogene (grant number 205419), the European Union Regional Development Fund through a Centre of Excellence in Genomics award and a Bhatnagar Fellowship from Council of Scientific and Industrial Research, Government of India.

Cambridge ̽��ֱ�� researchers have discovered that lactose tolerant milk-drinkers in India and Europe could be related to the same person who lived at some point in the last 10,000 years.

To our surprise we found that the -13910T mutation was also common in India – especially in those populations with a tradition of milk drinking.

Dr Toomas Kivisild

kakie; from Flickr Creative Commons

milk

This work is licensed under a Creative Commons Licence. If you use this content on your site please link back to this page.

Yes