Placing Ancient DNA Sequences into Reference Phylogenies
Rui Martiniano, et al 2022
Abstract
Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree. Key words: ancient DNA, phylogenetic placement, Y chromosome haplogroups.
Posts: 42918 | From: , | Registered: Jan 2010
| IP: Logged |
posted
Materials and Methods Y-Chromosomal Data Whole-genome sequenced present-day Y-chromosomal data from 1,208 males from Hallast et al. (2021) was complemented by two Y-haplogroup A00b samples from Karmin et al. (2015), 41 from de Barros Damgaard, Martiniano, et al. (2018b), 16 from Wong et al. (2017), and 1,071 samples from the low coverage 1000 Genomes Project data set (Poznik et al. 2016). These were combined with ten ancient samples from Fu et al. (2014), Gamba et al. (2014), Lazaridis et al. (2014), Jones et al. (2015), Llorente et al. (2015), de Barros Damgaard, and Martiniano, et al. (2018), Sikora et al. (2019). Genotype calling and filtering are described in detail in Hallast et al. (2021). Additionally, 334 samples from the 1000 Genomes Project were removed due to ≥10% missing data across the ∼10.3 Mb analyzed Y-chromosomal regions. The vcf files of samples mapped to GRCh37 were lifted over to GRCh38 using picard (v2.7.2)
Placing Ancient DNA Sequences into Reference Phylogenies Rui Martiniano, 2022
Posts: 42918 | From: , | Registered: Jan 2010
| IP: Logged |
posted
It clearly discredit the theory of E-m81 being ultimately of phoenician origin.
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Breath of fresh air from names I don't recall from earlier African MSY phylogeny articles: Martiniano, De Sanctis, Hallast, and Durbin.
Great find Lioness, thx 4 sharing.
Interesting hypotheses can be developed following this new data. So far, after skimming the peer reviewed release, it looks solid. Could complain about sampling but the goal was to align newer aDNA nrY data into the related living data sets. Right? Still, hope you can understand my wish for Fulani (Senegal-Sudan) inclusion. Not to downplay Tamasheq, Hausa, and Tabu importance.
Love Fig 3, the way a lot of data gets visualized for immediate intuitive impression and peoples, sometimes surprisingly, related by ancestry. When you shake the family tree, stand back. No telling who might fall on you!
One of the few articles I trust reading before poring over the data for myself first.
An 'interesting hypothesis' can be made about PN. Data here doesn't align at all with a scythe like MSY flow from the Sahra to the Med to the Nile to the Lakes?
What about the Levant to Caucasus and Gulf E1b1b1b2? Does it indicate Africa based uni, bi or no directional population movement?
Apparently Tamazight linked male ancestry is relatively recent, as is the language, and does not go back to the Epi-Paleolithic Maurusian males?
Mende are known for links to current southwestern Africa groups but this is the first I've seen Yoruba with such link. Did I slip up?
What else are you guys seeing in this data?
Whaddayez make of this new pathPhynder tool?
Ok lemme go dwnld the supplement.
CAVEAT Yeah nrY's just one uni-parental and the autosomes will retain alleles from disappeared Y chromosome lineages once present among a region of female continuity.
Tazarah
Why are you stalking my social media?
Member # 23365
posted
I see two people in here who were both trying to argue that the descendants of the proto-semitic/afro asiatic natufians (haplogroup E) somehow transformed into people with haplogroup J over time. Kind of makes you wonder how credible any of their other genetic positions are
Posts: 2491 | From: North America | Registered: Mar 2021
| IP: Logged |
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
I am surprised how nobody is calling out the blatant omission of ancient Saharan populations from this study as if there were no populations there over the last 15,000 years. How else would lineages originating in the horn wind up in Morocco? And as we have been discussing for years, it is obvious these lineages in North Africa have an African origin but these people in these institutions have been determined to create another origin for these lineages outside of Africa. And skipping over thousands of miles of territory and history is just the obvious way they try and stack the deck towards their favor.
quote: he origins of E-M215 were dated by Cruciani in 2007 to about 22,400 years ago in the Horn of Africa.[3][Note 1] E-M35 was dated by Batini in 2015 to between 15,400 and 20,500 years ago.[7] In June 2015, Trombetta et al. reported a previously unappreciated large difference in the age between haplogroup E-M215 (38.6 kya; 95% CI 31.4–45.9 kya) and its sub-haplogroup E-M35 (25.0 kya; 95% CI 20.0–30.0 kya) and estimated its origin to be in Northeast Africa, where the node separating the E-V38 and E-M215 branches occurs about 47,500 years ago (95% CI: 41.3–56.8 ka).[1]
All major sub-branches of E-M35 are thought to have originated in the same general area as the parent clade: in North Africa, the Horn of Africa, or nearby areas of the Near East. Some branches of E-M35 are assumed to have left Africa thousands of years ago, whereas others may have arrived from the Near East. For example, Underhill (2002) associates the spread of the haplogroup with the Neolithic Revolution, believing that the structure and regional pattern of E-M35 subclades potentially give "reagents with which to infer specific episodes of population histories associated with the Neolithic agricultural expansion". Battaglia et al. (2007) also estimate that E-M78 (called E1b1b1a1 in that paper) has been in Europe longer than 10,000 years. Accordingly, human remains excavated in a Spanish funeral cave dating from approximately 7,000 years ago were shown to be in this haplogroup.[11] Two more E-M78 have been found in the Neolithic Sopot and Lengyel cultures too.[12]
Concerning E-M35 in Europe within this scheme, Underhill & Kivisild (2007) have remarked that E-M215 seems to represent a late-Pleistocene migration from North Africa to Europe over the Sinai Peninsula in Egypt.[Note 2] While this proposal remains uncontested, it has more recently been proposed by Trombetta et al. (2011) that there is also evidence for additional migration of E-M215 carrying men directly from North Africa to southwestern Europe, via a maritime route (see below.)
According to Lazaridis et al. (2016), Natufian skeletal remains from the ancient Levant predominantly carried the Y-DNA haplogroup E1b1b. Of the five Natufian specimens analysed for paternal lineages, three belonged to the E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), E1b1(xE1b1a1,E1b1b1b1) and E1b1b1b2(xE1b1b1b2a,E1b1b1b2b) subclades (60%). Haplogroup E1b1b was also found at moderate frequencies among fossils from the ensuing Pre-Pottery Neolithic B culture, with the E1b1b1 and E1b1b1b2(xE1b1b1b2a,E1b1b1b2b) subclades observed in two of seven PPNB specimens (~29%). The scientists suggest that the Levantine early farmers may have spread southward into East Africa, bringing along Western Eurasian and Basal Eurasian ancestral components separate from that which would arrive later in North Africa.
Additionally, haplogroup E1b1b1 has been found in an ancient Egyptian mummy excavated at the Abusir el-Meleq archaeological site in Middle Egypt, which dates from a period between the late New Kingdom and the Roman era.[13] Fossils at the Iberomaurusian site of Ifri n'Amr or Moussa in Morocco, which have been dated to around 5,000 BCE, also carried haplotypes related to the E1b1b1b1a (E-M81) subclade. These ancient individuals bore an autochthonous Maghrebi genomic component that peaks among modern North Africans, indicating that they were ancestral to populations in the area.[14] The E1b1b haplogroup has likewise been observed in ancient Guanche fossils excavated in Gran Canaria and Tenerife on the Canary Islands, which have been radiocarbon-dated to between the 7th and 11th centuries CE. The clade-bearing individuals that were analysed for paternal DNA were inhumed at the Tenerife site, with all of these specimens found to belong to the E1b1b1b1a1 or E-M183 subclade (3/3; 100%).[15]
Loosdrecht et al. (2018) analysed genome-wide data from seven ancient Iberomaurusian individuals from the Grotte des Pigeons near Taforalt in eastern Morocco. The fossils were directly dated to between 15,100 and 13,900 calibrated years before present. The scientists found that five male specimens with sufficient nuclear DNA preservation belonged to the E1b1b1a1 (M78) subclade, with one skeleton bearing the E1b1b1a1b1 parent lineage to E-V13, another male specimen belonged to E1b1b (M215*).[16]
quote:Originally posted by the lioness,: Mods please delete the off topic stuff, thanks
Will do.
Everyone STAY ON TOPIC in regards to the study in the OP. Any further derailment will be deleted.
Posts: 1891 | From: NY | Registered: Sep 2014
| IP: Logged |
quote:Originally posted by Antalas: It clearly discredit the theory of E-m81 being ultimately of phoenician origin.
Why would anyone think that... M81 predates a pheonecia by millennia? M183 (the most dominant subclade known so far) though... we need some more resolution.
Kakapel 3,9 belonging to B2 is interesting. Possibly ore evidence that we're pigeon-holing Ancient African diversity.
Posts: 1781 | From: New York | Registered: Jul 2016
| IP: Logged |
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
quote:Originally posted by Askia_The_Great:
quote:Originally posted by the lioness,: Mods please delete the off topic stuff, thanks
Will do.
Everyone STAY ON TOPIC in regards to the study in the OP. Any further derailment will be deleted.
I can only hope the same courtesy's extended to rank and file ES members who also have their threads derailed by dissenters without a clue.
quote:Originally posted by Doug M: I am surprised how nobody is calling out the blatant omission of ancient Saharan populations from this study as if there were no populations there over the last 15,000 years. How else would lineages originating in the horn wind up in Morocco? And as we have been discussing for years, it is obvious these lineages in North Africa have an African origin but these people in these institutions have been determined to create another origin for these lineages outside of Africa. And skipping over thousands of miles of territory and history is just the obvious way they try and stack the deck towards their favor.
.
Well I did mention the articles sampling was not robust for central-southern Sahra. West African Sahel, Savanna, and Gulf of Guinea is missing. Only Mandenka and Yoruba moderns but is not this same West Africa full of nrY E?
Gambian A0 and no other GWD MSY did surprise me.
Anyway, excuse me but where is the published DNA of any ancient Saharan individuals because I missed out on that.
I also missed this article's author placing any reported MSY as originating elsewhere than continental Africa. It looks to me this team supports continental origins for Natufian nrY E-Z830 and Arabian Plate/Gulf E-L677. They do not posit "another origin for these lineages outside of Africa."
Tazarah
Why are you stalking my social media?
Member # 23365
posted
^ my last comment was removed, but I essentially said the same thing as Tukuler and it was directed toward the lioness because she derails threads in the kemet forum (she's tried to derail at least two of mine) without shame, but then she tries to make others play by the rules when it comes to threads that she creates.
"I can only hope the same courtesy's extended to rank and file ES members who also have their threads derailed by dissenters without a clue."
* But I will say, the ancient DNA (or should I say the lack thereof) in certain parts of africa (especially west africa) debunks the eurocentric fantasy that so-called black people have always been stuck in sub-saharan or west africa.
Posts: 2491 | From: North America | Registered: Mar 2021
| IP: Logged |
Tazarah
Why are you stalking my social media?
Member # 23365
posted
I made that post because I had just finished having a dialogue with you in another thread where you were misrepresenting genetic information (Y-DNA), so I was simply pointing out how you aren't 100% honest when it comes to DNA and how that fact needs to be taken into account when dealing with posts you make concerning DNA.
Completely on topic.
Posts: 2491 | From: North America | Registered: Mar 2021
| IP: Logged |
Tazarah
Why are you stalking my social media?
Member # 23365
posted
Yes, all you did was post an article, but I'm sure you have an opinion/position regarding it's content and that you have a reason for posting it.
It's perfectly normal for me or anyone else to logically deduce that you have a certain position based on comments you've made in other threads.
Therefore, it's completely rational for me or anyone else to reference other comments you've made, and other positions you've taken, especially since it's all DNA-related.
You don't get to choose who responds to what or how they respond.
You of all people should know that.
Posts: 2491 | From: North America | Registered: Mar 2021
| IP: Logged |
quote:Originally posted by Antalas: It clearly discredit the theory of E-m81 being ultimately of phoenician origin.
Why would anyone think that... M81 predates a pheonecia by millennia? M183 (the most dominant subclade known so far) though... we need some more resolution.
Kakapel 3,9 belonging to B2 is interesting. Possibly ore evidence that we're pigeon-holing Ancient African diversity.
I remember it was proposed by that dutch "scholar" who wrote a paper on it it was also supported by member like BrandonP...
Posts: 1779 | From: Somewhere In the Rif Mountains | Registered: Nov 2021
| IP: Logged |
Well I did mention the articles sampling was not robust for central-southern Sahra. West African Sahel, Savanna, and Gulf of Guinea is missing. Only Mandenka and Yoruba moderns but is not this same West Africa full of nrY E?
Gambian A0 and no other GWD MSY did surprise me.
Anyway, excuse me but where is the published DNA of any ancient Saharan individuals because I missed out on that.
I also missed this article's author placing any reported MSY as originating elsewhere than continental Africa. It looks to me this team supports continental origins for Natufian nrY E-Z830 and Arabian Plate/Gulf E-L677. They do not posit "another origin for these lineages outside of Africa."
Agreed, but this is a pattern at this point which is intentional and not just "an omission". Just look at a few other threads posted here recently on African DNA and they all omit anything north of Central Africa deliberately. This paper excludes Northern Sudan, Southern Algeria, Southern Libya, Mauretania, Niger and Chad altogether as if there arent populations there or relevant to how such DNA from East Africa would make it to "North Africa".
For example some other thread omitting all these same regions as if they aren't part of Africa as in saying the ONLY way these African lineages got there is due to non Africans "back migrating" into coastal areas. As if Africans couldn't have crossed the Sahara directly.
quote:Originally posted by Tukuler: I can only hope the same courtesy's extended to rank and file ES members who also have their threads derailed by dissenters without a clue.
You're free to go into details in the DMs...
Posts: 1891 | From: NY | Registered: Sep 2014
| IP: Logged |
UBBFriend: Email this page to someone!
![[Wink]](wink.gif)
Printer-friendly view of this topic