quote:Biologists find clues to a 'ghost' species of ancient human in Africa and say interbreeding between early hominin species was 'the norm'
Study found a saliva protein in modern sub-Saharan Africans to be very distinct
This suggests the ancient species interbred with another archaic human species
But, there are no fossils linked to this discovery, making it a 'ghost' species
Ancient human ancestors that can be traced to populations alive today may have engaged in ‘sexual rendezvous’ with a ‘ghost’ species of archaic humans.
In a new analysis of a protein found in saliva, researchers discovered evidence of archaic admixture in modern people living in sub-Saharan Africa, indicating that another species had contributed to the genetic material of their ancestors.
The experts say it appears that interbreeding was common among early hominin species – but, with no fossils of the mysterious species in question, it’s considered a ‘ghost.’
‘It seems that interbreeding between different early hominin species is not the exception – it’s the norm,’ said Omer Gokcumen, PhD, an assistant professor of biological sciences at the University at Buffalo’s College of Arts and Sciences.
‘Our research traced the evolution of an important mucin protein called MUC7 that is found in saliva.
‘When we looked at the history of the gene that codes for the protein, we see the signature of archaic admixture in modern day Sub-Saharan African population.’
The researchers were investigating the purpose and origins of the MUC7 protein.
This protein is, in part, responsible for the slimy consistency of saliva, and helps it to bind to microbes.
"...The Mal'ta genome reveals that these Paleoindian progenitors were an admixed population. They were mainly of East Asian origin, but about a third of their genome was derived from a northern Eurasian “ghost” population..."
The Mal'ta child and cultural artifacts surrounding him identify this culture as a very northerly branch of the Gravettian culture:
Joseph Leydon: "The pygmies may have entered the area (Australia) around 65k ago, but they weren't the first. The first had a mito DNA genome that is now extinct, and only preserved today in an erroneous insertion into chromosome 11.
Since Amazonians, Ainu, and Papua New Guinea tribes have the most of this insertion, it can be concluded that their shared ancestor was the one who assimilated this "ghost population" of homo sapiens.
"Our research traced the evolution of an important mucin protein called MUC7 that is found in saliva," he says. "When we looked at the history of the gene that codes for the protein, we see the signature of archaic admixture in modern day Sub-Saharan African populations."
The research was published on July 21 in the journal Molecular Biology and Evolution. The study was led by Gokcumen and Stefan Ruhl, DDS, PhD, a professor of oral biology in UB's School of Dental Medicine.
A tantalizing clue in saliva
The scientists came upon their findings while researching the purpose and origins of the MUC7 protein, which helps give spit its slimy consistency and binds to microbes, potentially helping to rid the body of disease-causing bacteria.
As part of this investigation, the team examined the MUC7 gene in more than 2,500 modern human genomes. The analysis yielded a surprise: A group of genomes from Sub-Saharan Africa had a version of the gene that was wildly different from versions found in other modern humans.
The Sub-Saharan variant was so distinctive that Neanderthal and Denisovan MUC7 genes matched more closely with those of other modern humans than the Sub-Saharan outlier did.
"Based on our analysis, the most plausible explanation for this extreme variation is archaic introgression -- the introduction of genetic material from a 'ghost' species of ancient hominins," Gokcumen says. "This unknown human relative could be a species that has been discovered, such as a subspecies of Homo erectus, or an undiscovered hominin. We call it a 'ghost' species because we don't have the fossils."
Given the rate that genes mutate during the course of evolution, the team calculated that the ancestors of people who carry the Sub-Saharan MUC7 variant interbred with another ancient human species as recently as 150,000 years ago, after the two species' evolutionary path diverged from each other some 1.5 to 2 million years ago.
posted
Nice, but who was this "northern Eurasian “ghost” population"?
They were mainly of East Asian origin, but about a third of their genome was derived from a northern Eurasian “ghost” population, no longer extant today, represented by the Mal'ta boy and related individuals from Afontova Gora.
There was indeed a “ghost” population, but it is not what they claim. But I love how they put in “ghost” population".
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by DD'eDeN: 3 Ghost species interbred
"...The Mal'ta genome reveals that these Paleoindian progenitors were an admixed population. They were mainly of East Asian origin, but about a third of their genome was derived from a northern Eurasian “ghost” population..."
The Mal'ta child and cultural artifacts surrounding him identify this culture as a very northerly branch of the Gravettian culture:
This is false. The population was not East Asian. The Gravettan, like the Aurignacian and Solutrean were cultures that originated in South Africa. The ghost population is just an African population Eurocentric geneticists refuse to aknowledge until they can flip the script, as they did with making L3c into a U haplogroup.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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About Mal'ta, "No ancestral connection between Malta1 and samples from the Vĕstonice Cluster", note that though they both had Venus Figurines, Mal'ta's were clothed in ways similar to Eskimo figurines, Vestonice Venus's were naked.
quote:Originally posted by DD'eDeN: [QB] 3 Ghost species interbred
"...The Mal'ta genome reveals that these Paleoindian progenitors were an admixed population. They were mainly of East Asian origin, but about a third of their genome was derived from a northern Eurasian “ghost” population..."
The Mal'ta child and cultural artifacts surrounding him identify this culture as a very northerly branch of the Gravettian culture:
The above Mal'ta specimen from Siberia has nothing whatsoever to do with the gene variant found in African saliva that is the topic of the thread.
So this term "ghost" is not linking any of the "ghost populations" in any way except that they haven't found fossils for them
It's as if you were to go into a morgue and they had several corpses that were identified by relatives but there were two they couldn't identity and then to suggest they are linked because they are both "unidentified".
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quote:Originally posted by the lioness,: "Ghost population" just means they have no fossil
That is a possibility in some cases, but it's certainly not factual. It can mean they leave out certain populations for "convenience".
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by DD'eDeN: the lioness,: "Ghost population" just means they have no fossil"
Ok, thanks, I didn't know that. Then, as you said, there isn't any significant linkage among them.
errata: I meant ghost population, not ghost species, above.
Montgomery Slatkin
Received 12 July 2004; revision received 29 September 2004; accepted 29 September 2004
In 2004, the term ‘ghost population’ was introduced to summarize the effect of unsampled subpopulations that exchange migrants with other subpopulations that have been sampled.
quote:Originally posted by the lioness,: "Ghost population" just means they have no fossil
That is a possibility in some cases, but it's certainly not factual. It can mean they leave out certain populations for "convenience".
Wrong. You don't know what you are talking about. It's the opposite of what you are saying. They insert a population between two specific populations that went extinct and it's based on statistical analysis
Posts: 42918 | From: , | Registered: Jan 2010
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quote:Originally posted by the lioness,: "Ghost population" just means they have no fossil
That is a possibility in some cases, but it's certainly not factual. It can mean they leave out certain populations for "convenience".
Wrong. You don't know what you are talking about. It's the opposite of what you are saying. They insert a population between two specific populations that went extinct and it's based on statistical analysis
This is from your favorite source:
Population studies[edit]
In 2004, it was proposed that Maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes using coalescent theory can use datasets which contain a population that has no data. This is referred to as a "ghost population".
The manipulation allows exploration in the effects of missing populations on the estimation of population sizes and migration rates between two specific populations. The biases of the inferred population parameters depend on the magnitude of the migration rate from the unknown populations.[1] The technique for deriving ghost populations attracted criticism because ghost populations were the result of statistical models, along with their limitations.[2]
datasets which contain a population that has no data
Or willingly has no data! This happened often with African populations. They simply use a data set and postpone it to some random group, via supposed "statistic analysis".
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
^ And you are still wrong, nothing is left out, it's a hypothetical population put in not left out and it could be African or non-African depending on which ghost population they are talking aboput
Posts: 42918 | From: , | Registered: Jan 2010
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quote:Originally posted by the lioness,: ^ And you are still wrong, nothing is left out, it's a hypothetical population put in not left out and it could be African or non-African depending on which ghost population they are talking aboput
Fact is that African populations have been regarded mostly as ghost populations, since most African populations never have been tested genetically. This is why they aren't visible, but simply are clustered in by bayesian statistic, "progressive African American woman ".
quote:The addition of unsampled or ghost populations can not only modify parameter estimations but also alter our interpretation of the results (see e.g. [75], [76]).
—Laurent Excoffier et al. Robust Demographic Inference from Genomic and SNP Data
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by Ish Gebor: most African populations never have been tested genetically.
Whose responsibility is it?
African countries?
That is completely irrelevant. What is relevant here is that most haven't been tested, yet have been clustered with groups that have nothing to do with them, yet with this relatively small set of samples Africans genetically are already more diverse, "progressive African American woman ".
Next you're going to tell me again, that I don't know what I am talking about. Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation
Duo Xu1, Pavlos Pavlidis2, Recep Ozgur Taskent1, Colin Flanagan1, Michael DeGiorgio4, Ran Blekhman5, Stefan Ruhl6*, Omer Gokcumen1*
ABSTRACT One of the most abundant proteins in human saliva, mucin-7, is encoded by the MUC7 gene, which harbors copy number variable subexonic repeats (PTS-repeats) that affect the size and glycosylation potential of this protein. We recently documented the adaptive evolution of MUC7 subexonic copy number variation among primates. Yet, the evolution of MUC7 genetic variation in humans remained unexplored. Here, we found that PTS-repeat copy number variation has evolved recurrently in the human lineage, thereby generating multiple haplotypic backgrounds carrying 5 or 6 PTS-repeat copy number alleles. Contrary to previous studies, we found no associations between the copy number of PTS-repeat copy number and protection against asthma. Instead, we revealed a significant association of MUC7 haplotypic variation with the composition of the oral microbiome. Furthermore, based on in-depth simulations, we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans.
The unusually high divergence of haplogroup E from other haplogroups suggests an increased coalescence time to the most recent common ancestor in the MUC7 locus. To investigate the coalescent depth of the haplogroups, we used the BEAST software (Drummond and Rambaut 2007) to construct a phylogeny of two haplotypes from each haplogroup described above, including the chimpanzee and rhesus macaque reference haplotypes as outgroups (Figure 4B). This allowed us to estimate the most likely coalescence time for haplogroup E and the other human MUC7 haplotypes to approximately 4.5 million years before present (95% confidence interval ranges from 3.2 to 6.3 million years before present). This indicates that for MUC7 both tree depth among humans and divergence between humans and chimpanzees date back further than most other parts of the genome (Schiffels and Durbin 2014). Our analysis also confirms that the depth of the tree is primarily due to the divergent haplotype group E. Based on the coalescent tree, we noticed that haplogroup E originated prior to the assumed Human-Neanderthal population divergence, previously dated to between 260 to 765 thousand years before present (Prüfer et al. 2014). To quantify this, we first calculated the number of nucleotide differences between each human haplotype in a pairwise fashion. Then we plotted these differences as a histogram (Figure 4C). Based on this plot, nucleotide differences between haplotypes generate “clusters” of similar haplotypes, while more distant haplotypes are further apart. We found that human and chimpanzee haplotypes clustered separately. We also found that human-Neanderthal and human-Denisovan haplotypes, as well as most human- human haplotypes clustered together. Strikingly, haplogroup E haplotypes when compared to other haplotypes form a distinct cluster, suggesting that haplogroup E is unusually divergent from other human haplotypes. Based on linkage disequilibrium analysis, we further showed that the haplogroup E covers entire MUC7 genes and is correspondence to an unbroken haplotype block of approximately 20kb (Figure 4D). The divergent MUC7 haplotype likely introgressed from an archaic African hominin We focused on three possible scenarios to explain the unusual divergence of haplogroup E. First, our null hypothesis was that ancient structure within the human lineage may be responsible for this divergent haplotype in the MUC7 locus. Ancient structure refers to the remnants of genetic structure of populations ancestral to modern humans, which have been maintained across the human genome. It has been reported previously that such variation is especially detectable in regions with low recombination and high mutation rate (μ) (Plagnol and Wall 2006; Lin et al. 2015). Second, we considered long-term balancing selection as a possibility to explain the maintenance of highly divergent lineages within MUC7 region. Indeed, our previous work as well as that of others have shown evidence of such loci where ancient lineages have been maintained within human populations (Gokcumen, Zhu, et al. 2013; Leffler et al. 2013; DeGiorgio et al. 2014; Key et al. 2014; Pajic et al. 2016). However, based on the phylogenetic tree (Figure 4B) and distribution of pairwise distributions (Figure 4C), both ancestral structure and balancing selection scenarios are unlikely. To be more specific, the depth of the branches within haplogroup E are relatively shallow despite the fact that they are highly divergent from other haplogroups. This indicates that haplogroup E’s origins within the human population is relatively recent as compared to other haplogroups. Corroborating this observation is that the haplotype block that defines haplogroup E remained intact (i.e., did not undergo recombination or gene conversion events, Figure 4D), also indicating that the haplogroup did not have the time to recombine within the human lineage. These observations fit neither to ancestral structure nor to balancing selection scenarios very well (Charlesworth 2006; Green et al. 2010; Yang et al. 2012).
Third, we considered introgression from an archaic hominin as a source of this haplotype, which will explain the divergence of haplogroup E from other haplogroups, as well as the apparently short coalescence of this haplogroup within the human lineage. This assumption was based on recent observations of similarly divergent haplotypes that were due to archaic introgression (Huerta-Sánchez et al. 2014; Dannemann et al. 2016). However, introgression of haplogroup E from Neanderthals or Denisovans is unlikely, because haplogroup E is exclusively found in sub- Saharan African populations, whereas introgression events between Neanderthals or Denisovans with modern humans happened after modern humans migrated out of Africa (Vernot and Akey 2014) (Figure 5A, Figure S5). As such, we hypothesize that an archaic hominin, at that time still roaming in Africa, contributed haplogroup E to the ancestors of extant Africans. The possibility of such an introgression has been discussed in recent studies (Hammer et al. 2011; Hsieh et al. 2016).
Taken together, our analyses collectively support the hypothesis that ancient introgression has influenced modern African genomes and that genetic variation in MUC7 locus is influenced by this introgression event.
The most important contribution of our study to the understanding of human evolution is the serendipitous discovery that introgression from an enigmatic African population likely contributed to the noteworthy genetic variation of the MUC7 gene at both single nucleotide and copy number variation levels. Our finding agrees with recent reports of such an introgression in sub Saharan African populations (Hammer et al. 2011; Hsieh et al. 2016), as well as the unexpectedly old human remains (Hublin et al. 2017) and lineages (Schlebusch et al. 2017). The role of MUC7 in host-microbe interaction adds an important novel aspect to the ongoing discussion about the impact of archaic introgression in the human genomes. Indeed, recent studies have shown that haplotypes introgressed from Neanderthals have shaped the variation in the immune system of modern humans (Quach et al. 2016). For example, even though all other 5-copy alleles have the haplogroup G background in Eurasia, the introgressed haplogroup
alone constitutes the majority of 5 PTS-repeat alleles in Africa. Therefore, it is plausible that adaptive forces, that favored 5-copy alleles, may have maintained the introgressed haplogroup E in African populations. Within contemporary datasets, we found no obvious trends in pathogenic pressures or geophysical factors (e.g., humidity or temperature) that explains the distribution of MUC7 PTS-repeats copy number variation in contemporary human populations (data not shown). However, additional analyses, especially among indigenous or ancient populations may reveal such patterns. Lachance et al. suggested that another locus with known copy number variation involving the CSMD1 gene shows evidence of archaic admixture among Sub-Saharan African populations (Lachance et al. 2012). Thus, our results contribute to the emerging notion that functional variation introgressed from an African hominin into modern humans and has been maintained among contemporary African populations.
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quote:Originally posted by Ish Gebor: most African populations never have been tested genetically.
Whose responsibility is it?
African countries?
That is completely irrelevant.
That is most relevant point, you don't know what you are talking about
Lol I already explained it, and backed it up. Stop dancing around the facts with your Eurocentric garbage. Most of Africa has NOT been sampled!!! This is why they represent ghost populations. They are unknown and that is the relevant point!!!
quote:The addition of unsampled or ghost populations can not only modify parameter estimations but also alter our interpretation of the results (see e.g. [75], [76]).
—Laurent Excoffier et al. Robust Demographic Inference from Genomic and SNP Data
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
Getting back to the article, they theorize that African E carrier humans mixed with another African hominid in Africa that was not Neanderthal or Denisova. Without a fossil the evidence is not strong for this but they had found a unique gene in saliva samples
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posted
Furthermore, based on in-depth simulations, we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
Like I said on another site this "Ghost" population was most likely not "archaic." Even if they were these African farmers most likely got it indirectly via mixing with Hunter Gatherers in Africa.
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This happened often with African populations. They simply use a data set and postpone it to some random group, via supposed "statistic analysis".
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