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Tuesday, October 31, 2017

Genetic ancestry online store (to be updated regularly)


It's an unfortunate reality that most commercial genetic ancestry tests out there are rather lame. They're not wrong per se, but that's probably the best that can be said about them. And let's be honest, that's no longer enough considering how far this area of science has come in recent years.

To try and remedy this problem, I'll be offering a wide range of highly accurate and unique, but low cost, ancestry tests here, in my makeshift online store, based on analyses on this blog. These tests will focus on either recent or ancient ancestry, or both, using the latest reference samples from scientific literature whenever possible. To make a purchase, send your request, autosomal genotype data (from AncestryDNA, FTDNA or 23andMe) and money (via PayPal) to eurogenesblog [at] gmail [dot] com.

Let's start things rolling with my genetic and linguistic landscape of Europe north of the Alps, Balkans and Pyrenees (see here). For a mere $6 USD I will pinpoint your location on the plot below amongst a variety of modern-day and ancient individuals. You'll also receive the principal component coordinates, which you can use to model your ancestry proportions or produce heat plots (for instance, like here). Please keep in mind, however, that to ensure sensible results in this particular analysis, practically all of your ancestry has to derive from Central, Eastern and/or Northern Europe. Most of my other tests won't be so restrictive.


I'll be updating this plot regularly with many more ancient samples as they become available, but your coordinates will remain relevant as I do so.

Please note that my online store will be closed throughout December, but stay tuned next year for many more offers.

See also...

Fund-raising offer: Basal-rich K7 and/or Global 10 genetic map

79 comments:

Lee Albee said...

So how do we get you our sequences and where is the online store?

Davidski said...

You're at the online store now. And you get your sequence(s) at FTDNA, 23andMe or AncestryDNA.

Twasztar said...

FTDNA, 23andMe or AncestryDNA

Which one is the best in your opinion?

Davidski said...

At the moment FTDNA, as far as the raw data is concerned.

Slumbery said...

Is Genographyc 2 data usable?

Helgenes50 said...

Here's what I get by modeling myself with this new PCA
( full Norman)

[1] "distance%=0.8119 / distance=0.008119"


French:France10 35.1
England_Anglo-Saxon:NO3423 27.2
French:France16 18.5
French:France1 11.6
England_Anglo-Saxon:HS3-I0161 7.5

Pretty similar to my first IBD test, a few years ago
Without ancient samples, only with modern populations
In these two results, 1/3 of German Ancestry ( continental+ Nordic)

West British (Britonic?) 42.3%
Continental Northern and Eastern European 36.6%
Central French 21.1%

Twasztar said...

I see, thanks.

jv said...

Thanks! So your closed in December but will reopen in January? I didn’t get my modern genetic components because I’m fortunate enough to know where my ancestors come from: Germany, England, Ireland & Switzerland( don’t think there will be any surprises). My Grandmother’s Crane side goes back to 1200 AD in England. The Cranes were Normans. Oliver de Cranne was one of the first recorded in England. However, in the 1600’s, the Cranes of Suffolk moved to Massachusetts & Connecticut and were Puritans. (1200-1600 AD is not that long ago. I like Epipaleolithic to Early Bronze Age history!)

Romulus said...

Ancestry and 23andme are both awful. Ftdna is the only way to go.

Samuel Andrews said...

@Helgenes50,

How accurate are your results? Are you actually French and British?

Samuel Andrews said...

@jv,
" However, in the 1600’s, the Cranes of Suffolk moved to Massachusetts & Connecticut and were Puritans."

Oh, Sweet. The impression from history class is all 17th century Americans were Puritans. But I never got an explanation for what happened to them. I imagine their community disappeared but the people didn't. I also have ancestors who were Puritans.

Lee Albee said...

I assume we would email you the FT or Ancestry DNA files?

Davidski said...

Lots of requests came in over night. I'll get onto them shortly.

Open Genomes said...

@David, what about the aDNA IBD offer?
Does that include all the new samples on the PC plot?

jv said...

Well, Benjamin Crane my 9th Great Grandfather ( wife Mary Backus) had a Tannery in Wethersfield, Ct. in mid/late 1600’s. His descendants moved to South Putnam, NY. in the early 1700’s. Dr Joseph Crane, Jr my 6th Great Grandfather(wife Esther Belden) was a doctor in NYC during the Revolutionary War. His descendants moved to Western New York from South Putnam. My Great Grandfather Charles Fredrick Crane(father John Crane, mother Betsy Wakefield) moved to Iowa then California. ( wife Lucy Battle) My Great Grandfather OB Crane moved from California and back to Jones Co. Iowa. Married Susie Allen born to German ( Hein)& Swiss (Allen) immigrates (1850’s) to Jones Co. Iowa. My Grandmother was Anita Crane Fox born in Iowa 1911. Her MtDNA is H6a1a2b1. I’m a Greenfield & Niehaus(MtDNA K2) from my father’s side. A Fox & Crane from my mother’s side.

jv said...

@ Samual Andrews,
I enjoy researching my recent Surnames/lineages too! Traced my maternal ggg Grandmother Anna Barbara Schoner Hein to Ansbach, Germany. My paternal Grandmother, Esther Niehaus Greenfield’s maternal line was from Venne, Germany.

Arkaim said...

@Davidski
How would you rate this?

Ancestral DNA tests: what should I know before I start?
https://eupedia.com/europe/dna_project_faq.shtml

ytro said...

Can you work with data from LivingDNA?

Davidski said...

@Open Genomes

The samples in the upcoming IBD run will be exactly the same as in the previous run.

@Arkaim

I'll have to decline your invite to read Eupedia. Lief's too short.

@ytro

Yes, I can use LivingDNA data.

Helgenes50 said...

@ Samuel Andrews

I am not a mix of French and English, but as norman I share the same ancestors
than my British neighbors, Saxons, Anglo-Saxons, Nordic, Bretons
Without forgetting that the original population, the Armoricans, was already very close to the Bretons. And in Western Normandy we were Armoricans

In a lot of the previous tests, I get 1/3 of Germanic
This percentage makes sense with the study of Leicester in my region, study based on the Y haplogroups.
Our percentage of germanic ancestry is probably very similar.

Ryan said...

I think you could and should charge more for this... at least $20? Your time is valuable.

Gansguoter said...

As I understand you need the raw data from FTDNA. Do you prefer build36 or build37?

Chad Rohlfsen said...

Hey, another Iowan.. Sioux City area here.

Samuel Andrews said...

@Helegenes50,

Interesting. Do all Normans show German and British influence?

Helgenes50 said...

@ Samuel Andrews

In Normandy from area to area, the ratio Celtic/Nordico-Germanic must be different, more Nordico-germanic on the coasts than in the south or inside of the country, more Gaulish.

In Cotentin and " Pays de Caux", the number of place names of Nordic origin ( Scandinavian and AS) is very high, but absent in much of the country.
In the peninsula of Cotentin, there are almost no place names before the Viking period

Unfortunately, as Normans we are not legion in the databases.

Two examples, on Anthrogenica, we are often talking about a Norman lady from Cotentin, very very English.
And a Blogger from Norfoks often gets results very similar to mine

Sorry if I am a little off-topic

Davidski said...

Seems like only people with FTDNA files are now sending through their data.

Please note that I can run AncestryDNA, FTDNA, 23andMe, and LivingDNA files.

jv said...

I found some Schoenherr’s in Sioux City. Just found out a couple of days ago the CORRECT spelling of my maternal 3rd Great Grandmother’s maiden name: Schoenherr and from Ansbach, Germany.

jv said...

My Crane Family came from Normandy before moving to England in the 1200’s. I believe there is an area called Cranne. One of the first recorded Crane’s in England was OLIVER DE CRANNE. I need to research the Cranne/Crane Family in Normandy. I have the Crane Family Tree beginning in 1270 in England, then 1600’s Connecticut, then 1700’s New York and 3 Crane Grandfathers belonged to Sons of the American Revolution, and then Jones Co Iowa( my much loved Grandmother Anita Crane Fox.)

huijbregts said...

I prepared a heat map of averaged scores.
Most of the variance is concentrated on dimensions PC1-PC4.
http://www.anthrogenica.com/showthread.php?12539-Eurogenes-Northern_Europe-PCA&p=305893&viewfull=1#post305893

Matt said...

As I was bored, a few more comparisons of the positions of samples / populations in Globe10 vs this PCA (NorthEuropePCA?):
https://imgur.com/a/c4NkD

N_Europe PC1 vs Global10 PC4: PC1 is the main PCA in N Europe, splitting Baltic from NW Europe, and PC4 in Global 10 roughly measures HG ancestry and distinguishes Europeans from Near Eastern populations. Generally these correlate, however there are differences in correlation from Eastern Europe and populations ancestral to present day Eastern Europe including Scythians, Samartians, Hungary_BA, Hungary_IA and Slav_Bohemia, against others.

N_Europe PC2 vs Global10 PC6: PC2 is the secondary PCA in N Europe, splitting Volga-Ural from Baltic-Slavic populations, while PC6 in Global10 is the East-West split in West Eurasia. There's not a lot of correlation between these two.

Running some nMonte with these two sets in the same datasheet: https://imgur.com/a/WQjTc

The Slavic populations seem to fit best in these 10+Global10 together as mostly derived from the I1502 (BR1) Hungary_BA sample, with the remainder 50-40% being about 20-10% late steppe (Poltavka or Samaritan/Scythian) and either Slav_Bohemia or Bell Beaker Germany.

Possibly this could be a real signal that these populations derive ancestry from individuals like I1502 together with late Bronze-Age to early Iron-Age Volga-Ural Steppe groups...?

(see: https://pastebin.com/294Beqhx for the datasheet)

Davidski said...

@huijbregt

Nice heat map. Can you post the R script?

Samuel Andrews said...

Off topic. Maybe WHG originated in Ice age Italy. DNA from the Iberian Refugium decended Magdalenians don't look like WHG's main ancestor.

The oldest example so far of a typical WHG mtDNA sequence comes from Italy.....

19ky, Paglicci71, U5b2b*

huijbregts said...

@Davidski

library(gplots)
myData <- as.matrix(myAverages)
heatmap.2(myData, distfun=dist, hclustfun=function(d) hclust(d, method="ward.D2"), key=TRUE,
col=redgreen(10), notecol="black", notecex=0.8, cexRow=0.8, cexCol=1, margins=c(8,10))

Maybe I should not have averaged Slavic_Bohemia. The pair is far apart

Simon_W said...

@ Matt

"The Slavic populations seem to fit best in these 10+Global10 together as mostly derived from the I1502 (BR1) Hungary_BA sample, with the remainder 50-40% being about 20-10% late steppe (Poltavka or Samaritan/Scythian) and either Slav_Bohemia or Bell Beaker Germany."

On a related note, it's still an open question where these BR1-like people exactly came from... They're not like typical Yamnaya steppe-folks, with their strong WHG and their lack of CHG. And although BR1 is often used as a representative of early Bronze Age Hungary altogether, there were also many less extreme people in EBA Hungary; if you check the PCA in Mathieson et al., it can be noted that most Vatya individuals are not far from the Bronze Age Balkan samples. There is just one HG rich Vatya outlier which is close to BR1 in that PCA; that's RISE479, I suppose. Whether BR1 is more typical for the Mako culture is an open question, as there's only one of them. Someone suggested GB1 from Chalcolithic Romania (Gonzalez-Fortes et al.) looks similar to BR1.

And I definitely don't think it's the best idea to merge BR1 and BR2 to a Bronze Age Hungary average. They were 900 years apart and from different cultures, and from what I've gathered BR2 isn't very north European-like either, he has relatively low Steppe ancestry. BR2 may be related to the Protovillanovans in Italy, as he belongs to the eastern Urnfield culture.

Matt said...

@Simon_W, yes, points taken, though I would note that in the broad West Eurasian context, neither the Hungarian BR1 and BR2, or the rest of the Hungarian cline, look like outliers when we consider the Tollense samples as well -

https://4.bp.blogspot.com/-0X53ULQMZ6U/WfhwdhmT9zI/AAAAAAAAGNQ/zs34s9OzA00HFftgKc-s10cus_wWLAwGQCLcBGAs/s1600/WEZ_West_Eurasia.png

It's doesn't look like the Tollense are autosomally the same as Bell Beaker or Unetice in the broad autosomal and then BR1 and BR2 and the other Hungarian samples are something else, and that BR1 and BR2 are outliers. BR1 and BR2 look within Tollense variation, in terms of what look like both the broad West Eurasian components and what looks like drifts that specifically distinguish present day NW->East Europe

Rob said...

@ Simon W & Matt

I hadn't been following the Tollensee samples too closely yet (because of the limitations) but w.r.t the BA Hungary samples, they seem like a mix of south-central European MNE (Baden, Remedello, Iberia Chalc.) & a yet difficult to define north/ eastern mix (? epi-Corded Ware E.C.E, giving a high "Latvia HG" signal). On the other hand, the Y lineage often encountered in BA Hungary is W-C European, an I2a2 distinct to, both, GAC and Carpatho-Pontic Chalc - Yamnaya type.

Putting everything together, could the Welzin type, looking at the plot, be a product of West European (~ French) M.N.E + epi-/ post- Corded admixing in north-central Europe in the post-2000 BC period

Arza said...

@ Matt

https://s6.postimg.org/5io77r23z/pca_Welz_Hung_RISE598.png

Matt said...

@Arza, that's a pretty interesting prediction, and on the basis of geography it seems fairly plausible, hope we can get the samples from Trzcinienc / East Trzciniec to test it and see what happens.

CleverPrimate said...

David,
When I first had you analyze my DNA data I only had 23andMe results. I have since had Ancestry.com analysis done. Do you think it would be worth my while to send those to you for further analysis? Do you think it would add anything significant?

Davidski said...

@CleverPrimate

Nope, unless I run you in a test that you haven't done before.

CleverPrimate said...

I believe you have done them all so far. I'll hold out until you come up with a new test and then I'll send them both in.

Matt said...

@ Rob, thanks for the response by the way, I think that "epi-Corded Ware E.C.E, giving a high "Latvia HG" signal" could be a very viable idea (based on the lack of any particularly HG other groups in Hungary, Balkans, GAC, that we've sampled so far).

Re: specific W-C European I2a2, pointing to the Hungary_BA samples having a specific W-C MN link, I'm leerier of ideas that are less geographically simple on very specific subclades, just because of population structure and unsampled populations in y-haplogroups. But you may well be right, and there may be enough samples that its reasonable to make the conjecture, and I don't have a very good grasp of y-tree for ancients at the fine detail, esp. with so many more samples out there.

Rob said...

@ Matt
Yes still hypothetical but it was based on the stratigraphy of samples from ancient Hungary, not modern data, and we have a reasonable number of the former to date (although still patiently waiting for the release of Lipson, Mathieson and Olalde for further detailed analysis).

Simon_W said...

@ Matt

At least BR2 isn't set apart from the cline defined by modern Europeans in the way the two "outliers" and the bulk of the Welzin samples are. But agreed, at close inspection there is still a little something peculiar about him, too. According to
https://docs.google.com/spreadsheets/d/1Rd332olbtYQs7dfVcEMnBCBRR0ILSLXCgDtZWm93XtA/edit#gid=661987578
he has less Steppe_EBA than Bergamo, but more WHG than Belarusians.

Moreover he seems to have a little bit of extra-CHG coming from southeastern Europe. The increase in CHG relative to BR1 is paralleled by a decrease of EHG, so it's hardly Steppe CHG we're seeing there:

https://docs.google.com/spreadsheets/d/1g-cEJmS9cZ6r-_9p0qj1f2qszxiJbactk89DOd0TlHg/edit#gid=1320636554

Matt said...

@Simon, I must actually admit that I had forgotten that it was Vatya:RISE479 and BR1 that were the Hungarian "outliers" and not BR2 and BR1.

Here's all the Hungarian samples on Global10 in PC4 and PC6 (which mostly correlate with the major "West Eurasian" PCA directions) and I think the fit with what you are saying here: https://imgur.com/a/z3HvP (Black = modern population average, Grey = ancient, Red = ancient Hungarian BA)

Rob said...

BR2 is J2a1 (Y) and K1a1 (mtDNA). Dates c. 1200 BC, i.e. at the cups of the 'Bronze Age collapse'.
His extra CHG could be from Balkans and/ or directly from Caucasus.

Matt said...

@Rob, that's a good point. Would not be surprised at all if Hungary in the Bronze Age was experiencing gene flow with both Balkans as well as other regions in Eastern Europe (and potentially in Western Europe given your earlier comment re:the potential kind of MN found in Hungary BA samples).

@OT: All who are interested, updated version of a preprint about Polygenic Adaptation:

https://www.biorxiv.org/content/early/2017/11/06/167551, updated with a bunch more adna tests.

Few interesting graphs from the paper, which might inform some of our basic anthropometric ideas of ancient people, at least in terms of what would happen under similar nutrition: https://imgur.com/a/aH1gF

1) Genetic height differences between present day Europeans quantified put pan-Northern Europeans (e.g. English in west to Ukrainian and Lithuanian in the east) at about 179-181cm (5 foot 11), mostly without much correlation with longitude, Bulgarians and Spanish at 178cm (5 foot 10), Sardinians and Southern Italians at 176cm (5 foot 9). East Asians are placed at around 168cm (5 foot 6), and the South Asian 1000 Genomes GIH at 174cm (5 foot 8.5).

2) Among ancients, STP seem to have the same score as modern day British and CEU, so about 179-181cm for Yamnaya, while EEF are exactly a third of the way between the predicted East Asians and GBR/CEU in polygenic height, and slightly above GIH, so should be (genetically) 176cm as well (5 foot 9).

Central European Bronze Age are intermediate STP and EEF and seem slightly shorter than present day people with similar ancestry proportions so selection may have operated slightly in most European post-Bronze Age populations to some extent since then, to increase robusticity or height.

3) Strangely, CHG seem tall (just above 180cm) and EHG seem shorter (the same 176cm range as EEF) in their analysis, and STP are accordingly intermediate. Not necessarily what I would've been expected, but Allen's Rule may have been at play in adapting EHG to be short, sturdy and robust compared to taller and proportionately slimmer WHG / CHG or Anatolians of the same height and more generally gracile proportions, all perhaps evolving in more temperate regions. Anyway, seems like trading a bit of CHG for EEF or EHG might make some populations slightly taller than expected?

(Not sure it's all totally complete. Should be better for West Eurasians and less true, but not totally wrong for more distant populations. Some East Asians, e.g. Northern Han Chinese may be more likely to have a genetic score 6 cm higher once unique East Asian variation is more accounted for. Mbuti, as pygmies and a much more genetically distant population to Europeans, likely to be much shorter than predicted here.)

(I thought this may be of interest, though as this is kind of off topic, I'll happily move the comment to another thread or delete, if Davidski wants to keep this discussion here more focused on customer support and not clutter it up.)

Davidski said...

@Matt

1) Genetic height differences between present day Europeans quantified put pan-Northern Europeans (e.g. English in west to Ukrainian and Lithuanian in the east) at about 179-181cm (5 foot 11), mostly without much correlation with longitude, Bulgarians and Spanish at 178cm (5 foot 10), Sardinians and Southern Italians at 176cm (5 foot 9). East Asians are placed at around 168cm (5 foot 6), and the South Asian 1000 Genomes GIH at 174cm (5 foot 8.5).

Where are these estimates in the paper?

Matt said...

@Davidski: Apologies, thought this would be self explanatory from my linked imgur gallery so forgot to actually state it! Figure S12 provides polygenic scores "placed on phenotypic scale" (so converted to actual heights), so that's valid for the modern populations and where the cm differences I mentioned come in.

Figure 4A provides differences between ancient West Eurasians and modern European, East Asian and South Asian populations. It expresses these differences in terms of Polygenic Height Scores, but since there are overlapping modern populations (CEU, IBS, GIH, etc.) between the "phenotypic scale" Figure S12 and Figure 4, it's easy to convert ancients on to the phenotypic scale.

Salden said...

http://journals.plos.org/plosone/art...l.pone.0187408

>A glimpse at the intricate mosaic of ethnicities from Mesopotamia: Paternal lineages of the Northern Iraqi Arabs, Kurds, Syriacs, Turkmens and Yazidis

>Serkan Dogan , Cemal Gurkan, Mustafa Dogan, Hasan Emin Balkaya, Ramazan Tunc, Damla Kanliada Demirdov, Nihad Ahmed Ameen, Damir Marjanovic

>Published: November 3, 2017
https://doi.org/10.1371/journal.pone.0187408

>Abstract

>Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others. As such, the genetics of the contemporary Iraqi populations are of anthropological and forensic interest. In an effort to contribute to a better understanding of the genetic basis of this ethnic diversity, a total of 500 samples were collected from Northern Iraqi volunteers belonging to five major ethnic groups, namely: Arabs (n = 102), Kurds (n = 104), Turkmens (n = 102), Yazidis (n = 106) and Syriacs (n = 86). 17-loci Y-STR analyses were carried out using the AmpFlSTR Yfiler system, and subsequently in silico haplogroup assignments were made to gain insights from a molecular anthropology perspective. Systematic comparisons of the paternal lineages of these five Northern Iraqi ethnic groups, not only among themselves but also in the context of the larger genetic landscape of the Near East and beyond, were then made through the use of two different genetic distance metric measures and the associated data visualization methods. Taken together, results from the current study suggested the presence of intricate Y-chromosomal lineage patterns among the five ethic groups analyzed, wherein both interconnectivity and independent microvariation were observed in parallel, albeit in a differential manner. Notably, the novel Y-STR data on Turkmens, Syriacs and Yazidis from Northern Iraq constitute the first of its kind in the literature. Data presented herein is expected to contribute to further population and forensic investigations in Northern Iraq in particular and the Near East in general.

The curious part is that Syriacs and Yazidis have very high levels of R1b compared to the other sampled populations. It's moderate in Turkmen and low in Arabs with Kurds.

Simon_W said...

@ Arza

"https://s6.postimg.org/5io77r23z/pca_Welz_Hung_RISE598.png"

It's quite amazing how much Baltic LBA RISE598 differs from modern Balts in that PCA. And although he's LBA, it has to be kept in mind that he dates to the first millennium BC, between 908 and 485 BC, according to calibrated C14 dates, a time when in central Europe the Iron Age was already flourishing.

Simon_W said...

I wouldn't say he was a Proto-Slavic invader, though. That's far too early and at the wrong place. RISE598 was found at a place where in Medieval times the Sudovians were living, a West Baltic tribe closely related to the Old Prussians. Actually, he might rather represent the real Proto-Baltic invaders who reached the Baltic region in the Bronze Age from the South.

Simon_W said...

The PCA Matt posted - https://4.bp.blogspot.com/-0X53ULQMZ6U/WfhwdhmT9zI/AAAAAAAAGNQ/zs34s9OzA00HFftgKc-s10cus_wWLAwGQCLcBGAs/s1600/WEZ_West_Eurasia.png - makes sense of the rumors I have heard about Wielbark samples. Apparently they were also of this WHG-shifted kind, and hence should be similar to Welzin_BA.

Simon_W said...

Quite exciting for me to note that my East Prussian German grandmother ("P_grandma" in the lefthand PCA) also seems to have some shift towards the more eastern-like ones of the Welzin samples. Under the reasonable assumption that one part of her ancestry is like average modern north-central Germans, her deviation doesn't go straight towards modern Balts, but instead is pulled a little to the WHG side: https://jpst.it/1792r

Romulus said...

@Matt

"Strangely, CHG seem tall (just above 180cm) and EHG seem shorter (the same 176cm range as EEF) in their analysis, and STP are accordingly intermediate. Not necessarily what I would've been expected, but Allen's Rule may have been at play in adapting EHG to be short, sturdy and robust compared to taller and proportionately slimmer WHG / CHG or Anatolians of the same height and more generally gracile proportions, all perhaps evolving in more temperate regions. Anyway, seems like trading a bit of CHG for EEF or EHG might make some populations slightly taller than expected?"

That can't be right. A recent paper had a graphic on height of Ancient groups and placed CHG as short as EEF. I can probably find it.

Matt said...

@Romulus, Martiniano et al 2017 (http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006852).

Martiniano's result was from completing imputation on samples, then used data from the GIANT study (https://www.broadinstitute.org/news/giant-study-reveals-giant-number-genes-linked-height) for markers and scores on the imputed data.

This study used the same markers (Wood et al (2014) page 29.) I do not think they carried out an imputation step.
I can't say which method should work better...

Samuel Andrews said...

Food for thought.

We all know genetic distinctiveness forms when a collection of individuals and their descendants continuously only breed with each for many generations. Evolution supposedly usually occurs in those small-inbred populations, but can also occur in multuple barely related populations if the same trait is selected for in each population.

Hypothetical scienro....

As a genetic experiment, two brothers from a tiny tribe are split at birth. One brother remains in that village. For 30,000 years that tribe's descendants are forced, by evil geneticists, to be genetically isolated from the rest of humanity, they were only allowed to breed with each other.

The evil geneticists placed the other brother into a society but not a genetically interlinked society. For 30,000 years, in this society people are only allowed to "breed" with completly unrelated humans. I know it is impossible for people in a society to remain completly unrelated for 30,000 years but let's just say somehow the geneticists found a way.

How would the people in the inbred world and the non-inbred world differ genetically?

Here's what I think.

The people in the non-inbred world be "less evolved", closer to the ancestral state the two brothers were in 30,000 years earlier. While, in the population that remained inbred for 30k years all kinds of new traits and new genetic distinctive markers would have formed in their DNA.

Inbredness, Relatedness, whatever you want to call it is the bread and butter of geneticists right? It's the source of diversity of life? Therefore, if no inbreedness, relatedness exists then no genetic changes, no new diversity, will occur, right?

Davidski said...

Seems like you're basically confusing evolution with speciation.

And by the way, inbred populations with low effective population sizes and genetic diversity are at high risk of extinction, because they can't adapt to changing pressures as well as large, genetically diverse groups.

Samuel Andrews said...

I asked that question for three reasons. One, some populations are more inbred than others and I know this has to be significant, I'm just not sure how.

The second reason what does this say about the difference between the genetics of "New World" people and "Old World" people? All New WOrld people are a mixture a distinct, inbred Old WOrld populations.

For example, what does this say about the difference between Dereck Jeter (New World) and a Pygmy (Old World)? Dereck Jeter must have something like x4 more ancestors than a Pygmy person.

What, will human genetics look like in 10,000 years? More and more the world population keeps growing and people are migrating and "breeding" with unrelated persons, both of which prevent inbreedness.

Samuel Andrews said...

@Davidski,
"Seems like you're basically confusing evolution with speciation."

Yep, by "evolved" I guess really meant speciation. I plan on doing a genetics 101 study project so I'll learn the basics.

In an inbred population everyone eventually, after so long, "evolves" to become genetically really similar and eventually a new species. What I'm wondering is since inbreedness is the driver of genetic diversity (and speciation) do indviduals from non-inbreed populations remain more in the ancestral state, don't "evolve" into a new species?

Davidski said...

Well, even so, isolated, inbred populations are unlikely to get the chance to speciate because they're at a higher risk of dying out due to their low diversity and thus inability to adapt to changes.

New species do form as a result of populations becoming isolated from each other, but this doesn't need to be accompanied by high inbreeding, and as I say, generally isn't.

For instance, one part of a large, genetically diverse plains population might be forced to live in the nearby forests as a result of intense competition on the plains, and over time the plains and forest groups stop breeding with each other, evolve in separate ways as they continue to adapt to their environments, and form new species. Just one example.

Ric Hern said...

I think a static inbred population will probably die out. If they migrate as a group to another ecosystem new pressures will result in drastic mutations and selection within that group....

EastPole said...

Colin Renfrew will have a lecture on DNA and Indo-European Origins today:

https://www.eventbrite.com/e/lecture-marija-rediviva-dna-and-indo-european-origins-tickets-36757838685

Richard Holtman said...

Hello David

Keep up the good work. I'll take you up on your offer.

epoch2013 said...

@David

Mark Lipsons paper is on Nature. That would mean that from now om the Blatterhohle samples are available, wouldn't it? Had a look at it yet?

Davidski said...

Yes, the Lipson et al. dataset is now available at the Reich Lab website at this link...

https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/LipsonEtAl2017.tar.gz

I haven't had a look at it yet.

Samuel Andrews said...

Btw, Blatterhohle R1b is pre-R1b1a1a2-M269.

Rob said...

@ Sam

Genetiker has him as pre-V88, apparently .

@ All

An mtDNA from Maglemoisan 8500 BC, Koelbjerg, Denmark
http://www.tandfonline.com/doi/abs/10.1080/21662282.2017.1381418

Is U5a2c.
Full genome to follow apparently in new paper

Salden said...

Genetiker is run by a White Nationalist hostile to the Kurgan Hypothesis and advovate of a White presence in Mesoamerica before the Age of Exploration.

Rob said...

Yes he's had some odd theories, but usually his SNP called are okay
Anyhow, if Blatterhohle is actually V88 instead of pre- M269, that kinda confirms the steppe hypothesis (for Northern Europe), doesn't it ?

Rob said...

Whilst on new papers, a look at mobility in Bronze Age north Kazakhstan

"Pastoralist Mobility in Bronze Age Landscapes of Northern Kazakhstan: 87Sr/86Sr and δ18O Analyses of Human Dentition from Bestamak and Lisakovsk"

They find - "The strontium and oxygen isotopic results from Bestamak (MBA) and Lisakovsk (LBA) suggest that pastoral groups in northern Kazakhstan engaged in small-scale movements that remained largely local to settlement sites. At the same time, these data hint at slight differences between MBA and LBA mobility patterns based on the presence of a few non-local strontium values observed in individuals from Bestamak...A shift in patterns of landscape
use from the MBA to LBA indicates that individuals were more mobile in the earlier period when large settlements dominated the southern Urals region. Our findings are in direct contrast to archaeological models claiming that increased mobility, often associated with
nomadic pastoralism, was the impetus behind the spread of Andronovo materials across Kazakhstan during the LBA. Further, contrary to genomic evidence, our results suggest that if long-distance migratory events were occurring during the Bronze Age, they did not impact the communities under study. Bronze Age groups in the region appear to have been exploiting
resources at the local and regional level rather than at pan-regional scales across the steppe."

So, IIUC, they argue that populations they studied suggest that mobility was greater during the EBA Sintashta period (characterised by large, fortified settlements) than during the subsequent Andronovo phase, where smaller more dispersed settlements dominate over a much greater territorial span.

John Smith said...

I don't care if he's pre-R1b1a1a2-M269 or pre-V88 in any case genetiker is pretty reliable but I did see him post something inconsistent about I/C1a for like Paglicci I asked him but he never responded so I still don't know whos right him or the paper someone made a mistake. How did Sam get the idea he's pre-R1b1a1a2-M269?? I hope we know for a fact what he had soon however I am betting on pre-V88 per the general reliability of genetiker. The only way genetiker would be wrong is if he sequenced the wrong sample and I doubt he did that. I think 95-99% chance its v88 and only a 1-5% chance Sam knows what he's talking about but we will know soon enough 100%.

Samuel Andrews said...

On the R1b, Bell Beaker discussion thread it's an assumed fact that Bla16 is pre R1b M269. The Lipson preprint says he was derived for some M269 equivalent SNPs and negative for others.

http://www.anthrogenica.com/showthread.php?3474-Bell-Beakers-Gimbutas-and-R1b/page459

Davidski said...

Apparently the new Mathieson et al. paper and data are coming very soon.

Samuel Andrews said...

About damn time.

Davidski said...

There's a presentation coming up later this month at Human Evolution 2017 about the genetic origins of the Roopkund skeletons. Some of them show affinities to Greeks and Levant populations. The rest look basically Indian.

https://en.wikipedia.org/wiki/Roopkund#Human_skeletons

Davidski said...

And Nick Patterson and David Reich are co-authors of that Roopkund talk.

Samuel Andrews said...

It's interesting that many current Europe-wide subclades in K and H only appear in the Iberian Neolithic and are absent in the German and Hungarian and Barcin Neolithic. Also, how do we explain the almost complete lack of N1a1a in modern European but a high frequency of N1a1a in the German and Hungary and Barcin Neolithic?

I'm working with loads of rich modern European mtDNA data. I'm running lots of scienores through tests. One scenario I'm pretty confident of is a tiny contribution from Barcin, LBK, Hungary Neolithic-type to modern Europeans.

Ric Hern said...

So some legends and Myths have a certain percentage of truth to them as seen at Roopkund. Without political or other manipulation some stories can be transferred intact for at least a thousand years. Very interesting.