tag:blogger.com,1999:blog-4123559132014627431.post4817971359450549837..comments2024-03-18T22:01:02.498-07:00Comments on Eurogenes Blog: "Heavily sex-biased" population dispersals into the Indian Subcontinent (Silva et al. 2017)Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger148125tag:blogger.com,1999:blog-4123559132014627431.post-33025685100828361202017-04-05T20:13:45.656-07:002017-04-05T20:13:45.656-07:00Matt,
Those are some pretty interesting patterns....Matt,<br /><br />Those are some pretty interesting patterns.<br /><br />For South Central Asia + South Asia, this data seems to provide evidence for a few ideas that were first articulated by RK.<br /><br />RK has often noted that the best way to differentiate scheduled-caste populations from Brahmins (across all of India) is by looking at affinity towards Steppe_MLBA populations.<br /><br />Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-31112886330184551462017-04-05T16:17:32.620-07:002017-04-05T16:17:32.620-07:00In both Lazaridis and the Eurogenes Fst, does seem...In both Lazaridis and the Eurogenes Fst, does seem like Fsts for ancient dna and modern dna tend to be systematically closer to each other, comparing ancients to closest (or one of closest) modern: http://i.imgur.com/Jj9o50q.png / http://i.imgur.com/oHlZieN.png / http://i.imgur.com/f096AFZ.png :/. E.g. not simply the case that Bell Beaker is systematically closer to some ancients compared to Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-25924127196902953342017-04-05T15:03:39.010-07:002017-04-05T15:03:39.010-07:00@ Davidski, I do think it's probably worth run...@ Davidski, I do think it's probably worth running off an Fst matrix and running these and other analyses when substantial amounts of new samples come out *but* yeah I'm pretty cautious about these stats being a better method. They can be comparable in some ways and have advantages and disadvantages.<br /><br />@ Sein, that's pretty cool as a fit for Pashtuns. Got some interesting Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-33603533260432412072017-04-05T11:42:42.669-07:002017-04-05T11:42:42.669-07:00Matt,
Not having the Kalash, Zoroastrian, Potapov...Matt,<br /><br />Not having the Kalash, Zoroastrian, Potapovka, and the Onge really seems to clean things up.<br /><br />Pashtuns (Pathans):<br /><br />37.40% Sarmatian_Pokrovka + 3.10% Andronovo + 0.10% Yamnaya_Samara<br />34.30% Iran_Chalcolithic + 10.80% Iran_Neolithic + 2.55% AG3-MA1<br />9.20% Dai + 2.50% Australian<br /><br />distance=6.9555<br /><br />I wouldn't worry about not having Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-416201813220069262017-04-05T07:03:00.560-07:002017-04-05T07:03:00.560-07:00Ah, just noticed that, of course, if I remove some...Ah, just noticed that, of course, if I remove some outliers, other outliers eventually take their place, and it's impossible to decide which populations and dimensions to use.<br /><br />Think I'll stick to qpAdm for now, and Global 10 when more ancient samples come out.<br /><br />On a positive note, I like the way the Fst is more sensitive than D-stats and f3-stats for population Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-50033470980130604712017-04-05T01:25:32.380-07:002017-04-05T01:25:32.380-07:00@ Sein: "Also, I can now see why you utilize ...@ Sein: <i>"Also, I can now see why you utilize PAST, lots of interesting functions (I copy and pasted David's Fst matrix earlier today, and quickly played around with K-means, PCA, PCoA, etc. Fun stuff)."</i><br /><br />Yeah, I don't know if I ever conveyed properly that there are many multivariate functions in Past3 that basically run in *seconds* and allow very quick Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-32290467243832039012017-04-04T23:34:20.987-07:002017-04-04T23:34:20.987-07:00New sheets. I tweaked a couple of things.
Fst mat...New sheets. I tweaked a couple of things.<br /><br />Fst matrix<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQUmxXWFliaHhaQWs/view?usp=sharing<br /><br />PCoA coords<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQLVV6TjJOX0tmUHM/view?usp=sharingDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-7056912659452368452017-04-04T23:30:00.168-07:002017-04-04T23:30:00.168-07:00David,
Just 25, although I do want to see if thin...David,<br /><br />Just 25, although I do want to see if things change with more dimensions (tomorrow).<br /><br />Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-30223050508596462802017-04-04T22:40:53.974-07:002017-04-04T22:40:53.974-07:00@Sein
How many dimensions (PCoA coords) are you u...@Sein<br /><br />How many dimensions (PCoA coords) are you using there?Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-43956224709496702212017-04-04T20:36:11.265-07:002017-04-04T20:36:11.265-07:00Matt,
Thanks for the data-sheets!
Also, I can no...Matt,<br /><br />Thanks for the data-sheets!<br /><br />Also, I can now see why you utilize PAST, lots of interesting functions (I copy and pasted David's Fst matrix earlier today, and quickly played around with K-means, PCA, PCoA, etc. Fun stuff).<br /><br />Regardless, (thankfully) I think David's efforts have payed off.<br /><br />Just to see if things make sense, I tried some basal Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-17172456618324354702017-04-04T15:32:16.501-07:002017-04-04T15:32:16.501-07:00@ Davidski, thanks for taking the time for this.
...@ Davidski, thanks for taking the time for this.<br /><br />Here are a few graphics based on the data:<br /><br />Neighbour Joining Structure: http://i.imgur.com/7dBelZY.png<br /><br />PCoA of all world: Axes 1 vs 2- http://i.imgur.com/hrrcTFe.png / http://i.imgur.com/OukHp2Y.png, Axes 4 vs 6 - http://i.imgur.com/2YNfXwz.png, <br /><br />"West Eurasians": Axes 1 vs 2 - http://Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-21890140088862374882017-04-04T12:12:05.574-07:002017-04-04T12:12:05.574-07:00David,
Thanks! I truly appreciate this. We're...David,<br /><br />Thanks! I truly appreciate this. We're looking at a massive treasure trove of data here.<br /><br />I'll let Matt do what he does, and then we'll see how well this works (although, I'm pretty confident that this will work great).<br /><br />But before that, I'll do some fits just using the Fsts, to see how things look.Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-56182017678707383742017-04-04T05:17:08.088-07:002017-04-04T05:17:08.088-07:00@Matt and Sein
Here's my first attempt at an ...@Matt and Sein<br /><br />Here's my first attempt at an Fst matrix.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQYWtGYlBtMEx6eFE/view?usp=sharing<br /><br />Can't add the British Iron Age and AS samples to this. Might be able to at some point when better sequences are released.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-22587885039025978482017-04-03T15:03:14.653-07:002017-04-03T15:03:14.653-07:00Couple bits of potential food for though David (fo...Couple bits of potential food for though David (for after if you get comfortable that you're able to get an autosomal matrix that is similar to that from Lazaridis 2016 and works well with this):<br /><br />1) Given the Goldberg sex asymmetric migration paper, it might be cool to make an fstX matrix for a good set of populations. Maybe Lazaridis 2016 plus extra world populations in Asia and Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-20866244834730043552017-04-03T13:46:04.534-07:002017-04-03T13:46:04.534-07:00David,
Thanks!
If it works as well as the Lazar...David,<br /><br />Thanks! <br /><br />If it works as well as the Lazaridis et al. Fst matrix (when subjected to the PCoA technique), it'll be of considerable interest.<br /><br />Just spit-balling here, but if merging MA1 with AG3 isn't sensible in this context, and if only MA1 can't be added, would it work with your old synthetic ANE samples? <br /><br />They behaved just like MA1/Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-60783849706336479792017-04-03T13:18:33.733-07:002017-04-03T13:18:33.733-07:00I'll try and knock out an Fst matrix with a fe...I'll try and knock out an Fst matrix with a few extra pops that weren't featured in literature yet, but I'm not sure merging AG3 and MA1 will work.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-30042323845296501882017-04-03T01:05:12.213-07:002017-04-03T01:05:12.213-07:00Couple more technical details (put in a separate p...Couple more technical details (put in a separate post to not data dump you lot in one post):<br /><br />--------------<br /><br />1) Comparing the PCoA on the matrix to trying to run PCA on the West Eurasian subset of the matrix: http://i.imgur.com/FsqFLrt.png. There are similarities, but there's obviously a strange "horseshoeing" in the PCA data where a big major axis forms Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-82236369849508955142017-04-03T00:44:28.263-07:002017-04-03T00:44:28.263-07:00@ Davidski, yeah, to replicate pretty much the ext...@ Davidski, yeah, to replicate pretty much the extent is the steps as follows :<br /><br />1. Download Fst matrix file from Lazaridis 2016 supplement - http://biorxiv.org/highwire/filestream/16360/field_highwire_adjunct_files/3/059311-4.xlsx<br /><br />2. Download Past3 - https://folk.uio.no/ohammer/past/<br /><br />3. Adjust formatting on Fst data. In the raw table the standard error was above Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77318169948088346852017-04-02T18:56:48.843-07:002017-04-02T18:56:48.843-07:00Obviously, Matt can explain this far better, and h...Obviously, Matt can explain this far better, and he can also go into much richer detail; but yeah, it seems that he just ran an Fst matrix through some kind of MDS.<br /><br />By far, this is the best data I've ever seen for inferring admixture proportions. I'd say that it works better than nMonte with unlinked genotype PCA data, works better than nMonte with D-stats, and it also seems toSeinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-58645929659659141892017-04-02T17:19:49.406-07:002017-04-02T17:19:49.406-07:00What is this stuff based on, just Fst?What is this stuff based on, just Fst?Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-81677330371497947152017-04-02T15:54:58.854-07:002017-04-02T15:54:58.854-07:00Matt,
I'd say that this is vastly superior to...Matt,<br /><br />I'd say that this is vastly superior to using D-stats with nMonte.<br /><br />In fact, after exploring some "basal" modelling, it's quite clear (at least to me) that this also performs better when compared to qpAdm.<br /><br />For example, if my memory serves me right, Lazaridis et al. had Anatolia_N construed as 40% WHG, 30% Iran_Neolithic, and 30% Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-28130566993499318902017-04-02T13:17:45.258-07:002017-04-02T13:17:45.258-07:00Few more experiments.
This time ran a PCoA on the...Few more experiments.<br /><br />This time ran a PCoA on the Fst matrix from Mathieson et al 2015. Compared to Lazaridis 2016, this one has many fewer modern West Eurasian populations, and world populations, and ancient populations but has a potential advantage that the ancients were split into more specific cultures. So rather than Europe_MNChl or Europe_EN or Steppe_EMBA, it has Iberia_MN, Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-818764903889079942017-04-02T03:44:54.502-07:002017-04-02T03:44:54.502-07:00@ Alberto and @ Sein, thanks, yeah, actually surpr...@ Alberto and @ Sein, thanks, yeah, actually surprising to me how well this seems to fit with other methods and work, for such a brutally simple method unexplored in the literature (just the Fst matrix through a sort of MDS). Also in case you didn't spot, Davidski released a post of mine above from the spam folder purgatory with a few more of the fits for European populations. <br /><br />Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-41908104179258339802017-04-02T01:57:10.293-07:002017-04-02T01:57:10.293-07:00@Matt
Thanks for that Fst based PCA. It seems to ...@Matt<br /><br />Thanks for that Fst based PCA. It seems to work really good. I ran European modern populations with the same sources used by David in his qpAdm tour of Europe (http://eurogenes.blogspot.mk/2017/01/qpadm-tour-of-europe-mesolithic-to.html) and the results are very similar:<br /><br />https://docs.google.com/spreadsheets/d/1xcix-erUisL3UjRHpXgmU5QZF_jOrIFCx4iYLx5tlL8/edit?usp=Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-52770069910098462992017-04-01T12:06:06.244-07:002017-04-01T12:06:06.244-07:00Matt,
Thanks! The PCoA output proportions look pr...Matt,<br /><br />Thanks! The PCoA output proportions look pretty sensible for both Sindhis and Mala.<br /><br />I've done some models for West Asians/Caucasus pops, using the Lazaridis Fst PCoA, and I must say that these results are the most reasonable I've ever seen:<br /><br />Iranians<br /><br />66.9% Iran_ChL<br />24.6% Steppe_MLBA<br />5.6% Kharia<br />1.9% She<br />1.0% Yoruba<br />Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.com