What if there are two or three human species today?

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M.S. Islam

Ad Honorem
Jul 2012
3,333
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And yet was strongly argued by many palaeoanthropologists throughout.
It had been the dominant model until 1980s.

In addition to the original Altai Neanderthal genome sequence, there's now another high-coverage genome from Vindija, along with a low coverage genomes from the same site, plus the genomes from El Sidron and Mezmaiskaya, and the Neanderthal genome found in Denisova cave. Along with the Denisovan genomes themselves, of course. Probably some others I'm forgetting or not aware of.

So, no, research does not all refer to the same sequence.
There is only one (supposedly) full sequencing of Neanderthal DNA done, all others refer back to that as frame of reference.
 

M.S. Islam

Ad Honorem
Jul 2012
3,333
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Giving the overwhelming evidence we gathered in the last 10 years, scientific consensus supports that both the single Out-of-Africa model and Multi-regional model are right. The origin and dispersal of homo sapiens came out to be more complex than previously believed.

We still know little about the history of Homo sapiens in Africa - prior the out-of-Africa migration, I should say. But we have enough evidence to determine that all current non-African people do overwhelmingly descend from one single migration out of Africa which took place between 100kya and 50kya. Nevertheless, there was also some admixture between these Out-of-Africa homo sapiens group and other extant homo species - and those were the Neanderthals and Denisovans. That admixture was also crucial for the divergence and diversity of many human populations today inhabiting Eurasia, Oceania and the Americas (and also many parts of Africa).

All modern human populations outside Africa do descend from one single group of Africans that ventured outside the continent, but they also mixed with other hominids as they went to repopulate the Eurasian landmass.
That conclusion again is based on that faulty Neanderthal interbreeding study.

So, you are saying that most scientists dealing with this issue for the last 10 years are absolutely wrong, but you somehow know more than all of them? That's quite a big statement to make.
Judge for yourself:

"More recently, researchers have been successful in isolating and sequencing DNA from the Neanderthal nuclear genome. Ancient DNA entered the genomics age with the publication of around 27,000 bp of Pleistocene cave bear sequence [12] and more than 13 million bp of woolly mammoth DNA [13]. These studies used cell-based and emulsion-bead approaches to create metagenomic libraries of fossil DNA extracts [12-14]. Such libraries contain both endogenous DNA from the fossils and exogenous microbial DNA from modern contaminants and from microbes that colonized the organism after death or lived in the soil matrix. These approaches were applied to Neanderthals. A 38,000-year-old fossil from Vindija in Croatia (Vindija 80, Figure Figure22 and Table Table1)1) was chosen for analysis because a preliminary PCR and subcloning of the fossil's mtDNA indicated well preserved DNA that was largely free of contamination [15]. Noonan et al. [16] obtained 65,250 bp of Neanderthal genomic sequence using a cell-based approach, while Green et al. [15] obtained more than 1 Mb of genomic sequence using an emulsion-bead based approach.

Both groups made alignments of their sequences with orthologous chimpanzee and human sequences and characterized the substitutions along each lineage. From these, an average sequence divergence time between Neanderthals and modern humans could be calculated. This parameter does not, however, necessarily measure the time that the two populations actually split. To estimate that, the two groups compared their Neanderthal sequence with information on single nucleotide polymorphisms (SNPs) in present-day humans collected by the HapMap project [17]. If the split between humans and Neanderthals is ancient, Neanderthals should rarely, or almost never, carry the 'derived' variant of a human SNP – that is, a variant that is present in some modern human lineages but not in the ancestral human lineage from which both Neanderthals and modern humans descend. On the other hand, if the split is recent, derived variants will be common in the Neanderthal genome and we should expect alleles to be shared between modern Europeans and Neanderthals.

Although they were working with DNA from the same specimen, the two teams came to very different conclusions. Noonan et al. [16] arrived at an average divergence time between Neanderthals and humans of 706,000 years and an estimated time for a population split at 370,000 years ago. They found derived human SNP variants at only three sites in the Neanderthal DNA, two of which are only found in sub-Saharan Africans and not in Europeans. They concluded that the Neanderthal contribution to modern genetic diversity was zero. Green and colleagues [15], on the other hand, calculated the average sequence divergence time between Neanderthals and humans as 516,000 years. To check whether this degree of divergence is comparable to that found within humans, they resequenced a modern human using an identical approach and compared the data to the chimp and human reference genomes. They found the average sequence divergence time between the resequenced human and the reference genome to be 459,000 years. And when Green et al. compared their Neanderthal sequence with the corresponding HapMap data, they found that around 30% of the SNPs were of the derived human type. They therefore concluded that a single ancient split between Neanderthals and humans is unlikely, and there must have been some level of recent gene flow.

Such conflicting conclusions from the same DNA sample not surprisingly led to a reanalysis of the data. Contaminating modern DNA should be less fragmented than genuine ancient DNA. To check their data for evidence of contamination, Noonan et al. [15] had compared their long sequence reads to their short sequence reads and confirmed an equal sequence divergence from modern humans across their data, indicating the absence of contamination. Green et al. [14] had not taken this step. Wall and Kim [18] reanalyzed Green et al.'s dataset and found that their long sequence reads showed significantly lower sequence divergence from modern humans than their short sequence reads, and that their short sequence reads showed an indistinguishable level of sequence divergence from Noonan et al.'s data. Wall and Kim concluded that the sequence used by Green et al. had been contaminated by human DNA – and, using a maximum likelihood analysis, estimated the contamination to be as high as 78%. We also note that Noonan et al. found that 1.3% of their metagenomic library was Neanderthal in origin, whereas Green et al. found 6.2% to be Neanderthal. If this difference is due to contamination, then it is in close agreement with Wall and Kim's likelihood estimates. We believe these findings serve as a cautionary tale that even with extremely stringent protocols, contamination of fossils with modern human DNA will remain a problem."

Source: No evidence of a Neanderthal contribution to modern human diversity

Note: That Green et al study went to become the reference for Neanderthal DNA.
 
Sep 2012
927
Prague, Czech Republic
There is only one (supposedly) full sequencing of Neanderthal DNA done, all others refer back to that as frame of reference.
Why would you say such an odd thing when I just listed some?

There's the Altai Neanderthal:

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors.
There's the Vindija high coverage genome:

To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage.
There is also another full genome from Vindija, but it's composite - in that it's made up of DNA from three different individuals together. This is the original Neanderthal genome sequence.

The other genomes do not 'refer back' to anything; but they are either low coverage (meaning more likelihood of error); or partial, only covering part of the genome.
 
Sep 2012
927
Prague, Czech Republic
Source: No evidence of a Neanderthal contribution to modern human diversity

Note: That Green et al study went to become the reference for Neanderthal DNA.
I'm baffled by your insistence that the last decade never happened. The article you're citing was written in 2008. The authors note at the end of the article:

The continuation of the Neanderthal genome project, along with a better understanding of modern genomic diversity, will shed even more light on the origins of modern humans.
The continuation of the project did indeed provide a better understanding. Let's see what the same authors wrote just two years later:

The first two studies of untargeted Neanderthal genomic DNA recovered 65,000 and 1,000,000 base pairs of DNA sequence, respectively. Unfortunately, the larger study is known to be largely contaminated with modern human DNA probably introduced by laboratory workers and the smaller study may have significant contamination as well. Neither data set showed evidence of a close relaationship between Neanderthals and Europeans or any other living human population.

A team led by Svante Paabo has now sequenced the genome of three Neanderthal individuals to 1.3-fold genomic coverage. This means that each nucleotide in the Neanderthal genome has been read 1.3 times on average. (...) new, stringent methodologies have been employed that have reduced the modern human contamination that plagued previous studies to very low levels, and more than four billion nucleotides of of Neanderthal DNA have now been sequenced and analysed.

(...)

However, through a series of rigorous analyses, Green et al (2010) find a surprising genetic relationship between Neanderthals and the comparative genomes. They show that Neanderthals are more closely related to the three Eurasian genomes (French, Chinese and Papuan) than they are to the two African genomes (San and Yoruba). Though all humans share derived polymorphisms with Neanderthals, the Eurasian genomes have an excess of shared, dervied polymorphisms when compared to Africans. They interpret these results as recent admixture between Neanderthals and non-African modern humans and estimate that Neanderthals contributed 1-4% of the diversity seen in non-Africans.

(...)

The findings of the Neanderthal genome project require us to reevaluate our ideas about modern human origins. Though the majority of our genome follows the predictions of the recent African replacement model, a small but significant percentage of the genomes of Eurasians appear to descend from Neanderthals. Thus, we all primarily descend from a recent African population. However, early during the expansion out of Africa, a small amount of interbreeding occurred between these early modern humans and Neanderthals.
Note: That Green et al study went to become the reference for Neanderthal DNA.
No it didn't. This was the 2006 study referred to above as heavily contaminated. The Neanderthal draft reference genome is the composite genome sequenced by Paabo and his team from the Vindija Neanderthals. Since then, there are at least two more high-coverage genomes (these from individuals rather than composites); plus several low coverage and partial sequences. The collection spans a temporal range of tens of thousands of years and geographically from Spain to Siberia.

Lots of work has been done since 2008. Keep up.
 

M.S. Islam

Ad Honorem
Jul 2012
3,333
Dhaka
Why would you say such an odd thing when I just listed some?

There's the Altai Neanderthal:



There's the Vindija high coverage genome:



There is also another full genome from Vindija, but it's composite - in that it's made up of DNA from three different individuals together. This is the original Neanderthal genome sequence.

The other genomes do not 'refer back' to anything; but they are either low coverage (meaning more likelihood of error); or partial, only covering part of the genome.
They referred to it alright. DNA extracts from fossils come in bits, e.g. a 100 bp long bit. Now how would they know which part of the 3+ billion bp long DNA strands did it belong? They used references, for the first study they used human and chimp DNA as reference. Once a draft sequence of Neanderthal DNA was complete, that would be the one that will be used as reference for future studies, rather than human/chimp.
 

M.S. Islam

Ad Honorem
Jul 2012
3,333
Dhaka
I'm baffled by your insistence that the last decade never happened. The article you're citing was written in 2008. The authors note at the end of the article:



The continuation of the project did indeed provide a better understanding. Let's see what the same authors wrote just two years later:





No it didn't. This was the 2006 study referred to above as heavily contaminated. The Neanderthal draft reference genome is the composite genome sequenced by Paabo and his team from the Vindija Neanderthals. Since then, there are at least two more high-coverage genomes (these from individuals rather than composites); plus several low coverage and partial sequences. The collection spans a temporal range of tens of thousands of years and geographically from Spain to Siberia.

Lots of work has been done since 2008. Keep up.
It was the same Green et al study (Paabo had been part of it) that ultimately went on to publish draft sequence of Neanderthal DNA.
https://www.eva.mpg.de/neandertal/press/presskit-neandertal/pdf/Science_Green.pdf
 
Sep 2012
927
Prague, Czech Republic
It was the same Green et al study (Paabo had been part of it) that ultimately went on to publish draft sequence of Neanderthal DNA.
https://www.eva.mpg.de/neandertal/press/presskit-neandertal/pdf/Science_Green.pdf
When they wrote "Wall and Kim concluded that the sequence used by Green et al. had been contaminated by human DNA " they were referring to "Green RE, et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330–336". They were again referring to this in the quote I posted from two years afterwards when they note "Unfortunately, the larger study is known to be largely contaminated with modern human DNA probably introduced by laboratory workers and the smaller study may have significant contamination as well. " As they mentioned in both articles quoted, this sequence was about 1 million nucleotides long.

In the second article I quoted, the same authors refer to Green et al 2010, to which you now link. It's about this article that they report "new, stringent methodologies have been employed that have reduced the modern human contamination that plagued previous studies to very low levels, and more than four billion nucleotides of of Neanderthal DNA have now been sequenced and analysed."

The criticisms they noted in 2008 about Green et al 2006, are not relevant to Green et al 2010, as they themselves write very clearly.
 

M.S. Islam

Ad Honorem
Jul 2012
3,333
Dhaka
When they wrote "Wall and Kim concluded that the sequence used by Green et al. had been contaminated by human DNA " they were referring to "Green RE, et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330–336". They were again referring to this in the quote I posted from two years afterwards when they note "Unfortunately, the larger study is known to be largely contaminated with modern human DNA probably introduced by laboratory workers and the smaller study may have significant contamination as well. " As they mentioned in both articles quoted, this sequence was about 1 million nucleotides long.

In the second article I quoted, the same authors refer to Green et al 2010, to which you now link. It's about this article that they report "new, stringent methodologies have been employed that have reduced the modern human contamination that plagued previous studies to very low levels, and more than four billion nucleotides of of Neanderthal DNA have now been sequenced and analysed."

The criticisms they noted in 2008 about Green et al 2006, are not relevant to Green et al 2010, as they themselves write very clearly.
Continuation of same study.

The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.
Source: Neanderthal genome project - Wikipedia
 

sparky

Ad Honorem
Jan 2017
5,200
Sydney
an interesting side to both sub-species life is their parasite ,
I.E. the louse , this affectionate creature love its host
to the point that Sapiens and Neanderthal have a clearly distinct breed of the critter
things got somewhat more confusing with the Oh so human habit of killing anyone male and shagging anything female
this old human tradition make the genetic result looking like a police report on multiple rape ( consensual or not , who know )
the sad result , scientifically wise , is that there were several episode of interbreeding
probably more ,of which no trace remain
this got us some interesting venereal diseases too , there is a price for free love after all
for information , the East Asian population came , like the westerners , from central Asia
the divergence was quite recent then they went north , the epicanthic fold is an adaptation to hunting in snow country
they were successful enough to push (exterminate) the older East Asian populations

Paying a heavy price for loving the Neanderthals
 
Sep 2012
927
Prague, Czech Republic
Continuation of same study.

"The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006."

Source: Neanderthal genome project - Wikipedia
So, the Neanderthal genome project was founded shortly after Green et al's findings published in 2006. Good to know.

Now, having said that, it was in a sense the continuation of the work they had started. And in continuing their work they figured out how to fix the contamination problems your 2008 article noted. As was pointed out by the very people who wrote that article.

So, the issues discussed in the 2008 article are not relevant to the Neanderthal draft genome sequence. Which is not the only fully sequenced Neanderthal genome.
 
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