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Jean M
01-29-2014, 07:29 PM
Remnants of Neanderthal DNA in modern humans are associated with genes affecting type 2 diabetes, Crohn's disease, lupus, biliary cirrhosis and smoking behavior. They also concentrate in genes that influence skin and hair characteristics. At the same time, Neanderthal DNA is conspicuously low in regions of the X chromosome and testes-specific genes.

The research, led by Harvard Medical School geneticists and published Jan. 29 in Nature, suggests ways in which genetic material inherited from Neanderthals has proven both adaptive and maladaptive for modern humans. (A related paper by a separate team was published concurrently in Science.) ...

In the past few years, studies by groups including Reich's have revealed that present-day people of non-African ancestry trace an average of about 2 percent of their genomes to Neanderthals—a legacy of interbreeding between humans and Neanderthals that the team previously showed occurred between 40,000 to 80,000 years ago. (Indigenous Africans have little or no Neanderthal DNA because their ancestors did not breed with Neanderthals, who lived in Europe and Asia.)

Several teams have since been able to flag Neanderthal DNA at certain locations in the non-African human genome, but until now, there was no survey of Neanderthal ancestry across the genome and little understanding of the biological significance of that genetic heritage.


Read more at: http://phys.org/news/2014-01-neanderthals-genetic-legacy.html


Neanderthal lineages excavated from modern human genomes

A substantial fraction of the Neanderthal genome persists in modern human populations. A new approach applied to analyzing whole-genome sequencing data from 665 people from Europe and East Asia shows that more than 20 percent of the Neanderthal genome survives in the DNA of this contemporary group, whose genetic information is part of the 1,000 Genomes Project.

Previous research proposes that someone of non-African descent may have inherited approximately 1 percent to 3 percent of his or her genome from Neanderthal ancestors. These archaic DNA sequences can vary from one person to another and were aggregated in the present study to determine the extent of the Neanderthal genome remaining in the study group as a whole. The findings are a start to identifying the location of specific pieces of Neanderthal DNA in modern humans and a beginning to creating a collection of Neanderthal lineages surviving in present-day human populations.

University of Washington scientists Benjamin Bernot and Joshua M. Akey, both population geneticists from the Department of Genome Sciences, report their results Jan. 29 in Science Express. Vernot is a graduate student and Akey is an associate professor. Their paper is titled, "Resurrecting Surviving Neanderthal Lineages from Modern Human Genomes."

http://phys.org/news/2014-01-neanderthal-lineages-excavated-modern-human.html

Jean M
01-29-2014, 07:31 PM
Coverage in Nature News by Ewen Callaway

http://www.nature.com/news/modern-human-genomes-reveal-our-inner-neanderthal-1.14615


Modern human genomes reveal our inner Neanderthal

Cross-breeding boosted Homo sapiens' ability to cope with cool climates, but the hybrids may have had trouble breeding.

Sex with Neanderthals had its ups and its downs. Cross-breeding may have given modern humans genes useful for coping with climates colder than Africa's, but the hybrid offspring probably suffered from significant fertility problems. Those conclusions come from two papers published today in Science and Nature, which identify the slices of the genome that contemporary humans inherited from Neanderthals, the stocky hunter-gatherers that went extinct around 30,000 years ago.

Jean M
01-29-2014, 07:34 PM
The papers:

Sankararaman, S. et al., The genomic landscape of Neanderthal ancestry in present-day humans, Nature
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html


Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.


B. Vernot et al., Resurrecting Surviving Neanderthal Lineages from Modern Human Genomes, Science, Published Online January 29 2014
http://www.sciencemag.org/content/early/2014/01/28/science.1245938


Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.

Jean M
01-29-2014, 08:29 PM
And coverage from the BBC:

Neanderthals gave us disease genes


Genes that cause disease in people today were picked up through interbreeding with Neanderthals, a major study in Nature journal suggests. They passed on genes involved in type 2 diabetes, Crohn's disease and - curiously - smoking addiction....

That a gene variant associated with the inability to stop smoking should be found to be of Neanderthal origin is a surprise. The researchers are, of course, not suggesting that our evolutionary cousins were puffing away in their caves. Instead, they argue, this gene may have more than one function; the modern effect of this genetic marker on smoking behaviour may be one impact among several.

http://www.bbc.co.uk/news/science-environment-25944817

Mehrdad
01-29-2014, 08:31 PM
Do we know what haplogroups neanderthals belonged to?

Jean M
01-29-2014, 09:32 PM
Do we know what haplogroups neanderthals belonged to?

They did not fit onto the Y-DNA and mtDNA trees of present-day humans. They are not our ancestors. They belong on a different branch of the hominid tree.

Jean M
01-29-2014, 09:34 PM
Coverage in Science:

Which Genes Did We Get From Neandertals?


Tens of thousands of years ago along the balmy Mediterranean coast, or in some desert oasis in the Middle East, a hunky Neandertal male lusted after a modern human maiden. Or perhaps a sleek modern guy scored with an earthy Neandertal girl. Either way, living people in Europe and Asia still carry traces of those long-ago unions. Now two studies, the first to analyze Neandertal DNA in large numbers of living people, pinpoint genes we have inherited from our extinct cousins, including some that leave their mark on hair and skin and others implicated in disease.

The studies also show that those ancient mixed couples were not fully compatible. Both studies suggest that Neandertals and moderns came from such different genetic backgrounds that the descendants of their unions became less fertile over time, purging many Neandertal genes from modern genomes. “There were costs to interbreeding,” says population geneticist Joshua Akey of the University of Washington, Seattle, senior author of a report online this week in Science. Population geneticist David Reich of Harvard Medical School in Boston, who led the study reported in this week’s issue of Nature, agrees: “When Neandertals and modern humans mixed, they were at the edge of biological compatibility.”

http://news.sciencemag.org/archaeology/2014/01/which-genes-did-we-get-neandertals

newtoboard
01-29-2014, 09:37 PM
Surely a uniparental Neanderthal marker will be found in a human one day given Eurasians derive 3-5% of their autosomal ancestry from Neanderthals.

Mehrdad
01-29-2014, 09:41 PM
Surely a uniparental Neanderthal marker will be found in a human one day given Eurasians derive 3-5% of their autosomal ancestry from Neanderthals.

Exactly my thoughts

Jean M
01-29-2014, 10:12 PM
Dienekes weighs in to this discussion: http://dienekes.blogspot.co.uk/2014/01/neandertal-admixture-in-modern-humans.html


One of the lingering questions about Neandertal admixture is why there are no Neandertal Y-chromosomes or mtDNA in modern Eurasians. The disappearance of Neandertal mtDNA seems unlikely according to one study, but might be explained if negative selection was at play.

lgmayka
01-29-2014, 10:17 PM
Surely a uniparental Neanderthal marker will be found in a human one day given Eurasians derive 3-5% of their autosomal ancestry from Neanderthals.
Neanderthal yDNA is extremely unlikely to be found in any modern human. The newly published article says that the male offspring of sapiens-neanderthalensis matings were strongly selected against, probably via reduced fertility.

Moreover, we now know that yDNA is far more subject to social selection as well. It tends to reflect the rise of and fall of peoples and cultures. We can barely find any modern examples of Mesolithic C-V20 yDNA; why should we expect to find any of a much earlier and more catastrophically extinct people?

newtoboard
01-29-2014, 10:26 PM
What about mtDNA? How can you compare this situation with C-V20 when we don't know widely distributed or common it was during the Mesolithic? It's likely I was the major Mesolithic group of Europe and plenty of it seemed to survive. On the other hand we know Neanderthals were widely distributed all over Eurasia.

Mehrdad
01-29-2014, 10:28 PM
Dienekes weighs in to this discussion: http://dienekes.blogspot.co.uk/2014/01/neandertal-admixture-in-modern-humans.html

Wow, that's pretty recent. Thanks

GTC
01-30-2014, 04:33 AM
Coverage in Science:


... “When Neandertals and modern humans mixed, they were at the edge of biological compatibility.”

I like the way that is put.

J Man
01-30-2014, 04:22 PM
Does anyone know if 23andme tests any of these SNPs involved with keratin production or anything that could relate to Neanderthals from this study?

Jean M
01-30-2014, 04:56 PM
Does anyone know if 23andme tests any of these SNPs involved with keratin production or anything that could relate to Neanderthals from this study?

23andMe is still using a test for supposed "Neanderthal" DNA based on the paper by Green et al., A Draft Sequence of the Neanderthal Genome, Science (2010), which over-estimated Neanderthal input into the modern gene-pool. Whether they will update in line with all this new material, I don't know.

J Man
01-30-2014, 05:39 PM
23andMe is still using a test for supposed "Neanderthal" DNA based on the paper by Green et al., A Draft Sequence of the Neanderthal Genome, Science (2010), which over-estimated Neanderthal input into the modern gene-pool. Whether they will update in line with all this new material, I don't know.

Yes I know that but I don't know how accurate that test really is.

MitchellSince1893
01-30-2014, 05:56 PM
The 23andme average Neanderthal percentage for all users is currently 2.7%.

My ~60 matches range from 2.2% to 3.3%.

Jean M
01-30-2014, 06:36 PM
Yes I know that but I don't know how accurate that test really is.

There was a bit of a clue in my post that I doubt whether it is accurate at all.

rms2
01-30-2014, 07:36 PM
I never really took all that Neanderthal/Denisovan stuff seriously. My dad's Geno 2.0 results gave him 1.5% Neanderthal and 0.7% Denisovan.

Jean M
01-30-2014, 09:25 PM
Coverage from the Howard Hughes Medical Institute: When Populations Collide

http://www.hhmi.org/news/when-populations-collide



Highlights


More than thirty thousand years ago, Homo sapiens migrating out of Africa began encountering Neanderthals, a lineage that had diverged from modern humans hundreds of thousands of years before.
Despite their differences, Homo sapiens and Neanderthals mingled, and over time, produced children with genes from both lineages.
HHMI researcher David Reich and colleagues have now analyzed exactly which areas of the human genome retain segments of Neanderthal DNA, passed down throughout the generations.


In late 2013, Reich was one of the leaders of a team that published the complete genome of a Neanderthal woman, based on analysis of DNA isolated from a toe bone discovered in modern-day Siberia. To determine how the human-Neanderthal genetic mixing may have played out, Reich and his colleagues compared that completed Neanderthal genome with the genomes of 1,004 present-day humans from around the globe.

“If a gene variant is absent in Africans today, but present in modern day non-Africans as well as the Neanderthal genome, that’s good evidence that it originates from Neanderthals,” Reich says. Since humans met Neanderthals as they migrated out of Africa, those populations that remained in Africa had little contact or genetic mixing with Neanderthals. Reich’s group also leveraged other genetic information, including the size of different gene fragments, to determine whether genes were inherited from Neanderthals or not.

The researchers found that today, humans in east Asia have, on average, more of their genome originating from Neanderthals than Europeans, and modern-day Africans have little or none. Those findings confirmed previous studies. But then, the scientists took their analysis a step further and examined which genes most often have Neanderthal ancestry in present-day people. They found that some genes had variants of Neanderthal origin in more than sixty percent of Europeans or Asians, while other genes were never of Neanderthal heritage.

The scientists discovered that the genetic changes most often inherited from Neanderthals were disproportionately in genes related to keratin, a component of skin and hair.

J Man
01-31-2014, 01:18 AM
There was a bit of a clue in my post that I doubt whether it is accurate at all.

Ya I saw that as well.

lgmayka
01-31-2014, 03:41 AM
There was a bit of a clue in my post that I doubt whether it is accurate at all.
This "new" estimate is based entirely on the shockingly skewed 1000 Genomes Project. In other words, the "new" Neanderthal calculation does not take into account any human living between the Netherlands and China, nor any human living in the Balkans or the Middle East. Why didn't a peer reviewer point this out?

I continue to marvel at the naivete of scientists who imagine that the 1000 Genomes Project fairly represents the entire world's population and write their conclusions on that basis.

GailT
01-31-2014, 06:11 AM
John Hawks writes:


Today, ancient DNA has begun to provide vastly more data about some parts of our evolution. But comparing an ancient genome to the genomes of hundreds or thousands of living people is not straightforward. We require fairly sophisticated models to understand the evolutionary changes in these samples.

Models introduce the problem of overfitting. And models require assumptions, which are often hidden away in the supplementary information of high-impact papers. As we've seen recently, many of the initial conclusions about ancient genomes, made in the wake of the Neandertal and Denisovan discoveries in 2010, were overhyped.


John Hawk's blog is amazing, here he blogs about his visit to Ethiopia and the Omo valley (http://johnhawks.net/weblog/hawks/travel/omo-valley-trek-2014.html), with photos.

Jean M
01-31-2014, 12:04 PM
This "new" estimate is based entirely on the shockingly skewed 1000 Genomes Project. In other words, the "new" Neanderthal calculation does not take into account any human living between the Netherlands and China, nor any human living in the Balkans or the Middle East.

And the 2010 estimate was based on the genomes of five modern individuals: Han Chinese, Papuan, Yoruba, San and French. The result was probably skewed by the inclusion of the Papuan. Samples from Papua New Guinea are high in Denisovan.

Jean M
01-31-2014, 12:42 PM
John Hawks writes.

Yes I saw that. The full quote:


Models introduce the problem of overfitting. And models require assumptions, which are often hidden away in the supplementary information of high-impact papers. As we've seen recently, many of the initial conclusions about ancient genomes, made in the wake of the Neandertal and Denisovan discoveries in 2010, were overhyped. Along with some other anthropologists, I raised concerns about these at the time, pointing out which conclusions were very solid, and which other ones we should treat more cautiously. And I'll continue to do that. But many people who are applying sophisticated models to ancient DNA data are not quite so cautious -- they are looking for their publishable results. Negative results are, at the moment, less interesting or publishable in this field. I worry that the level of scrutiny at top journals may be relaxing.

http://johnhawks.net/weblog/topics/meta/irreproducible-research-nih-2014.html

I was frankly surprised, since he was hugely enthusiastic about the conclusions of the Green study when it came out. But we live and learn I suppose.

greystones22
01-31-2014, 01:37 PM
Surely a uniparental Neanderthal marker will be found in a human one day given Eurasians derive 3-5% of their autosomal ancestry from Neanderthals.

To date we only have genetic data from autosomes, X chromosome and mtDNA. No male neanderthal has been sequenced yet.