January 30, 2014

Resurrecting Neandertal Lineages (Vernot and Akey 2014)

Coinciding with the publication of Sankararaman et al. (2014) in Nature, another paper on Neandertal ancestry into modern humans appeared in Science. From the paper:
On average, we found 23 Mb of introgressed sequence per individual (Fig. 1F), with East Asian individuals inheriting 21% more Neandertal sequence than Europeans. Within subpopulations, we found small but statistically significant variation in the amount of introgressed sequence among Europeans (Kruskal-Wallis rank sum test; p-value = 4.2 × 10−12), but not among East Asians (p-value = 0.43).
and:
Consistent with recent inferences (5, 9), observed patterns of introgression were incom-patible with a one pulse model (Fig. 3B), suggesting that gene flow be-tween Neandertals and humans occurred multiple times. Although we varied many parameters of each model (10) (fig. S14), only the ratio of ancestral effective population size between East Asians and Europeans (NeASN/NeEUR) and the relative amount of introgression between the sec-ond and first pulse (m2/m1) had appreciable effects on model fit (Fig. 3B). We estimate that NeASN/NeEUR is 1.29 (95% CI of 1.15-1.57), and that East Asians received an additional 20.2% (95% CI of 13.4%-27.1%) more Neandertal sequence in the second pulse (10).

Science DOI: 10.1126/science.1245938

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

Benjamin Vernot, Joshua M. Akey

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.

Link

31 comments:

barakobama said...

When will people learn European is not a race. Laz 2013 and so many other things found before that show Europeans have multiple sources of ancestry and some Europeans can be very different from each other genetically. For example Greeks and Finnish. Most Europeans have similar admixture and because of that closely related but it is more complicated than many assume.

The light skin mutations within genes TYR, SLC24A5, SLC45A2 are about as popular in west Asians as they are in Europeans. Yet 23andme and others claim if someone has one of those mutations they have European ancestry. Now we know through DNA from Mesolithic Europeans and Neolithic Europeans that all those mutations except the one in gene TYR were brought to Europe from the near east with farming.

It gets so annoying how people use European to represent west Eurasian.

It seems this study made the same assumptions.

andrew said...

While a two pulse model may be parsimonious, in light of high Neanderthal admixture in Otzi, I think that a more complex model is needed.

In this model there is a first wave of Neanderthal admixture impacting all Eurasians.

People migrating to East Asia via a Southern route pick up a second wave early on that reaches fixation and is shared by all East Eurasians who migrated via this route. (A subset of these East Eurasians admix with Denisovans en route to Melanesia).

Hunter-gatherers migrating to Europe pre-LGM pick up a third wave.

Europe is then repopulated from West Asian populations that have experienced neither the second or third waves, thereby diluting previously elevated levels of Neanderthal admixture in Europe. The uneven proportions of pre-LGM European hunter-gather ancestry in various Europeans make the Neanderthal admixture proportions in them not fully homogeneous.

Grey said...

"skin phenotypes"

makes sense if Neanderthals had adapted to northern latitudes.

terryt said...

"with East Asian individuals inheriting 21% more Neandertal sequence than Europeans".

Surely it is extremely unlikely that admixture is from a 'southern' migration.

Grey said...

"East Asian individuals inheriting 21% more Neandertal sequence than Europeans"

Assuming the Neanderthals were in the north any reason East Asians might have had longer contact?

More mountains in the north of Asia?

http://www.nationsonline.org/oneworld/map/physical_world_map_1600.htm

Mark Moore (Moderator) said...

Andrew,

That is a very interesting hypothesis. I can't see all the data you see. Is it the N. European Hunter gathers that are lacking in Neandertal genes? I am gong by your statement " of pre-LGM European hunter-gather ancestry in various Europeans make the Neanderthal admixture proportions in them not fully homogeneous."

What is the difference in the proportions in various European groups?

andrew said...

"Surely it is extremely unlikely that admixture is from a 'southern' migration."

I would expect that wave one of admixture took place in Arabia, that wave two takes place in Eastern Iran, that wave three takes place in Europe, and that the admixturing diluting repopulation of Europe after the LGM involves people who are ancestral to wave one but not wave two (e.g. from the Middle East and Anatolia and the Caucasus).

" Is it the N. European Hunter gathers that are lacking in Neandertal genes? I am gong by your statement " of pre-LGM European hunter-gather ancestry in various Europeans make the Neanderthal admixture proportions in them not fully homogeneous."

What is the difference in the proportions in various European groups?"

I don't have full access to the paper either, although it indicates that the variation is quite modest even though it is statistically significant. My hypothesis is that high Neanderthal admixture in Europe is associate with pre-LGM European hunter gatherer ancestry which tends to be highest in populations with the most recent European hunter-gatherer roots, mostly in Northern Europe. There, pre-LGM hunter-gather root ancestry might be present in some single digit percentage in some individuals, in most of the rest of Europe, the percentage is likely at the very low end of that range to negligible. My estimate of Mesolithic European hunter-gatherer ancestry in modern populations is on the order of 15%-20% but higher in some populations mostly in Northern Europe, and lower in others (an average of the percentage of mtDNA U5 and Y-DNA I, respectively, in a population is a decent enough proxy for this ancestry even if it is crude), and the proportion of that which is pre-LGM is probably a pretty modest minority of that. My estimate, for a variety of reasons too involved to sum up in a blog comment, of the average Neanderthal admixture in pre-LGM, post-Neanderthal extinction European hunter gatherers is about 8%. Maybe the average modern European is 2% pre-LGM hunter-gatherer with significant variability in that percentage. The lowest Neanderthal admixture rates seen in Europe within the observed range of variation probably reflects the wave one only populations at the time of fixation, with additional Neanderthal admixture due to pre-LGM hunter-gatherer admixture. The East Asian 20% excess Neanderthal admixture probably reflects wave two admixture in Iran and its uniformity in amount suggests an admixture event at about the moment of the West Eurasian-East Eurasian genetic divide's emergence shared by all East Asians ca. 60-80kya that reached fixation early on, while the Mesolithic non-European forager migration in the repopulation of Europe after the LGM would have started around 18-14 kya and really taken off with the European Neolithic ca. 8 kya which was weakest in its impact in Northern Europe which still had hunter-gather populations as late as about 1-3 kya. Thus these genes haven't had nearly as much time to reach fixation in Neanderthal ancestry percentage.

Tobus said...

@barak:The light skin mutations within genes TYR, SLC24A5, SLC45A2 are about as popular in west Asians as they are in Europeans.

This isn't completely true, you are correct about SLC24A5 and TYR (although TYR isn't fixed in Europe to start with), but frequencies of SLC45A2 are notably lower in West Asia. While SLC24A5's distribution is consistent with a non-European origin, SLC45A2's distribution is consistent with it being a European-only allele spread via recent admixture... so 23&me are ~33% right.

The reason studies don't talk about West Eurasians as a group is because there is an assumed 3-way African/European/East Asian model and sampling strategy, based on phenotype and genetic distances. In this model in between populations are generally described as some mixture of these three, so including them doesn't help in explaining the genetic history of the three lineages. It's a bit misleading because 9 times out of 10 the studies don't mean people in geographical Europe when they use "European" in an ancient context, they mean "ancestors of Europeans" who may have been geographically located in West or Central Asia at the time in question. The don't however mean "West Eurasian" as this includes people with African or Asian admixture subsequent to the isolation of modern "Europeans".

eurologist said...

Andrew,

Quite a bit of speculation in your post... and what is that non-European post-LGM European re-population? Never heard of such a thing; the archaeological record shows the opposite.

Fig. 1F of the paper shows the distribution of the amount of introgressed sequences for all individuals, sorted by group. For Europeans, it typically varies between 18 and 25 Mb, where the intra-group variation (~+- 12-15%) is larger than the between-group variation (5-10% at the extreme positions (individuals with the lowest or highest amount) and also for the average (estimated from the figure).

Tuscans and CEU have individuals with the lowest amount, but CEU also has individuals with the highest amount, likely reflecting their broader ancestry. Finns have the highest amount of introgressed sequence - both for the extreme individuals as well as on average. Spanish also have a fairly high cut-off, meaning their people with the lowest amount have relatively a lot, followed by British.

For the average, the order from lowest to highest is TSI, IBS, CEU~GBR, FIN.

All Asians with the lowest amount of admixture still have more than the average European, and except for a few Finns, all Europeans with the highest amount of admixture have less than the average Asian. The difference between the three Asian populations (Southern Han, Han from Beijing, Japanese) is very small, just reflecting the smaller gene pool of the Japanese (fewer extreme individuals).

At a false discovery rate threshold of 5%, Europeans have a unique 206 Mb, Asians 245 Mb, with an overlap of 149 MB shared. So, each group has more unique sequences than the two share.

Rokus said...

Depletion of Neanderthal sequences may not be the result of hybridization, as has been proposed by McVicker et al. (2009). Negative selection of deleterious sequences and positive selection of mutated sequences by the replacement of older sequences are also very common autonomous genetic processes. Unfortunately, this is one out of two new papers on the apparent depletion of Neanderthal-like (~conservative?) sequences that take ongoing negative effects of hybridization for granted. Based on what? The biochemical mechanism behind such an ongoing process, that apparently even affects Neanderthal genetic material equivalent to modern human ancestors, remains unclear. Wouldn’t this process be somewhat similar in case the genome of a direct archaic ancestor of modern humans would have served as a reference?

The Depletion of Neanderthal Hybridization – Or Was It?

eurologist said...

Sorry for the second post, my last paragraph did not paste. Here is my speculation based on the distributions:

It is reasonble to assume that European individuals with extreme (high or low) Neanderthal admixture are due to admixture with an external population of mostly such individuals. The plots seem to indicate a very old such admixture (Gravettian adding extremes on the high side, up to 25Mb?), and two relatively recent ones (Neolithic to Iron Ages?), the second one or which generating the low-end tail - which is almost non-existant in Spanish, British, and Finns. I would estimate that this second admixture event is with a (West Asian?) population that had about 17-19 Mb Neanderthal admixture, while the Mesolithic Northern/ Central European average was about 22-23 Mb, with about 19-21 Mb in Neolithic Southern Europe.

Grognard said...

Rokus - X chromosome shows signs of negative selection, and this is an area that's long associated with cross-species infertility in other animals.

I wouldn't be surprised if this is where many appearant disease come from - you have one generally positive gene but not the other gene needed to keep it from being harmful. Not everything is going to play nice with everything else and we have other examples of this.

arch said...

Can someone explain the "Neandertal Mania" that has taken hold over 'researchers'?

I cant justify 3 papers on this flogged-to-death topic, that mostly rehash the same tired issues and claim to have new answers for the roadblocks to neandertal cross-breeding, which are really the same exact tired speculation about 'sterile' offspring that no proof actually supports.

It seems that their is a funding avail for some reason for this so-called neandertal research that is driving a outsized interest in this topic and resulting in a lot of papers that are really inconclusive but designed to lend some credence to the claims through sheer volume of papers.

None of these papers touch on the fact that we KNOW at least SOME (if not all) of what is being entirely labeled as 'neandertal' genetic material is actually common hominid ancestry from a common ancestor and not due to inter-breeding, yet all these theorists and 'scientists' so eager to publish re-hashed claims on this topic almost completely ignore common hominid ancestry.

Whatever the case.. I can see a paper or two on SPECULATED 0.1-0.2% of a modern human genome that MIGHT be related to Neandertal ingression, however there is virtually no ancient euro DNA studies on modern humans that would be relevant to the known 99.8% of our ancestry or discussion of the huge problems with claims concerning neadertal cross-breeding, nor any discussion at all of the certainty that some or all of this material actually results from a common hominid mutual ancestor - not neandertals.

Brad Foley said...
This comment has been removed by the author.
Brad Foley said...

Andrew: I happened to attend a seminar last week at which Akey spoke. I happened to mention that I found the discrete 2-event hybridisation model a bit unconvincing. He agreed that the actual hybridisation events (they estimate about 300 total) were surely spread out across time and space while Homo sapiens coexisted with Neanderthals.

They found by adding a single parameter (a later hybridisation event) they got very good agreement with the real data. Of course fitting a more complicated model (like the ~4 stage model you propose) would would require some hefty model fitting, and lots of detailed data.

Rokus said...

'Rokus - X chromosome shows signs of negative selection, and this is an area that's long associated with cross-species infertility in other animals.'
This particular chromosome, yes. And also the repatterning of the whole genome, but so far this hybridization process is thought to stabilize.

Meyer et al (2012), already suggested that 'reduced evidence of archaic gene flow may be a general
feature of chromosome X.'
This applies to Denisovan and Neanderthal introgression (Table S30). However, there is something strange going on: archaic ancesty compared with the genome-wide average varies much more for Denisovan chromosomes than Neanderthal, what I interpreted as a much more intensive hybridization contact for Neanderthal that smoothed out the erratic pattern (as with Denisovan admixture) that could be expected from each single hybridization event.
However, what I find difficult to accept, and I am unaware of any scientific foundation of the assertion, is that ongoing negative selection in F2-Fn offspring occurred and still occurs for non-male related introgressed (archaic) genes. At least this effect was never observed in Oca's hybridization experiment on mice (2004). So. since X also evolves faster, I wonder if it isn't about time for the scientific community first to fully understand the replacement process of mutated haplotypes.

About Time said...

Would be good to see a real global study of Neanderthal introgression across different populations. I have trouble with the study that finds a peak in Tuscans, when less formal 23andme postings show this maxing out more in Chinese, Brits, etc and less in S Europe.

And someone needs to call Milford Wolpoff and get him to dig into this with his comments and suggestions. He should make a new updated book with all the genomic stuff, people would love it.

arch said...

"Rokus - X chromosome shows signs of negative selection, and this is an area that's long associated with cross-species infertility in other animals."

Nope. Wishful (and) too convienient thinking.
What is long associated with infertile offspring in a family or genus is simple Chromosomal mis-match.

64 Horse chr. vs. 62 Donkey chr. = sterile mule offspring of two equines that are otherwise physically similar.

We know that no such condition exists between Neandertal and Anatomically Modern Humans. The End.

The theorists who have already proclaimed that Neadertal are on avg 3% of the modern humans genome need a answer to why not a single instance of a single admixed Neadertal line exists in even one modern human, so for them.. its not 'the end'. Its a huge a usually ignored or avoided problem that can really only be solved to their liking by assertions that Neadertal mixed offspring were infertile but at the same time managed to introduce enough genetic material to 50k years later constitute 3% of every modern human genome, and this is a hard thing to prove because its a fairly nonsensical assertion.

Thus the endless toying with infertile offspring with no proof of any sort, and the ignoring of the fact that the period of separation between most AMH populations and a Congo Pygmy or a New Guinea tribesman is larger that the time of separation from Neandertals who are alleged ancestors as well.

Congo Pygmy and New Guineans, Micronesians, Negrito Islands.. etc.. can all interbreed fertile offspring with any other Chromosomally normal modern human as would be expected of Neadertal as well, as they were chromosomally compatible. This is a major thorn in the sides of neandertal admixture promoters, and they can offer only bluster and weak unsupported suggestion of 'infertile' offspring that hold no water.

I am seriously tired of the desperate and constant Neandertal tall tales. Its a lot more easily explained that the material being referred to as Neadertal is inherited in the vast majority of cases from a common ancestor that Neandertal and AMH share. Simple. No tall tales or 'thorny' problems to address.

How about ENOUGH with the Neadertal claims and spam papers for a while.
Lets get some pertinent studies on ancient AMH DNA within cultures or historical populations-
the studies on the origin of wheat strains, pigs and the same 1/2 dozen or so Neandertal genomes that the same people all use have been exposed to us all to frequently, theoretically and unconvincingly at this point.

eurologist said...

And someone needs to call Milford Wolpoff and get him to dig into this with his comments and suggestions.

For what purpose? I am perplexed.

About Time said...

@Eurologist. Wolpoff was the lone voice reminding scientists that the "stones and bones" left some open questions for enthusiasts of a complete replacement hypothesis when the first y DNA and mtDNA studies were published. Ie, "Adam and Eve" had company.

terryt said...

"Nope. Wishful (and) too convienient thinking.
What is long associated with infertile offspring in a family or genus is simple Chromosomal mis-match. 64 Horse chr. vs. 62 Donkey chr. = sterile mule offspring of two equines that are otherwise physically similar".

Your theory on Chromosomal mis-match is inconsistent. Check out this link on Przewalski's horse:

http://en.wikipedia.org/wiki/Przewalski's_horse

Domestic horses have 64 chromosomes, yes, but Przewalski's horse, like donkeys, have 62:

"The karyotype of the domestic horse differs from that of Przewalski’s horse by an extra chromosome pair either because of the fission of domestic horse chromosome 5 in Przewalski’s horse or fusion of Przewalski’s horse chromosomes 23 and 24 in the domestic horse. In comparison, the chromosomal differences between domestic horses and zebras include numerous translocations, fusions, and inversions. Przewalski’s horse is known to have the highest diploid chromosome number among all equine species. Przewalski’s horse can interbreed with the domestic horse and produce fertile offspring (65 chromosomes)".

In fact the two types of horses interbreed so successfully that hybridism with domestic horses is the main obstacle to keeping a pure Przewalski’s horse population. As a result we can conclude it is not simply the number of chromosomes that matter but what is on those chromosomes.

"We know that no such condition exists between Neandertal and Anatomically Modern Humans. The End".

As far as I'm aware we have no ida how many chromosome pairs Neanderthal had. The original comment regarding the X chromosome is very likely to be correct. In the formation of hybrids between any two pairs of species the first thing that appears with increasing distance is male infertility. This is seen between cattle and yaks and between cattle and bison. And female mules are not always sterile, although males always are.

"The theorists who have already proclaimed that Neadertal are on avg 3% of the modern humans genome need a answer to why not a single instance of a single admixed Neadertal line exists in even one modern human"

Hang on. Surely that 3% of the genome is evidence of Neanderthal/human admixture. The paper claims sterility within the offspring was not absolute. Sterility depended on which genes from each parent were inherited by each particular individual.

"ignoring of the fact that the period of separation between most AMH populations and a Congo Pygmy or a New Guinea tribesman is larger that the time of separation from Neandertals who are alleged ancestors as well".

Not so. The maximum period of separation between AMH populations and a Congo Pygmy or a New Guinea tribesman is around 60,000 years while that between AMH and Neanderthal is at least half a million.

"Its a lot more easily explained that the material being referred to as Neadertal is inherited in the vast majority of cases from a common ancestor that Neandertal and AMH share".

Inadequate as an explanation. Many African have minimal Neanderthal admixture.

Locrian said...

arch — I am very confused by what you are claiming and what you are denying. You don’t think it’s impossible that Neanderthals and AMH interbred, I suppose you agree that this could have happened. And yet somehow you think that it is not interesting if it did happen — obviously not interesting to you, but why would it not be interesting to anyone else?

You seem to be claiming that what we are taking to be genes inherited into modern humans from Neanderthal admixture is all the result of common African ancestry. Then how can modern Africans, modern Europeans, Modern Asians differ in the amount? I’m sorry, but these claims of yours make no sense to me.

Rokus said...

Terryt

Domestic horses have 64 chromosomes, yes, but Przewalski's horse, like donkeys, have 62

Please count the result of a fission of domestic horse chromosome 5 in Przewalski’s horse, or a fusion of Przewalski’s horse chromosomes 23 and 24 in the domestic horse.
Answer: 66. Przewalski's horses are not like donkeys.

"Its a lot more easily explained that the material being referred to as Neadertal is inherited in the vast majority of cases from a common ancestor that Neandertal and AMH share".

Inadequate as an explanation. Many African have minimal Neanderthal admixture.

What is called Begging the question. The definition of Neanderthal admixture doesn't mind the shared part available at saturation level in modern humans. Eg. so far the shared part of Africans with Europeans doesn't show much variety, all the contrary. But I suppose you already have all the answers on the shelf that you only need to cite in biblical order.

terryt said...

"But I suppose you already have all the answers on the shelf that you only need to cite in biblical order".

You are quite welcome to ignore the facts on inter-specific hybrids. With your comments on the horses you conveniently forget that the different chromosome numbers between chimps and humans is also the result of combination or splitting.

arch said...

Your theory on Chromosomal mis-match is inconsistent. Check out this link on Przewalski's horse:
In fact the two types of horses interbreed so successfully that hybridism with domestic horses is the main obstacle to keeping a pure Przewalski’s horse population.


You are changing my argument that you cannot answer except with unsupported theory (chromosomal mismatch is the prime mover in preventing AMH/Neadertal interbreeding) into a argument that I did not make (chromosomal mismatch commands 100% sterility or infertility) Notably.. this Przewalski citation is not even convienient your OWN position (sterile offspring somehow account for no modern neadertal direct lines despite massive interbreeding with AMH) -
but is useful to you ONLY to rather clumsily seek to impeach my argument.
Like with Downs-Syndrome genetically affected Humans, chromosomal count mismatch need not 100% prevent mating/fertility although it often can, it generally results in supression or reduced fertility.


As far as I'm aware we have no ida how many chromosome pairs Neanderthal had. The original comment regarding the X chromosome is very likely to be correct.

We know that Denisovans share the same AMH chromosome fusion on Chr.2 that is not shared by primates,
http://biologos.org/uploads/static-content/denisovans_fig_3.jpg
and we know that Neandertal are downstream of Denisovans, so if Denisovans share the same 46 Chr fusion event as AMH. then its not honest to assert we could rationally expect Neadertal to carry 48 Chr. All the evidence is not on your side to assert they diverge chromosomally or could reasonably be expected to.


Hang on. Surely that 3% of the genome is evidence of Neanderthal/human admixture. The paper claims sterility within the offspring was not absolute. Sterility depended on which genes from each parent were inherited by each particular individual.

That 3% in my opinion overwhelmingly relates to common ancient ancestry between all groups (Denisovan/AMH/Neandertal).. you second sentence admits as much unwitttingly. The difference in modern populations relates to African inheritance from other precursor populations that made lesser contributions to Asian and European populations, and most importantly to the degree of inheritance and as you said, WHICH GENES were inherited into these bottlenecked and divergent populations.

arch said...

Not so. The maximum period of separation between AMH populations and a Congo Pygmy or a New Guinea tribesman is around 60,000 years while that between AMH and Neanderthal is at least half a million.

African divergence from Europeans has long been cited at 100 - 150k+. Recent papers have placed Neadertal divergence as recently as 170k. On top of that Neadertal ingression, which you assert on a large scale, would have begun as soon as these populations came into contact, which is not 500k years ago. From that time one their genes would be our genes if such large scale introgression took place.
These theoretical formulas and math-generated age estimates are generally laughable and you really only need to look at the insistent, serious pronouncements of Haplogroup and clade splits over the course of the last decade, which later under scrutiny fail miserably in their accuracy and construction to take extra caution when such mathematical based theories get offered as solutions to genetics issues that we have only a small part of the neccesary data to make a accurate calculation.

Inadequate as an explanation. Many African have minimal Neanderthal admixture.

Many Black Africans have a lot of Neandertal admix, unfortunately for your argument. Also, recent claims suggest humans have double the segments from Denisovans, not Neandertal, and Asians massively outstrip Europeans in what is claimed to be "Neadertal" admix analysis, despite the fact that they did not live in proximity to regions with Neadertal archaeological evidence.
Too many people have staked their careers on MAKING the Neadertal Humanitys, and particularly Europeans, ancestors, and when they could not find the evidence to prove this directly they started making it up using any anecdotal or math-formula based assertion, calling this manufactured theory evidence (which its not) and ignoring the huge problems that did not help their case. If you find a Neadertal Hg modern Human let me know-
TIL THEN, this is a bridge too far, there is no proof and you are ignoring the more probable reason these groups all share common ancestry which is that we know they ALL SHARE COMMON ANCESTRY!

AndyC said...

Chinese man with 44 chromosomes still can poroduce fertile offspring. See link below. Seems that the key issue in hybridization is the genes, not necessarily the chromosomes.

http://genetics.thetech.org/original_news/news124

terryt said...

"Seems that the key issue in hybridization is the genes, not necessarily the chromosomes".

Yes. But Rokus is quite prepared to ignore facts in this discussion. Further information regarding chromosome number and hybrid capability in horses (admittedly from Wikipedia but I have long been aware of the facts):

http://en.wikipedia.org/wiki/Zebroid

A few quotes:

"Donkeys and wild equids have different numbers of chromosomes. A donkey has 62 chromosomes; the zebra has between 32 and 46 (depending on species). In spite of this difference, viable hybrids are possible, provided the gene combination in the hybrid allows for embryonic development to birth".

So different chromosome number in no way prevents the formation of a hybrid, merely the fertility. But:

"" A hybrid has a number of chromosomes somewhere in between. The chromosome difference makes female hybrids poorly fertile and male hybrids generally sterile due to a phenomenon called Haldane's Rule".

Female hybrids are 'poorly fertile', not always 'infertile'. And another place where hybridism produces conseravtion problems:

http://www.princeton.edu/~dir/pdf_dir/2009_Cordingley_AnimConser.pdf

Quote:

"Two hybrids have successfully raised foals to over 3 months in age, including one
which has reached adulthood, indicating the fertility of female hybrids and
viability of their offspring".

So again we have two horse species with different chromosome numbers producing fertile female offspring.

"These zebra species diverged o1 million years
ago (Yang et al., 2003; Carbone et al., 2006) and only differ
in chromosome number by one – Grevy’s zebra have 23
haploid chromosomes and plains zebra possess 22 haploid
chromosomes".

The divergence of 1 million years may be relevant to human/Neanderthal divergence.

terryt said...

"you are ignoring the more probable reason these groups all share common ancestry which is that we know they ALL SHARE COMMON ANCESTRY!"

Are you claiming there has been no mixing of human types EVER? That is most unlikely, especially considering the substantial mixing happenning today.

"if Denisovans share the same 46 Chr fusion event as AMH. then its not honest to assert we could rationally expect Neadertal to carry 48 Chr"

I have never claimed Neanderthals and modern humans have a different number of chromosomes. I said that chromosome number is not the cause of reduced fertility between species. It is what is on the chromosomes that is important.

"You are changing my argument that you cannot answer except with unsupported theory (chromosomal mismatch is the prime mover in preventing AMH/Neadertal interbreeding)"

Is that last your quote or a claim made by someone else? We have no evidence that humans and Neanderthals had a different number of chromosomes.

"We know that Denisovans share the same AMH chromosome fusion on Chr.2 that is not shared by primates"

As do Neanderthals, from the same link.

"Recent papers have placed Neadertal divergence as recently as 170k."

Which 'recent papers'?

"Asians massively outstrip Europeans in what is claimed to be "Neadertal" admix analysis, despite the fact that they did not live in proximity to regions with Neadertal archaeological evidence".

But many of their ancestors apparently passed through regions where both Neanderthals and Denisovans were common.

"If you find a Neadertal Hg modern Human let me know-"

From the information on hybrids, and keeping Haldane's Law in mind, we can presume that if both Neanderthals and modern humans were matrilocal in social organization male hybrid sterility alone would explain the extinction of both Neanderthal mt- and Y-DNA today.

Rokus said...

'You are quite welcome to ignore the facts on inter-specific hybrids. With your comments on the horses you conveniently forget'

Whoever you met on the moon, it wasn't me.

'But Rokus is quite prepared to ignore facts in this discussion.'

Don't know what you are up to, sure not something ad hominem?

All I had to say is that the assertions on male-related infertility are not consistent with the selective expulsion of non-fertility related functional Neanderthal genes, and neither is such a relation supported by references or tested hypotheses.

Fertility problems based on Robertsonian translocations, not mentioned in the studies, may occur, though the suggested progressive influence of some distant hybridization effect remains equally unsupported by any evidence. Translocations are currently unknown as genetic markers of any population, so the human genome must have been stabilized soon after each hybridization event. Further spontaneous chromosomal changes should affect the basepairs of both parental lineages indiscriminately, and are hardly likely to hit mixed sequences differently for functional and non functional basepairs.

terryt said...

Sorry if I misunderstood but you seemed to be saying that a close chromosome number difference made hybrid incompatatbility unlikely. Chromosome number difference is not really important in the matter. It is what is on the chromosomes that is important. Robertsonian translocations seem to be random events are are unlikely to be a driver of in hybrid infertility. That is probably why the authors ignored them.