Europeans as much as 5% Neanderthal?

Are you part-Neanderthal?
Jennifer Viegas, Discovery News
 Wednesday, 23 August 2006 

There may be remnants of Neanderthal genes in the nuclear DNA of people with European ancestors. People of European descent may be 5% Neanderthal, according to a DNA study that questions whether modern humans left Africa and replaced all other existing hominids.

The same study, published in the latest issue of the journal PloS Genetics, also says West Africans could be related to an archaic human population.

As both groups spread, the findings suggest we all have a bit of archaic DNA in our genes.

“Instead of a population that left Africa 100,000 years ago and replaced all other archaic human groups, we propose that this population interacted with another population that had been in Europe for much longer, maybe 400,000 years,” says Vincent Plagnol.

Plagnol, a researcher in the Department of Molecular and Computational Biology at the University of Southern California, and colleague Assistant Professor Jeffrey Wall analysed patterns of ancestral linkage in 135 modern individuals.

They looked at people from Utah with ancestors from Northern and Western Europe and Yoruba people from West Africa.

Using statistics and computer modelling, the researchers focused on linkage ‘disequilibriums’, or sections within genes that did not make sense if only modern human matings are considered.

The missing genetic links only fit if some other hominid population is introduced into the model, the scientists say.

“We considered the data from modern human DNA and fitted a model to explain what we see,” explains Plagnol.

“We found that a simple model cannot explain the data if we do not add an ‘ancestral population’. If this population did not cross with modern humans, or almost did not, the effect is too small to explain the data. We find that a rate of 5% is what is needed to explain what we see.”

 The researchers agree with recent studies that conclude Neanderthals did not contribute any mitochondrial DNA, or mtDNA, genetic material that is passed from mothers to children.

But they say other portions of the European genome, such as those associated with nuclear DNA, may still harbour the Neanderthal imprint.

Plagnol says different parts of the genome have different ancestry, so an individual could have a fraction of a certain chromosome that is inherited from a Neanderthal, but then possess “very typical Homo sapiens mtDNA”.

The scientists are not certain which early human group could have contributed to West African DNA, but both Europeans and Africans in the study showed about the same 5% archaic contribution.

Neanderthals are believed to have originated in Africa around 400,000 years ago, but they left and then settled in Europe, hence the apparent lack of interaction with modern humans in Africa.

Alan Templeton, professor of Evolutionary and Population Programs at the University of Michigan, has also conducted DNA studies and comes to similar conclusions.

“The humans who were in Africa and the humans who were in Eurasia were regularly interchanging genes,” he says.

“There was interbreeding and when humans came out of Africa 100,000 years ago they did not replace these other human populations in Eurasia.”

New technologies are being developed to sequence nuclear DNA from fossils, so in the near future, scientists may learn more about how modern human genes compare with those of archaic humans, like Neanderthals.

The West African introgression is probably from a pygmy people, as I’ve seen an X chromosome paper by Garrigan suggesting that one group Africans has a very anomalous X chromosome. Article from this paper..

Possible Ancestral Structure in Human Populations
Vincent Plagnol * , Jeffrey D. Wall

1 Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America

Abstract
Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p ≈ 10−7), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.

Synopsis
The authors’ results have direct implications for the competing models of modern human origins. In particular, their estimates of non-negligible contributions of archaic populations to the modern gene pool are inconsistent with strict forms of the Recent African Origin model, which posits that modern humans evolved in a single location in Africa and from there spread and replaced all other existing hominines.

And a further contribution from Alan Templeton.

Out of Africa again and again
Alan Templeton

Abstract

The publication of a haplotype tree of human mitochondrial DNA variation in 1987 provoked a controversy about the details of recent human evolution that continues to this day. Now many haplotype trees are available, and new analytical techniques exist for testing hypotheses about recent evolutionary history using haplotype trees. Here I present formal statistical analysis of human haplotype trees for mitochondrial DNA, Y-chromosomal DNA, two X-linked regions and six autosomal regions. A coherent picture of recent human evolution emerges with two major themes. First is the dominant role that Africa has played in shaping the modern human gene pool through at least two—not one—major expansions after the original range extension of Homo erectus out of Africa. Second is the ubiquity of genetic interchange between human populations, both in terms of recurrent gene flow constrained by geographical distance and of major population expansion events resulting in interbreeding, not replacement.

Graph showing three waves of ‘out of Africa’

Haplotype Trees and Modern Human Origins
Alan R. Templeton

Abstract

A haplotype is a multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region. An evolutionary tree of the haplotypes can be estimated if the DNA region had little to no recombination. Haplotype trees can be used to reconstruct past human gene-flow patterns and historical events, but any single tree captures only a small portion of evolutionary history, and is subject to error. A fuller view of human evolution requires multiple DNA regions, and errors can be minimized by cross-validating inferences across loci. An analysis of 25 DNA regions reveals an out-of-Africa expansion event at 1.9 million years ago. Gene flow with isolation by distance was established between African and Eurasian populations by about 1.5 million years ago, with no detectable interruptions since. A second out-of-Africa expansion occurred about 700,000 years ago, and involved interbreeding with at least some Eurasian populations. A third out-of-Africa event occurred around 100,000 years ago, and was also characterized by interbreeding, with the hypothesis of a total Eurasian replacement strongly rejected (P < 10-17). This does not preclude the possibility that some Eurasian populations could have been replaced, and the status of Neanderthals is indecisive. Demographic inferences from haplotype trees have been inconsistent, so few definitive conclusions can be made at this time. Haplotype trees from human parasites offer additional insights into human evolution and raise the possibility of an Asian isolate of humanity, but once again not in a definitive fashion. Haplotype trees can also indicate which genes were subject to positive selection in the lineage leading to modern humans. Genetics provides many insights into human evolution, but those insights need to be integrated with fossil and archaeological data to yield a fuller picture of the origin of modern humans.

5 responses to “Europeans as much as 5% Neanderthal?

  1. All looks very theoretical work, hypothetical modelling. Personally, in order to confirm or (more probably) reject such papers and their daring conclussions, I am in wait of full Neandethal genome sequencing, which is ongoing and the subsequent comparison with modern human DNA.

    So far all the hard data seems to reject this admixture – but you can never be 100% sure. As you mention in the other post, mtDNA suggests no admixture. And this is also the conclusion for nuclear DNA in other papers (for instance: Wall JD, Kim SK 2007 Inconsistencies in Neanderthal Genomic DNA Sequences. PLoS Genetics 3(10): e175 doi:10.1371/journal.pgen.0030175).

    By the moment the conclussion seems to be that most likely it did not happen. People can model all they want but it’s just conceptual work, until hard evidence for such admixture is available (i.e. actual DNA strings shared by West Eurasians and Neanderthals but not by all other humans – none so far), we do have good reasons to think they are wrong.

  2. Mathilda: you might find this interesting. The study finds population structure in Africa before OOA. I can’t access the full study; you may be able to do so.

  3. From Dienekes

    Jul
    10
    2008 Campbell & Tishkoff review paper on African genetic diversity
    5 comments
    From the paper:
    Several studies of nucleotide and haplotype variation have indicated that ancestral African populations were geographically structured prior to the migration of modern humans out of Africa (70, 71, 79, 157, 197, 237). Additionally, a recent study of 800 short tandem repeat polymorphisms (STRPs) and 400 INDELs genotyped in more than 3000 geographically and ethnically diverse Africans indicates the presence of at least 13 genetically distinct ancestral populations in Africa and high levels of population admixture in many regions (F.A. Reed & S.A Tishkoff, unpublished data). Population clusters are correlated with selfdescribed ethnicity and shared cultural and/or linguistic properties (e.g., Pygmies, Khoisanspeaking hunter-gatherers, Bantu speakers, Cushitic speakers). This study reveals extensive admixture between inferred ancestral populations in most African populations. One exception is amongWest African Niger-Kordofanian (i.e., Bantu) speakers who are more genetically homogeneous compared with other African populations, likely reflecting the recent and rapid spread of Bantu speakers from a common origin in Cameroon/Nigeria (although fine-scale genetic structure can be detected amongst these populations). Thus, the pattern of genetic diversity in Africa indicates that African populations have maintained a large and subdivided population structure throughout much of their evolutionary history (Figure 2).
    As I have argued before, the great genetic diversity of Sub-Saharan Africans is due to the fact that they are composed of several long-differentiated populations admixed with each other. As Figure 2, mentioned above, indicates, NE Africans are related to Eurasians more closely than other Africans, although there has been subsequent gene flow into NE Africans from other Sub-Saharan Africans. Annual Review of Genomics and Human Genetics Vol. 9 (Volume publication date September 2008) (doi:10.1146/annurev.genom.9.081307.164258) African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping Michael C. Campbell­, Sarah A. Tishkoff­ Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. Link

  4. “But, but, but” I hear people saying. “That study is two years old”. People will still maintain we all come from just a small group of people, either from the Garden of Eden or from Noah’s Ark. Ancient myths die slowly.

    I thought the comment, “the ubiquity of genetic interchange between human populations, both in terms of recurrent gene flow constrained by geographical distance and of major population expansion events resulting in interbreeding, not replacement” was very relevant. It even happens today. “But” again I hear people say. “Australian Aboriginal and Native American genes still survive”. I ask “How easily detected will their genes be in the relevant populations in 30,000 years time?”

  5. As I’ve often pointed out, both the Y & X haplogroup can quickly disappear when inter breeding happens. A good example of this is often cited when attempting to prove native American ancestry. Suppose a European male produces a male offspring with a native American mother & a European female produces a female with a native American father. If these two offspring produce children, then all children would test as 100% european haplogroups due to the Mt & Y chromosomes showing only European haplogroups (the father passes down his European chromosome as does the mother).
    One could easily envision a situation where those 31/32 native American would test as 100% European unless extensive testing was done. Granted it is highly unlikely, but seems to have happened a number of times.

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