DNA Sequencing Megathread! Neanderthals, Denisovans and other ancient DNA!

[Razgovory]

Because the term was basically invented to distinguish the later arrivals from the original inhabitants in nations with colonial origins like ours.

Though...you know...maybe not.

After close examination of the flag I have come to the conclusion that the Russians have been backing Nativist elements in the US much longer than first supposed.

[Valmy]

But we still have blond beasts on horseback embedding axes in settled agricultural peoples from the Indus to Ireland to the tune of Carmina Burana, right?

Sure...

Though I read that the Celts were all dark haired and the red and blonde got introduced with the Germans and Vikings. But that is probably all proven to be bunk now.

[Josquius]

But we still have blond beasts on horseback embedding axes in settled agricultural peoples from the Indus to Ireland to the tune of Carmina Burana, right?

Sure...

Though I read that the Celts were all dark haired and the red and blonde got introduced with the Germans and Vikings. But that is probably all proven to be bunk now.

I'm not so sure. All is perhaps over stating it and perhaps victorian racism played a part but most stereotypes exist for a reason.

[jimmy olsen]

Humnaity is not unique in all of it's mixing and hybridizing among it's numerous populations. All large and wide spread mammalian genera seem to have behaved the same way. Among the most interesting, Elephants have proven to have had a fascinating history.

http://johnhawks.net/weblog/reviews/genomics/elephant/elephant-palaeoloxodon-hybrids-2018.html

Hybrid origins of the straight-tusked elephants

26 Feb 2018

Elephants are one of the most important comparisons for human origins. Like humans, they're long-lived animals that have complex social behavior, they require extensive home ranges and sometimes migrate over long distances.

What genetics has discovered about their evolution and diversification over the last few years provides some fascinating parallels to human evolution in the Pleistocene. Mammoths are their own fascinating story—I wrote about them several years ago, and again in 2016, and the story continues to develop.

But in the last year, the other ancient elephants have been at the forefront of new discoveries. In particular, the "straight-tusked elephant", Palaeoloxodon antiquus, has yielded two ancient genomes that have disrupted what paleontologists thought they knew about Pleistocene evolution.

Last summer I wrote about sequencing work on the ancient straight-tusked elephant: "Genomes of straight-tusked elephants".

At that time, Matthias Meyer and colleagues had demonstrated that the genomes of two individuals of Palaeoloxodon antiquus from Germany were closer to African forest elephants (Loxodonta cyclotis) than savanna elephants (Loxodonta africana).

That was newsworthy. Paleontologists had mostly thought that Palaeoloxodon was related to the Asian elephant and mammoth clade. It turns out that it's one of the African elephants. The result also emphasized the deep phylogenetic separation of the savanna and forest elephants in Africa. Those two living African elephant populations, once assumed to be part of a single species, are substantially different genetically from each other, perhaps as much as mammoths and Asian elephants were.

It also raised new questions about the relationships of the extinct African lineage, Palaeoloxodon recki. Once widely known as Elephas recki, this was the major component of the elephant fauna in the Pleistocene African fossil record. Today's savanna elephants, L. africana, are virtually unknown through much of the African Pleistocene. Nobody really knows where the living lineage may have been hiding, nor does anybody know why P. recki might have become extinct.

In my post last June, I hinted that there might be more to the story. Ewen Callaway had reported on a conference presentation by Eleftheria Palkopoulou that discussed evidence for hybridization among these ancient elephants: "Elephant history rewritten by ancient genomes".

Now, Palkopoulou's analysis has been published in PNAS: "A comprehensive genomic history of extinct and living elephants". The title is a bit overblown in my opinion, because I have many questions that the new paper doesn't answer. But the paper does add two important details to Meyer's results from last year.

First, Palkopoulou and colleagues show that the straight-tusked elephant genome from Neumark-Nord, some 120,000 years old, is not a simple branch of the elephant phylogeny. This individual's ancestry derives mostly from a branch that stemmed from the common ancestors of savanna and forest elephants. But it also has substantial ancestry from woolly mammoths. And up to a third of its genome came from a population genetically similar to today's forest elephants from Sierra Leone, in West Africa.

A third of the genome is pretty high to be interpreted as a "ghost population". The straight-tusked elephant population of Europe in the early Late Pleistocene was apparently a mixture of two source populations, one with a long independent evolutionary history, and one with continuing strong genetic connections to African forest elephants.

This strong African forest connection was not with every population of forest elephants. The Sierra Leone L. cyclotis individual in the study bears strong similarity to the ancient straight-tusked elephant, but the Central African Republic-sampled L. cyclotis genome does not.

Second, Palkoupoulou and coworkers used a combination of analyses to jointly examine the effective population sizes of elephant species and genetic divergence times between them. There are lots of details in this analysis, with so many lineages sampled, and I wouldn't trust many of these details too far until more individuals are added to the African elephant and Palaeoloxodon samples.

Still, these analyses reinforce what the evidence for introgression shows. The two sampled forest elephants demonstrate a long divergence, with an estimated divergence time between 463,000 and 609,000 years ago for the populations that these two sampled individuals represent.

These two populations of forest elephants from different parts of Africa are around as different from each other as Neandertals and Denisovans were.

Clearly, we are not going to understand the evolution of the forest elephants, or their connection with straight-tusked elephants, until geneticists sample a lot more of them. Two genomes from each are not enough.

Another detail of the new analysis bears upon the long-time absence of the savanna elephant from the Pleistocene African fossil record:

The two savanna elephants had lower Ne relative to forest elephants for hundreds of thousands of years (Fig. 4D), potentially reflecting ecological competition from the African elephant Palaeoloxodon recki (including Palaeoloxodon iolensis) that dominated the African savannas until the Late Pleistocene (2, 19), or the high levels of male–male competition documented in this species.

That's a possibility. I find it fascinating that the savanna elephant lineage is very ancient indeed, separated from forest elephants for the last 2 million years. The identity of the P. recki population remains obscure, and the great difference between today's forest elephant samples suggests that a better sample of elephant DNA from across Africa may yield additional genetically differentiated lineages. It's even conceivable that some lineage of forest elephant might turn out to be a close relative of P. recki or P. iolensis.

Or then again, maybe P. recki will turn out to be a true ghost, not closely related to P. antiquus at all. As I wrote last year:

Of course, without ancient DNA evidence, it's not certain that these other extinct Palaeoloxodon species are closely related to the forest elephants and P. antiquus.

I just want to reiterate this sentiment. Discovering that P. antiquus isn't what paleontologists once thought does not give me confidence that paleontologists really know where P. recki or P. namascus belong. For that matter, I have no confidence that P. recki within Africa is really a single lineage. Until recently, most biologists considered L. africana and L. cyclotis to be a single lineage.

I can't wait to see results from a bigger sample of ancient elephants. The story of the straight-tusked elephants is likely much broader than two German skeletal samples. There are many challenges to ancient DNA study in temperate and low-latitude situations, but if there's any species with plenty of tissue to sample, it should be elephants.

[KRonn]

Interesting stuff about the elephants, similar questions and finds which obviously goes for all or most species of flora and fauna on the planet. 

[crazy canuck]

I have to say this is a hilariously retarded newspaper headline by the Telegraph:

http://www.telegraph.co.uk/news/2018/02/21/no-one-living-britain-truly-british-scientists-find-stonehenge/

No one living in Britain 'truly British', scientists find as Stonehenge builders were replaced by European immigrants

The Britons were not Britons!

I mean do they think the Stonehenge builders popped out of the soil of Britannia or something? I mean how many centuries do have to inhabit a place before you are considered indigenous?

I think you misunderstood the article

The builders of Stonehenge were replaced by a different population

Here is perhaps a better article explaining the latest research I found on my Twitter feed

http://www.independent.co.uk/news/science/archaeology/stonehenge-neolithic-britain-history-ancestors-plague-archaeology-beaker-people-a8222341.html?utm_content=buffer0e272&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

[Valmy]

I think you misunderstood the article

The builders of Stonehenge were replaced by a different population

I know.

I think you misunderstood my post. The title of the article asserted that the people who replaced the Stonehenge builders were 'not truly British' despite, you know, being the very people that word comes from. I mean if being the Britons doesn't make you truly British than what does?

[crazy canuck]

I think you misunderstood the article

The builders of Stonehenge were replaced by a different population

I know.

I think you misunderstood my post. The title of the article asserted that the people who replaced the Stonehenge builders were 'not truly British' despite, you know, being the very people that word comes from. I mean if being the Britons doesn't make you truly British than what does?

The people who replaced the builders of Stonehedge were from central Europe and so necessarily were not from Britain. I'm not sure what point you're trying to make. Would you argue that a descendant from somebody stepping off the mayflower is part of North America?If you took the time to actually read the article I posted you would see the context

[Valmy]

The Stonehenge builders were not from Britain either. I stated that point in my original post.

And are you really comparing Paleolithic and Bronze Age migrations to 17th century colonialism as far as claims of being Indigenous is concerned? That makes  the term meaningless, IMO anyway.

[crazy canuck]

The Stonehenge builders were not from Britain either. I stated that point in my original post.

And are you really comparing Paleolithic and Bronze Age migrations to 17th century colonialism as far as claims of being Indigenous is concerned? That makes  the term meaningless, IMO anyway.

Again you should probably read the article I posted.  You will see that is where the analogy is made.  But as ever your way is to not actually consider what the other person is saying and perhaps learn something- keep citing yourself as an authority.  I am out.

[grumbler]

What's really interesting is that "the builders of Stonehenge" had to have been both groups of people, as the Beaker People replaced the Neolithic farmers in this scenario.  It's curious that the style of the place remained so consistent through a pretty complete turnover of builders.

[Valmy]

The Stonehenge builders were not from Britain either. I stated that point in my original post.

And are you really comparing Paleolithic and Bronze Age migrations to 17th century colonialism as far as claims of being Indigenous is concerned? That makes  the term meaningless, IMO anyway.

Again you should probably read the article I posted.  You will see that is where the analogy is made.  But as ever your way is to not actually consider what the other person is saying and perhaps learn something- keep citing yourself as an authority.  I am out.

I read the article you posted and I am aware of the issue. I already said I did. In fact I discussed the facts listed in the article earlier in this thread.

You never even addressed what I was saying. And actually I change my opinion all the time based on what people say here so what you are assertion is just factually incorrect.

But go ahead and go out and attack me personally. Whatever.

[Malthus]

What's really interesting is that "the builders of Stonehenge" had to have been both groups of people, as the Beaker People replaced the Neolithic farmers in this scenario.  It's curious that the style of the place remained so consistent through a pretty complete turnover of builders.

Stonehenge seems to have been "built" over a very long period of time - with stones added on, taken away, moved. The original "Stonehenge" looked nothing like what it does today ... though I'm not sure exactly when in the building sequence the Beaker People came onto the scene, or whether it was associated with any particular stylistic variation: it could be that they were responsible for "Stonehenge III", when the big stones were erected. 

So it may be the case, depending on the dating, that the Beaker People built the "Stonehenge" we are familiar with - on the site of the earlier structures to be sure, incorporating some of their elements, but not all that similar to them ("Stonehenge II" was in fact built largely of wood; "Stonehenge I" was basically a ditch and a raised embankment, with some mysterious holes that could have had either timbers or stones).

In addition, its function may have changed. The "original" Stonehenge(s) was built by tribes with very little social stratification (evidenced in part by mass interment in ossuaries) and the "henge" may have been associated with their funerary rites; by contrast, the later "henge" was surrounded by individual barrows, with rich grave goods (indicating a high level of social stratification).

A plausible theory, though of course far from proven, is that the site gained a reputation for sanctity that later peoples sought to take advantage of, by building on the exact same spot, even if their religions weren't the same - maybe deliberately as a sign of dominance (there are lots of examples of this - for example, the Al Asqua Mosque built on the location of the Temple of Jerusalem). 

[Caliga]

A guy who lives in Jaen, Spain contacted me via 23andme.  The end of our first chromosomes are identical indicating we are related.  Strange, since he is an ethnic Spaniard back as far as his geneaology research has taken him, and I have absolutely no documented Spanish ancestry.  23andme estimates we share a set of fourth great grandparents.  So, um yeah.  We are trying to figure out how we could possibly be relatives now.   I wonder what the chances are that we just randomly matched on the stub of that chromosome?

[Admiral Yi]

A guy who lives in Jaen, Spain contacted me via 23andme.  The end of our first chromosomes are identical indicating we are related.  Strange, since he is an ethnic Spaniard back as far as his geneaology research has taken him, and I have absolutely no documented Spanish ancestry.  23andme estimates we share a set of fourth great grandparents.  So, um yeah.  We are trying to figure out how we could possibly be relatives now.   I wonder what the chances are that we just randomly matched on the stub of that chromosome?

Maybe you've got some black Irish in you?