APOE gene is related to Alzheimer's disease, but also to Covid-19 vulnerability

 I made APOE gene statistics using the 1000 genomes data.  The APOE gene is bound to two SNPs, rs429358 and rs7412, both on the chr 19.  In the worst case both are homozygous for the allele C (e4  resulting vulnerability of 12x for late-onset Alzheimer's and 61x for early-onset disease.  If the first SNP is heterozygous and the latter CC (e3) the possbility is still >3x increased risk for Alzheimer's; 1.4x increased risk for heart disease.  Now, new studies connect these alleles also to increased risk for serious Covid disease.

Study

rs429358 freq/individual, rs7412 any value LWK 0.727 GWD 0.478 ESN 0.465 MSL 0.447 ACB 0.417 YRI. 0.389 FIN 0.364 ASW 0.344 CEU 0.333 GBR 0.330 CLM 0.277 STU 0.255 IBS 0.243 PUR 0.212 TSI 0.187 CHB 0.184 CDX 0.183 BEB 0.174 MXL 0.172 ITU 0.167 PJL 0.167 JPT 0.163 KHV 0.121 PEL 0.118 CHS 0.105 GIH 0.097 APOE4 FREQ/ind, rs7412=CC LWK 0.1515 GWD 0.0796 ACB 0.0729 ESN 0.0606 MSL 0.0588 GBR 0.0440 FIN 0.0404 YRI. 0.0370 ASW 0.0328 CLM 0.0213 CEU 0.0202 KHV 0.0202 STU 0.0196 JPT 0.0192 BEB 0.0116 PJL 0.0104 GIH 0.0097 IBS 0.0093 APOE3 FREQ/ind, rs7412=CC LWK 0.424 ESN 0.343 MSL 0.329 GWD 0.319 YRI 0.315 CEU 0.293 FIN 0.283 ASW 0.279 ACB 0.271 GBR 0.242 CLM 0.234 IBS 0.224 STU 0.216 PUR 0.212 TSI 0.187 CHB 0.184 CDX 0.183 MXL 0.172 ITU 0.167 BEB 0.151 PJL 0.146 JPT 0.125 PEL 0.118 CHS 0.105 KHV 0.081 GIH 0.078

European IBD statistics

 Many online genetic services provide individual  ancestry results but don't reveal their methods.  For me 9 of 10 services give Finnish plus minor 5-8% admixture of Greek or Italian.  I have seen a man of fully Croat ancestry getting additionally 12 % Orcadian ancestry.  Surprising Orcadian in Balkans, really? Only to mention two examples. Those ancestry testing companies looks like modern alchemists.  My advice is, don't pay, you can get ancestry tests for free from services using open source softwares.   Maybe results of open source softwares are not perfect, but at least you have a possibility to find out how the results are done. 

It is obvious that these companies use a special data adaptation and model putative ancestral pools to geographical locations according their own approaches, but they are not professional historians.  Maybe there is seen a growing genealogical demand in countries where the paper trail is incomplete or they simply try to give a shortcut bypassing paper trail, but according my experience there is no substitute for the old fashion genealogy work.  I am not going to start searching my Italian cousins, because  my paper trail, fully covering to the end of the 17th century, doesn't show Italian roots. 

 

A new Finnish study about yDna haplogroups

 A new study observes yDna haplogroup frequencies and CAD (Coronary artery disease), in Finnish sepelvaltimotauti) vulnerability of haplogoups in Finland.  Haplogroup frequencies show very close same number with the study Lappalainen et al. 2006, but differ from the study Neuvonen et al. 2015.  New haplogroup proportions are

N1c1 60,18 %
I1 26,44 %
R1a1 5,99 %
R1b 5,01 %
I2 0,97 %
E1b1 0,51 %

The study is dowloadable from the link in the end of the following text, link

Results figuring CAD are contradictory with another Finnish study.  This study (published in a Finnish medical magazin Duodecim by Joel Nuotio*, Tomi T. Laitinen* ja Markus Juonala, Link) gives following results, showing the highest vulnerability of CAD in East Finnish regions where the proportion of N1c1 is highest and the lowest vulnerability was found in Southwest regions where the N1c1 proportion is the second highest.  

Picture:

A - autosomal genetic structure in Finland

B - CAD incidence

C - genomewide CAD risk

I see two main factors involved with the disease vulnerability

- way of life

- autosomal inheritance

The Duodecim article shows the highest CAD incidence in the northeast and lowest in the southwest, both areas having the highest N1c1 proportions in Finland.  The way of life is today quite the same everywhere in Finland, thanks to the similar food markets and consistent culture  in the whole  country.  So what remains is differences in the autosomal inheritance.  Southwest and east have been isolated from each other hundreds years in the Finnish history and we can predict also significant difference in the autosomal inheritance of those two areas, the difference we can also see using autosomal genome tests.  Basically the areas of the HG I1 are between southwestern and eastern N1c1 areas and we can predict that the CAD vulnerability of I1 should be between the vulnerability of those two N1c1 areas. 

Patterns of genetic connectedness between modern and medieval Estonians and Finns

 A new Estonian study sets the connection between our countries to the 8th and 10th centuries AD and bases it on an assumed Estonian migration to Finland.  Sounds like Estonian self-seeking idea about  Estonian Vikings.  Heard before.  I have not knowledge about such Estonian migration.

  There have been a lot connections between our countries, but historians have never mentioned exactly aforementioned time frame as a significant event in our history.  Sure people have moved from Estonia to Finland, but also conversely.  Historians suggest that the main migration bringing the Baltic Finnic language happened during the Roman Iron Age and we know for sure that around 20-30% of the North Estonian population had Finnish origin after the Swedish era in the 17th century.  We know it because we have original documents.  Those times were very exhausting in Estonia due to many wars and the Estonian population size decreased remarkably.  

Such a Late Iron Age migration from Estonia should also be seen by an elevated R1a proportion in Finland, but the small R1a amount in Finland doesn't imply any Estonian origin.  I stay waiting for wider scientific stance.

Link

The grave of Viking female revealed many surprises

 It was long assumed that the grave was made for a woman, for a Viking queen or princess. Archaeological evidences spoke about a female, clothes and jewellery were typical for a female, but the luxurious sword gave a hint about a male.  The sword was so fine and luxurious that it has been a model for replicas sold under the topic "Sword of Suontaka Viking princess".  But genetic analyses  revealed that the buried one was not a typical man or woman, the remains showed signs of both, namely a chromosomal XXY structure.

Link

The dichotomy between Eurasian and African X chromosomal haplotypes

I made a statistics showing a full bifurcation between East-Asia and Africa. Showing high similarity in the whole Eurasia it is likely that the Eurasian haplotype is related to the OOA event. To see how much the African haplotype in Europe represents Near East migrations needs more investigation. The result implies however that not all and there have been different evolution and migration routes in Eurasia. The haplotype includes 15 SNPs.

Percentages of East Asian (pure African type is 100 - x)

Han Chinese	100
Southern Han Chinese	100
Japanese	100
Kinh Vietnamese	99.494949
Dai Chinese	98.92473
Punjabi	96.07639
Peruvian	94.70588
Bengali	92.48062
Sri Lankan	91.04575
Gujarati	90.64725
Mexican-American	89.8958
Indian	88.7255
CEPH (Utah Euro)	87.2727
Finnish	83.4007
Tuscan	82.0561
Colombian	81.5603
Spanish	80.9034
British	79.8535
Puerto Rican	70.1603
African-American SW USA	23.5519
African-Caribbean	8.1597
Luhya	7.71040000000001
Mende in Sierra Leone	3.098
Gambian	1.5044
Yoruba	0.987700000000004
Esan	0.808099999999996

 

Lost Finnish study

 I found newly some information about once lost Finnish study on the Eupedia forum, but still the source unknown.  If you know where is this data from, please inform me, I appreciate it.  I assume that the study can be published during this autumn, but can't be sure.   I suppose it has been on the agenda of the deleted symposium EAA2020.

This is interesting especially because of the certain illogicality between released yDna and autosomal data.

https://www.eupedia.com/forum/threads/40385-The-12th-century-communities-illuminates-the-genetic-makeup-in-the-southwest-finlandh

"The 12th century communities illuminates the genetic makeup in the southwest finland

Abstract author(s): Saari, Nelli-Johanna (University of Helsinki, Department of Philosophy, History, Culture and Art Studies; Max
Planck Institute for the Science of Human History, Department of Archaeogenetics; University of Helsinki, Faculty of Biological
and Environmental Sciences, Organismal and Evolutionary Biology Research Programme) - Majander, Kerttu (Institute of Evolutionary Medicine,
University of Zurich; Max Planck Institute for the Science of Human History, Department of Archaeogenetics)
- Salmela, Elina (University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology
Research Programme; Max Planck Institute for the Science of Human History, Department of Archaeogenetics; University of
Turku, Department of Biology) - Krause, Johannes (Max Planck Institute for the Science of Human History, Department of Archaeogenetics) -
Onkamo, Päivi (University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary
Biology Research Programme; University of Turku, Department of Biology)

Abstract format: Poster

Southwest Finland has rich Late Iron Age archaeological records that show diverse cultural and trade networks. Ancient DNA analyses
from human remains, however, have remained scarce due to the acidic Finnish soil that leads to a rapid decay of bone material.
Two large inhumation burial grounds from the Crusade Period (1050–1150 CE) in Southwest Finland, Raisio Kansakoulunmäki and
Masku Humikkala, represent the transition period towards Christianity. The favourable skeletal preservation on these sites offers a
possibility to analyse the genetic structure of the Iron Age communities behind the burial context. Combining this genetic data to
other periodically and regionally close individuals enables an in-depth examination of the population history of Late Iron Age Southwest Finland.
In this archaeogenetic study we investigate the genetic composition of altogether 29 individuals, 14 from Kansakoulunmäki and
15 from Humikkala. A closer analysis of kinship patterns and genetic ancestry provides comprehensive information of the Late
Iron Age communities, such as family relations and patrilocality. All samples in this study have been processed in dedicated cleanroom facilities.
Ancient DNA libraries have been enriched for ancestry-informative markers in human DNA, and the data retrieved
with high-throughput next-generation sequencing. The preliminary results for seven Raisio Kansakoulunmäki individuals indicate a
genetic continuity with contemporary Finnish populations. Our current analyses intend to provide a detailed view of the ancestry
components, kinship and genetic affinities for all successful samples.


SOURCE:

https://eaa.klinkhamergroup.com/eaa2020/full_paper/files/2647/NJS_EAA2020_poster_updated_final_pdf.pdf




Sample ID Sample Individual information Called SNPs Burial Osteological Genetic MT hg Y hg Radiocarbon age (BP)
RK2002 Petrous part Mature adult (35-64) 260.771 F F? F H5b2 NA 828±27 BP
RK2003 Petrous part Young adult (18-44) 166.090 NA NA F H27a NA 937±28 BP
RK2004 Petrous part Infant (2-3 years) 354.779 NA NA F H3h1 NA 988±28 BP
RK2006 Petrous part Juvenile (9-11) 114.529 NA F F H27a NA 950±28 BP
RK2007 Petrous part Mature adult (35-64) 16.998 F F? F NA NA 995±24 BP"

 

RK2009 Petrous part Young adult (18-44) 385.637 F M? F U5b1 NA 924±28 BP
RK3005 Petrous part Juvenile (12 years) 205.527 NA F? M T1a1 N1a1a1a1a 772±28 BP
RKA001 Petrous part Young adult (18-44) 102.282 NA M? M A12a N1a1a1a1a 871±30 BP

Are East Finns really eastern conquerors. Fiction and truth.

 Being active in the internet I often meet these ideas.  Russians often have opinion about eastern conquerors that populated Finland.  Westerners have another weird habit; they dig again and again 80 - 150 years old dusty papers to prove something.  We have in Finland our own stories, sometimes supported by our researchers, unfortunately.  Common for those people is denialism, they don't want to use up-to-date and comparable scientific  results and if they use available new data they will always find a loophole how to support those 80-150 years old dusty papers.  One of those ideas is to prove that the Finns came from the far east and so East Finnish people have to be an evidence because they are the most eastern Finnish group..

I made a series of Dstat-statistics to see where the East Finns locate on the east-west axis.  I have genealogically proven samples from all Finnish regions and also  classified samples from the 1000 genomes project. 

 

East Finns are closer Southwest Finns than they are from Karelians, despite of the historical Swedish connection of Southwestern Finns. 

Karelian

FIN-Southwest-2g

FIN-East-2g

Mbuti

-0.0014

0.001243

-1.152

58418

58585

973547

Karelian

FIN-Southwest-2g

FIN-East-proved

Mbuti

-0.003

0.001186

-2.515

19777

19895

314367

Karelian

FIN-Southwest-proved

FIN-East-proved

Mbuti

-0.0046

0.001608

-2.84

19625

19805

314366

 

I made more comparisons to see a bigger view and I can cast a challenge.  If someone can give any non-Finnish sample group being closer East Finns than East Finns are from Southwest Finns, I will publish the results and give all kudos to her/him.  Only group on the Russian side I rule out is Ingrians who actually are East Finns who migrated to Russia during the historic era.

FIN-Southwest-proved is from the seaside of Finland Proper and consists of 5 samples.

1800 years old golden Odin neck ring was found in Finland

 Picture

It was found 1770 from Nousiainen in Southwestern Finland and soon after the discovery moved to Stockholm.  Being from the 200 AD it is probably one the oldest artefact related to Scandinavian mythology.  Taking into account the age and representing the heathen time before Swedish crusades it is hard to see it as a Swedish era product.

Relations of Finnish groups

 I did a new test searching admixtures of Karelians.  Academic Karelians given by Russian researchers are likely from the White Sea region.  As far as I know they are relatives of Finnish Karelians, but still a different group.  In Finland only people living in the Karelian Isthmus were considered as original Karelians, but probably in Russia the Karelian ethnicity is a wider concept and those figured as more southern Finnic people are called Ingrians, while in Finland they are called Izhorians.  For better or worse, the Karelians published by Russian researchers are not easy to determine by any Finnish ancestry, neither those called Ingrians by Russian researchers are what they should be (in my opinion).  The Ingrians as understood in Finland were an eastern migration of East Finns in the 17th century while Izhorians are considered as an old Baltic Finnic group.  What we see later, the published Karelians seems to be quite an archaic group and the best but not qualitatively confirmed match for them was Baltic_BA (Baltic Bronze Age) plus even older Bolshoy Olegi Ostrov samples from the Kola Peninsula, both samples not belonging to any known Finno-Ugric speaking people.  The  published Ingrians seem to be a very Finnish group, which is reasonable, but being closer Southwest Finns than East Finns I would say that they actually are Izhorians.  After this prologue I want also say that I probably will not do more these Finnish analyses, not before Finnish researchers publish new Iron Age Finnish samples. They published some data of them already two years ago, plus I found accidentally a newer international study citation and results figuring Iron Age Finnish samples showing unprecedented results.  I linked this study in my older letter, but the study disappeared later, so I can't tell if it was anything noteworthy or only a misconception, which was later removed (link: http://terheninenmaa.blogspot.com/2020/09/study-southwestern-finnish-samples-from.html?m=1 ).

 

Best f3-results.  It seems like Karelians, Tavastians and East Finns compose a partly mixed entity, while Southwestern Finns belong to another entity. 

Karelians - probably White Sea Karelians

Ingrians - probably Izhorians

FIN-East - Savolaxians

FIN-West - Tavastians

FIN-North - likely samples from Torne River Valley

FIN-Southwest - samples from Finland Proper

 

 Common ancestries:

 

East Finns, best fits

I have two East Finnish sample groups, one (EFinn) consisting of my project members from Eastern Finland, another (FIN-East) derived from the first one using samples from the 1000 genomes project.  The 1000 genomes gives gives better result quality due to sample amount and quality.  My 1000 genomes samples are grouped into 3 groups:  Southwest Finns resembling my project members from Finland Proper,  West Finns resembling Tavastians and East Finns resembling people from the Savo district.  Now I have a new group resembling medieval Estonians under abbreviation Estonian_MiddleAge_N1c1.  N1c1 comes from the allocation of researchers.  There is no reason to assume that medieval Estonians could have been genetically extremely diverse though.  The new Finnish group is named as  Estonian_med_Finns.

 

Some explanations.  Z-score values over 3 or below -3 are considered to be meaningful.  It doesn't mean that all other results are not "true", only that they are not mathematically reliable.  The reliability depends on SNP amount among other things ( ! mark). Good  Z-score doesn't tell about a superiority of the result itself, neither the margin of error, column 5. 

F3 uses only two sources and admixed results can be achieved by several combinations.  Real admixture could be achieved by some combination of these sources giving admixed results, or not, or even by a combination of fitting and non-fitting results.  Using qpAdm I could have found these combination, but qpAdm is a challenging tools to use with already admixed modern populations. 

Trying to find the Finnish admixture

 After hundreds candidates from every compass points I succeeded to find a meaningful combination using 3Pop.  You can try, it is not easy to find acceptable results, negative f3 results with over 3 Z-value.  After finding the Finnish admixture I made a few estimates with some other present-day populations, with less success.  This is of course only one possibility among many other similar combination and in a real world admixtures are more complex. I found that Ingrians are the most similar group with Southwestern Finns, giving similar admixtures, East Finns and Karelians didn't fit in this admixture.  Ancient samples in the first row represent Iron Age Scandinavians, Levaluhta Iron Age Saami-like people, Baltic_BA Bronze Age people from Latvia. Don't shoot the pianist.

 

 

Was there a genetic shift from the Bronze Age Estonia to the present day through the Iron Age

 While we experience heat in Finland and people spend time in air-conditioned rooms and the secrecy keeps going on as to the Finnish Iron Age samples (which we know being analysed), I started to think what can I do.  Something definitely.  I can look if there is any continuation from the Baltic Bronze Age to modern populations through the Iron Age Estonia.  We remember studies finding out that the Iron Age Estonia met a migration holding male haplogroup N1c.   This observation keeps inside the idea of a larger migration of N1c to Latvia, Lithuania and Finland.  I also picked Estonian Medieval samples carrying this particular haplogroup to extend observations about possible replacement of Bronze Age Estonians by eastern newcomers.  All right, in case my tests fail to see any replacement, it doesn't mean that any replacement didn't occur, it proves only that the migration didn't change the genetic profile of Bronze Age Estonians.  So I did a dStat-test comparing whether I can see notable change between Bronze Age, Iron Age and medieval Estonians compared to present-day populations.  If there is any shift to the present-day it would mean that there is a continuum from a dedicated migration.  If there is no notable shift it would mean that  no notable eastern or any kind of notable migration existed changing present-day populations through the Iron Age Estonia.  

 

Looking at results and using the Swedes as a threshold my conclusion is that only Latvians and Estonians show in some extent drift towards the change in Iron Age Estonia.   Only Latvians and Estonians show notable shift towards Medieval Estonia (again using the Swedes as a threshold), which sounds weird, because the common idea is that this shift should be strongest is Estonia and Finland, not in Latvia.  The row mauri is my result made by an imputed genome I got from 23andMe.  The imputation was done by a reputable US university.  

Significant results are colored.

New HG N sample found - do we have now the home land of Proto-Uralic people

Kılınç et al. 2021 brought forth a new ancient Bronze Age sample belonging to Y-DNA haplogroup N.  I have tested it and it shows an extreme Siberian ancestry. This is the second time we have a Bronze Age sample carrying haplogroup N.  The first time we saw this happening a couple years ago with Bronze Age Kola Peninsula samples.  Both samples, Kola and now the new one from Krasnojarsk Russia belong to the clade L1026/L392, but now I have an unconfirmed evidence about the latter one belonging to the downstream mutation L1022, which is known to be Estonian and Southwest Finnish in modern samples.  So far so good, but while recent Estonians and also Iron Age Estonians show a negligible amount of Siberian ancestry, whether they belong to the HG N or not, the new sample is fully Siberian.  While the new Krasnojarsk sample is 100% Siberian, Kola samples show roughly 50/50% Siberian and Baltic HG-like ancestry and Iron Age Estonians are of later Baltic ancestry with CWC admixture or of mixed Scandinavian-Baltic ancestry.  So we have still a big puzzle with the origin of the HG N in the Baltic Sea region and also with the origin of Baltic Finnic genetic home land.  If I had to choose between the Krasnojarsk and Kola samples  would prefer the Kola samples due to their large European autosomal admixture and the situation near strongest modern European N clusters.

 I made a PCA plot locating the new sample and it was placed near Koryak people, maybe Chukchis too, but I had not them in my analysis. Koryaks are one of the most distant people in all Siberian people.    I also made a qpAdm test in aim to see the best Siberian admixture population for modern Saamis to evaluate the fit with the new Krasnojarsk sample.  The Krasnojarsk sample did fit as a Siberian admixture of the Saami and present-day Nenets were a better fit. So we can say  that the Krasnojarsk sample is a poorer fit than Nenets figuring Siberian ancestry in Fennoscandinavia and we don't need the new sample to explain the origin of Baltic-Finnic people and their assumed Siberian admixture origin.  Additionally the ancient Kola sample set explains the N-L1026 in Fennoscandinavia better than any other sample so far, because the Siberian admixture in Fennoscandinavia and in the living area of Baltic Finns today shows an evident gradient from north to south diminishing to zero in Iron Age Estonia.  Whether the original Finno-Ugric speakers were genetically Koryak-like or not, I wouldn't yet bet on it.