1. Genes might not be so selfish after all

Comment #249303 by B.L.Z. Bub on September 18, 2008 at 1:06 am

An example of Linklater's careful "research"

Linklater wrote
"these changes may remain through cell divisions for the remainder of a cell's life, and sometimes these changes can last for multiple generations".

Wikipedia wrote
These changes may remain through cell divisions for the remainder of the cell's life. Sometimes the changes last for multiple generations.

Plagarism?

2. Neanderthal DNA Shows They Rarely Interbred With Us Very Different Humans

Comment #228536 by B.L.Z. Bub on August 12, 2008 at 7:22 am

"So if I find a Neanderthal who is the great-great-great-great.....great grandchild of a female hybrid produced by a male Neanderthal and a female sapiens around 70,000 years ago, that individuals mtDNA is going to be a lot closer to modern humans than 660,000 years."

Now you are moving the goal posts, I said in an earlier post that this paper is only relevant to female Neanderthal x male sapiens interbreeding. So you are arguing a point I have already conceded. The individual you postulate above will possess H. sapiens mtDNA and that individual's mtDNA is going to fall exactly into the range of modern human mtDNA and will differ from the mtDNA from the individual reported in this paper to the same extent and give a separation of 660,000 yrs ago.

Can you propose a scenario where male Neanderthal x female sapiens interbreeding is likely to be MORE frequent than the reverse? The assumption of the study is that the only really likely mating would be male sapiens x female Neanderthal for the following reasons.

1. Hominids expanding into new territory will not be short of resources so inter-group warfare will be rare. Thus male mortality will be low relative to female mortality (child birth), therefore there will be a shortage of women in sapiens groups.
2. More sophisticated weaponry and ruthlessness will allow sapiens to steal Neanderthal women without losing their own.
3. There would be little incentive for male sapiens to join Neanderthal groups.
4. It is highly improbable that male sapiens would accept male Neanderthals into their groups.

So only female Neanderthal x male sapiens matings are likely to be frequent and they will nearly always occur within sapiens groups.

"I think it is safe to assume that mtDNA diversity was less 70,000 years ago than it is today (less people), but even if it wasn't, you would still be cutting about 300,000 years off of your maximum convergence date for sapiens and Neanderthal mtDNA. Why? Because the mtDNA you pulled out of that Neanderthal fossil was really mtDNA from a sapiens female who lived about 70,000 years ago"

Yes it would be but her mtDNA still diverged from Neanderthal mtDNA 660,000 yrs ago. So no it would not give any different result re. divergence, but sapiens mtDNA in a morphologically Neanderthal fossil will show at least one male Neanderthal x female sapiens mating, it will not confirm extensive interbreeding or a different divergence date.

I am signing off from this now, got to do some work, but look forward to renewing your acquaintance if you start a similar discussion on the forum.

3. Neanderthal DNA Shows They Rarely Interbred With Us Very Different Humans

Comment #228429 by B.L.Z. Bub on August 12, 2008 at 3:40 am

Christopher

Not sure we are making much progress, shame no one else is joining in as I am running out of steam, perhaps you would like to start a thread on the forum.

"What I mean by "resetting the DIVERGENCE clock" is that individual mtDNA strains have become widely distributed throughout an interbreeding population. When that population splits, it is possible (or probable, depending on the amount of interbreeding) that the diverging groups will contain individuals who share the same mtDNA. Therefore, mtDNA extracted from any descendents of those individuals will show a divergence date compatible with the timeframe when the interbreeding population parted ways."

Your premise seems indisputable but your conclusion seems to me to be a non sequeter. In both populations post-split, individuals will contain either neanderthal mtDNA or sapiens mtDNA. The descendants of these will have inherited one or the other. I am completely at a loss to understand how you conclude that "any descendents of those individuals will show a divergence date compatible with the timeframe when the interbreeding population parted ways." You will have to show me a diagram.

I think there is a confusion between populations and individuals here. mtDNA strains part company with each other at every generation. Imagine a female having two daughters, one of which experiences a single point mutation. We now have two sisters with different mtDNA sequences. n generations later (assuming a continuous maternal line) you could test each of these sisters descendents and, by counting the number of differences in their mtDNA, can calculate how long ago their common mother lived. They might all have lived in the same village for a thousand years, or one sister might have emigrated to China and married a chinaman and all her daughters and grand daughters married locally. While the nucleic DNA will become entirely chinese, the mtDNA will not have been affected one jot by mate choices or degree, or timing of separation from parental population.

The conclusion of the paper is that there cannot have been sufficient interbreeding for neanderthal genes to have persisted to the present day. Sure there cold have been limited interbreeding that left no descendents, either because it was rare so by misfortune all lines went extinct, or because offspring were sub-fertile. But I think it does falsify the hypothesis that neanderthals were hybridised out of existence as their gene pool was subsumed into the larger one of the fast-breeder sapiens.

4. Neanderthal DNA Shows They Rarely Interbred With Us Very Different Humans

Comment #228376 by B.L.Z. Bub on August 12, 2008 at 1:26 am

Christopher
So where have we got to, I think we agree on this
1. mtDNA can be used to deduce points of specific divergence because of regular mutation rates which is analogous to a biological clock, the greater the number of differences between two mtDNA sequences, the further back in time was their common parent.

And as such we agree that the finding of this paper of a divergence c.660,000 yrs ago is valid. Even if a second fossil gave a more recent date, this would not invalidate the original finding.

However do you agree with this?
2. Every maternal line is passing down its mtDNA to its offspring unchanged irrespective of her partner other than any random mutations that might occur.

This comment "If after a few thousand years this interbreeding gene-pool split the mtDNA divergence clock is reset." Suggests that you don't. I think this is the nub of our differing interpretations of this paper.

As far as I understand it, the mtDNA "clock" cannot be reset, irrespective of a female's mate, the female's mtDNA passes on unchanged (apart from random, regular mutation) to the nth generation.

Am I wrong? If so can you tell me how mtDNA can be "reset"? what mechanisms are involved? If mtDNA can be reset than I cannot see how it could ever be used to deduce points of divergence. It would be no more useful than nucleic DNA. Also I don't think you can talk about a gene-pool with regard to mtDNA, every maternal lineage is its own little gene-puddle, never mixing with others to make up a pool.

I presume your belief that interbreeding has happened is based on fossils apparently showing intermediate characteristics. Well these are not incompatible with the findings of this paper. Recognisable intermediate fossils would probably be first or second generation individuals. Perhaps hybrid offspring were infertile or sub-fertile so left no offspring.

Sorry I have not addressed all the points you made in your last two posts but this is enough to be going on with and I must get to work.

5. Neanderthal DNA Shows They Rarely Interbred With Us Very Different Humans

Comment #227553 by B.L.Z. Bub on August 10, 2008 at 9:37 am

Christopher

Perhaps I misunderstand something then, please tell me where my error is.

1. mtDNA can be used to deduce points of specific divergence because of regular mutation rates which is analogous to a biological clock, the greater the number of differences between two mtDNA sequences, the further back in time was their common parent.

2. Every maternal line is passing down its mtDNA to its offspring unchanged irrespective of her partner other than any random mutations that might occur.

"They spread out. Some groups come back into contact with the descendants of the H. erectus rootstock they split from so long ago...which has now evolved into (you guessed it) H. sapiens. Some groups don't."

This would be about 100,000 yrs ago, this group would have been separated from the common ancestor for as long as those groups still living in northern Europe and not contacting the dispersing H. sapiens. Thus their mtDNA will be just as divergent.

"If the mtDNA was taken from an individual who was a descendant of a group that never came back into contact with H. sapiens, then that individual would trace his/her mtDNA back to the original split."

Agreed.

"On the other hand, mtDNA taken from an individual who belonged to a group that did make contact with H. sapiens would almost certainly indicate a closer common ancestor IF interbreeding had occurred."

Why? The Neanderthal mtDNA would pass unchanged into her offspring. Having a sapiens as a mate will not change this, no mtDNA comes from the male line. Even if her hybrid daughters also had sapiens mates the Neanderthal mtDNA would pass down unchanged. After a few generations of this the decedents might look outwardly indistinguishable from their pure sapiens contemporaries, the nucleic DNA having been multiply diluted, but they will still posses the Neanderthal mtDNA unchanged but for random mutations. If this had occurred to any extent then these variant (Neanderthal) mtDNA sequences should still be found in the human population today.

But of course the fossil record must not be ignored, the more data the better. This paper only seems to suggest that female Neanderthal x male sapiens interbreeding, if it happened at all, was rare and has left no trace in contemporary the H. sapiens population.

6. Neanderthal DNA Shows They Rarely Interbred With Us Very Different Humans

Comment #227518 by B.L.Z. Bub on August 10, 2008 at 5:41 am

65 "I think it was named in the 1860's by an irishman or brit? So you are correct in the old spelling of Thal vs. Tal"

Homo neanderthalensis King, 1864

William King (1809-1886), an Anglo-Irish geologist

7. Neanderthal DNA Shows They Rarely Interbred With Us Very Different Humans

Comment #227515 by B.L.Z. Bub on August 10, 2008 at 5:32 am

44. "Fair enough. I'll buy the genetic split. But how does this in any way tell us to what degree sapiens and neanderthals interbred? I mean, this is one individual...what if he/she is a descendent of a neanderthal line that essentially bred true, while other neanderthals migrated to different areas (I'm thinking of the Levant) and generously interbred? If that were the case, wouldn't an analysis of mtDNA from one of those individuals indicate a much more recent common ancestor?"

I dont think so.

Assuming exogamy (females moving from natal group to mate) then if a female neanderthal bred with a male sapiens then offspring with neanderthal mtDNA would be reared in sapiens group. Therefore it can be expected that neanderthal mtDNA be present in the extant population of H. sapiens. The sequencing of this single individuals mtDNA is enough to show that this has not happened (assuming that neanderthal mtDNA does not vary wildly).

Of course it does not rule out male neanderthals mating with female sapiens, that needs to await y-chromosome sequencing. Nor can it exclude widespread interbreeding within now extinct neanderthal groups, any offspring bought up in such groups have left no decendents to test. This posibility could only be excluded by testing very many neanderthal individuals to search for sapiens mtDNA or y-chromosome.

Lots of assumptions but none outragous so i think the conclusions of this research, while far from difinitive, are reasonable.

8. Non-voters: It's all in God's hands

Comment #200276 by B.L.Z. Bub on June 27, 2008 at 8:24 am

Could be just a correlation? I think there is evidence to suggest that those who have been poorly educated or not done well in education (i.e. bit dim) tend to take less interest in politics and are less likely to get involved in civic affairs. Such people might also be the ones most readily suckered into the type of church talked about above.

9. How Darwin won the evolution race

Comment #198993 by B.L.Z. Bub on June 25, 2008 at 1:40 am

I am sure this is a good article but I am afraid I was put off by as soon as I started to read. When you see three factual errors in the first sentence it rather destroys confidence in the piece as a whole. If it does contain anything I did not already know, could I believe it? Not without doing my own research. And it would have been so easy to check these facts.

In early 1858, on Ternate in Malaysia, a young specimen collector was tracking the island's elusive birds of paradise when he was struck by malaria.

In case anyone is interested the three errors are:-

1. Ternate is not in Malaysia (a modern country) but the Malay Archipelago made up of Malaysia (British Malaya in Wallace's time) and Indonesia (Dutch East Indies in Wallace's time). Ternate is in Maluku Utara, Indonesia (North Moluccas in Wallace's time).
2. There are no birds of paradise native to Ternate (although it was a trading station for skins from New Guinea but if the writer was referring to these then he would hardly have described them as elusive, expensive perhaps).
3. Even if we expand "Ternate" to include the adjacent Halmahera (Gilolo), where there are two birds of paradise, Wallace could not have been in search of them. He was aware of only one, the Paradise Crow, but he believed this to be a kind of starling. The other, Wallace's Standardwing, would not be discovered till the end of the year when Wallace (actually his assistant Ali) found it on Bacan. At the time all birds of paradise were thought to come from New Guinea and Australia. Indeed Wallace left Ternate in March for Dory (Manokwari) in New Guinea where he was to search for birds of paradise.