Tag Archives: genomes

Melanesia

Long strand of DNA from Neanderthals found in people from Melanesia

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Many of us have at least a little Neanderthal DNA inside us Marcin Rogozinski / Alamy Stock Photo Read more: https://www.newscientist.com/article/2220381-long-strand-of-dna-from-neanderthals-found-in-people-from-melanesia/#ixzz630AemCaX
Many of us have at least a little Neanderthal DNA inside us Marcin Rogozinski / Alamy Stock Photo Read more: https://www.newscientist.com/article/2220381-long-strand-of-dna-from-neanderthals-found-in-people-from-melanesia/#ixzz630AemCaX

Many people have DNA inside them that they inherited from extinct hominins like the Neanderthals – and now we know that in some cases it isn’t just tiny snippets but long stretches.

Over the past decade, genetic analysis of human DNA has revealed that ancient humans must have interbred many times with other hominins such as Neanderthals. The result is that DNA from these extinct groups can be found in many human populations today.

In particular, everyone whose primary ancestry was outside Africa carries some Neanderthal DNA, while many people from Asia – especially South-East Asia – have DNA from the mysterious Denisovans. Some of this DNA may have been advantageous for modern humans.

Read more: Denisovans: The lost humans who shared our world

However, these studies were limited to small pieces of DNA. “Most people have focused on looking at single nucleotide changes,” says Evan Eichler at the University of Washington in Seattle. This means just one “letter” of a gene has been altered.

Now Eichler and his team have gone further. “This is one of the first papers that looks at bigger events like deletions and duplications of sequence,” he says. These larger genetic changes will have had more important effects on human biology.

The researchers looked at the DNA of people from Melanesia, as the levels of Neanderthal and Denisovan DNA are highest in these populations. They found evidence of much longer chunks of archaic DNA in this population.

Two large pieces of DNA were found that originate from ancient hominins. One is on chromosome 16 and comes from Denisovans. It contains two duplicated sections. The other is on chromosome 8 and comes from Neanderthals. It includes both a deletion and a duplication.

Duplications are significant because they allow the original gene to be kept, if it is useful, while the copy is free to change and potentially develop a new function. “A duplication is a type of mutation that lets you have your cake and eat it too,” says Eichler.

Both chunks of DNA show signs of having been selected for by evolution. They seem to have been advantageous and thus become more common in the Melanesian population over the centuries.

Test run

“The archaics have contributed to the success of humans that left Africa,” says Eichler. Neanderthals and Denisovans lived in Europe and Asia for hundreds of thousands of years before modern humans emerged from Africa, so they would have evolved adaptations to the different climates, foods and diseases. These useful genes “were kind of test-run in our precursors”, says Eichler. “They’re basically borrowed.”

However, it is unclear what the advantages have been. “I think the biggest challenge is proving the function,” says Eichler. This will be difficult because the genes are only found in humans, so animal studies will not help, and they have been duplicated and then subtly altered. “You’re talking about a set of genes which are a geneticist’s worst nightmare.”

Journal reference: Science, DOI: 10.1126/science.aax2083

Read more: https://www.newscientist.com/article/2220381-long-strand-of-dna-from-neanderthals-found-in-people-from-melanesia/#ixzz630AR7mwx

Melanesia

Genetic ‘trace’ in Papuan genomes suggests two expansions out of Africa

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Date:September 21, 2016

Source: University of Cambridge

Summary:

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.  

Abstract:

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. The third, however, may have found that ‘trace’. 

This study, led by Drs Luca Pagani and Toomas Kivisild from the University 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.  

The 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: “The 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. The 2% of the Papuan genome is the only remaining trace of this otherwise extinct lineage.”

The 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.

Story Source:

Materials provided by University of Cambridge. The original story is licensed under a Creative Commons Licence. Note: Content may be edited for style and length.

Journal Reference:

  1. Luca Pagani, Daniel John Lawson, Evelyn Jagoda, Alexander Mörseburg, Anders Eriksson, Mario Mitt, Florian Clemente, Georgi Hudjashov, Michael DeGiorgio, Lauri Saag, Jeffrey D. Wall, Alexia Cardona, Reedik Mägi, Melissa A. Wilson Sayres, Sarah Kaewert, Charlotte Inchley, Christiana L. Scheib, Mari Järve, Monika Karmin, Guy S. Jacobs, Tiago Antao, Florin Mircea Iliescu, Alena Kushniarevich, Qasim Ayub, Chris Tyler-Smith, Yali Xue, Bayazit Yunusbayev, Kristiina Tambets, Chandana Basu Mallick, Lehti Saag, Elvira Pocheshkhova, George Andriadze, Craig Muller, Michael C. Westaway, David M. Lambert, Grigor Zoraqi, Shahlo Turdikulova, Dilbar Dalimova, Zhaxylyk Sabitov, Gazi Nurun Nahar Sultana, Joseph Lachance, Sarah Tishkoff, Kuvat Momynaliev, Jainagul Isakova, Larisa D. Damba, Marina Gubina, Pagbajabyn Nymadawa, Irina Evseeva, Lubov Atramentova, Olga Utevska, François-Xavier Ricaut, Nicolas Brucato, Herawati Sudoyo, Thierry Letellier, Murray P. Cox, Nikolay A. Barashkov, Vedrana Škaro, Lejla Mulahasanovic´, Dragan Primorac, Hovhannes Sahakyan, Maru Mormina, Christina A. Eichstaedt, Daria V. Lichman, Syafiq Abdullah, Gyaneshwer Chaubey, Joseph T. S. Wee, Evelin Mihailov, Alexandra Karunas, Sergei Litvinov, Rita Khusainova, Natalya Ekomasova, Vita Akhmetova, Irina Khidiyatova, Damir Marjanović, Levon Yepiskoposyan, Doron M. Behar, Elena Balanovska, Andres Metspalu, Miroslava Derenko, Boris Malyarchuk, Mikhail Voevoda, Sardana A. Fedorova, Ludmila P. Osipova, Marta Mirazón Lahr, Pascale Gerbault, Matthew Leavesley, Andrea Bamberg Migliano, Michael Petraglia, Oleg Balanovsky, Elza K. Khusnutdinova, Ene Metspalu, Mark G. Thomas, Andrea Manica, Rasmus Nielsen, Richard Villems, Eske Willerslev, Toomas Kivisild, Mait Metspalu. Genomic analyses inform on migration events during the peopling of Eurasia. Nature, 2016; DOI: 10.1038/nature19792

MLA: University of Cambridge. “Genetic ‘trace’ in Papuan genomes suggests two expansions out of Africa.” ScienceDaily. ScienceDaily, 21 September 2016. <www.sciencedaily.com/releases/2016/09/160921131119.htm>.

APA: University of Cambridge. (2016, September 21). Genetic ‘trace’ in Papuan genomes suggests two expansions out of Africa. ScienceDaily. Retrieved October 20, 2019 from www.sciencedaily.com/releases/2016/09/160921131119.htm