Ranis UP Human genomes

[Norfern-Ostrobothnian]

Seems we are about to get the Ranis genomes soon. They seem to be mostly N except with one R which is interesting. Ranis belongs to the LRJ and reportedly they are related to Zlaty Kun which make her also LRJ genetically speaking too. LRJ was the first proper Human culture in Europe. They left no admixture to other populations as far as I can tell. I however wonder if the LRJ split off before Basal Eurasian did?

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups. One such technocomplex where the maker is unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which covers an area in northwestern and central Europe from the UK to Poland. This paper presents the morphological and proteomic species identification, mitochondrial DNA analysis, and direct radiocarbon dating of human remains directly associated to an LRJ assemblage at the cave site of Ilsenhöhle in Ranis (Germany).  

https://www.ebi.ac.uk/ena/browser/view/PRJEB67776

https://zenodo.org/records/10064946


R10875 N
R10396 N
R10355 N
16/116-159199 R
16/116-159327 N
16/116-159416 N
R10876 N
R10874 N
R10879 N
R10873 N

[TanTin]

Did someone convert it to plink format? I'm curious to see where it will project between the ancients.

[TanTin]

I just noticed the detail: it is only MitDNA . ( Mitochondrial DNA from Ilsenhöhle in Ranis )

[Kale]

What a tease! I thought one of the conference abstracts talked about autosomal dna also? Maybe that will be a separate paper sometime soon (hopefully)?

[Desdonas]

If ranis do not have any mtdna M, then the M-ENA connection may not be just an accident.

[Desdonas]

https://www.nature.com/articles/s41586-0...3-7#MOESM1

[parasar]

https://www.nature.com/articles/s41586-0...3-7#MOESM1

Are they indicating that L and M are on a separate branch wrt N?

[Ebizur]

https://www.nature.com/articles/s41586-0...3-7#MOESM1

Are they indicating that L and M are on a separate branch wrt N?

That would not be a new finding. Many previously published phylogenetic trees of human mtDNA likewise have shown haplogroup M and (extant African branches of) haplogroup L3 to share a more recent common ancestor than either of those shares with haplogroup N. I have always thought of the distribution of mtDNA M-L3 as a decent analogue to the distribution of Y-DNA haplogroup DE-YAP.

[alchemist223]

https://www.nature.com/articles/s41586-0...3-7#MOESM1

Are they indicating that L and M are on a separate branch wrt N?

That would not be a new finding. Many previously published phylogenetic trees of human mtDNA likewise have shown haplogroup M and (extant African branches of) haplogroup L3 to share a more recent common ancestor than either of those shares with haplogroup N. I have always thought of the distribution of mtDNA M-L3 as a decent analogue to the distribution of Y-DNA haplogroup DE-YAP.

Interesting. Wonder if there will ever be another version of the Phylotree for mtDNA that is standardized. Just weird to see different trees even for old, major haplogroups, especially compared to Y-DNA.

[crashdoc]

It is just a question of outgroups.  What is identified as L on the diagram are actually only L3 branches. M and the other branches of L3 do not share common mutations. What they have in common is that they don't have N's mutations.  If they had added L4, L6 or L2 samples as outgroups to the graph, we would see the normal branching, but they only rooted it using a Neandertal mitogenome which is far removed.  It is not really a flaw of the study as they were analyzing branches under N and having M and other L3 branches as outgroup was quite enough to root N's branches.

Here's a part of the mtdna tree from yfull as a reference, with defining mutations indicated:

L2: T146C!, C150T, T152C!, T2416C, G8206A, A9221G, T10115C, G13590A, C16311T, G16390A
L3'4'6: G4104A, A7521G
L3'4: T182C!, T3594C, T7256C, T13650C, T16278C
  L3: A769G, A1018G, C16311T
  L3a: C151T, T152C!, C12816T, A16254G, A16316G
  L3b'f: T15940d
  L3c'd: T152C!, A13105G!
  L3e'i'k'x: C150T, A10819G
  L3h: T7861C, G9575A
  M: T489C, C10400T, T14783C, G15043A
  N: G8701A, C9540T, G10398A, C10873T, A15301G!
  L4: T195C!, G5460A, T16362C
L6: T146C!, T152C!, G185C, G709A, C770T, T961C, A1461G, C4964T, T5267C, A6002G, A6284G, C9332T, A10978G, T11116C, C11743T, G12771A, A13710G, C14791T, C14959G, A15244G, T15289C, C15499T, C16048A, T16224C

Edit: the indentation has not worked as intended, L4 is sister group to L3 and the others below L3 are all daughter clads of L3. L6 is sister to L3'4.

[CLTVTE]

That would not be a new finding. Many previously published phylogenetic trees of human mtDNA likewise have shown haplogroup M and (extant African branches of) haplogroup L3 to share a more recent common ancestor than either of those shares with haplogroup N. I have always thought of the distribution of mtDNA M-L3 as a decent analogue to the distribution of Y-DNA haplogroup DE-YAP.

BachoKiro F6_620 is actually mtDNA M+yDNA F. It is thought that ancient yDNA F could accompany yDNA M in China. Despite being assigned to an ancient variant of mtDNA N, the Oase yDNA K2a* specimen has a mutation A8701G, which is common in mtDNA M.

[Megalophias]

Did they actually provide the mtDNA variants anywhere? If they did I couldn't find them, and wasted a good bit of time extracting them from the sequences.

These trees always seem to have weird unsupported branches, like grouping L and M, and so forth. I think for some reason they are forced to produce binary branchings, which is terrible for mtDNA and results in all these meaningless fake clades, when what you should have is a whole lot of primary branches.

As far as I can tell Bacho Kiro F6-620 shares nothing with the Andamanese under M (or anyone else last I checked, including the Goyet M). CC7-2289 seems to just have the root sequence of R with no additional mutations, so no idea why she is nested within R, albeit with garbage levels of support. They do at least manage to put Oase 1 in his correct position basal to all N.

Salkhit shares 3 mutations (G4113A, G8153A, G9456A) under N with Bacho Kiro BB7-240 and CC7-335; the latter 2 each have one unique mutation more, and Salkhit has 7 more mutations. (We must have known this already, but apparently I forgot.) So this lost branch of N lasted quite a long time and was shared between Germany and Mongolia.

Zlaty Kun and R10873 from Ranis share 4 mutations under N (T14025C, T16093C, T16172C, and a C insertion at 16265). R10874 has these 4 plus G14249A. 4 others from this site are supposed to be the same individual as or maternally related to R10874. The others have a lot of missing data, so they could have additional mutations that were not found. R10875 has T16172C and T16093C but not T14025C or ins16265C. R10876 is like R10875 but missing data for 16093. 16/116-159416 is missing data for both 16093 and 16172. So anyway we have here an extinct clade of N shared between Ranis and Zlaty Kun.

Fumane2 (Proto-Aurignacian Italy IIRC) and 16/116-159199 from Ranis (that's a mouthful) share T16304C, which is the only mutation the latter has under R. Fumane2 has 2 more as well. They don't share these with Tianyuan or Ust Ishim or anyone else. T16304C is found in R5, R9, and R22, so maybe recurrent, or pre-one of these, but probably not. So these two are probably in a very early lost branch of R.

[Norfern-Ostrobothnian]

They are in the zenodo repository I posted in the thread. From what I remember when I checked them myself, they had a few unique variants common to them. I might check them out deeper later.

[Quint]

TheYtree now has R10355 under mtDNA R2'JT, 16/116-159253 under R0 and R10876 under R. What do you think?

[Norfern-Ostrobothnian]

R10355 doesn't have T4216C so it isn't R2'JT
16/116-159253 doesn't have G73A or A11719G so it isn't R0
It does seem it may be R.
R10876 doesn't have T12705C or T16223C so it isn't R