Maternal lineages from 10-11th century commoner cemeteries of Hungary

[Dunai]

A very exhaustive study was done by Hungarian archeogeneticists regarding the maternal ancestry of the commoner population in Hungary, which haven't been done on this scale thus far on this very important group, only on the elite population. I will quote some of the most important finds, but the whole study should be read since it provides further explanations.

"Hungarian history was profoundly determined by the conquering Hungarians (succinctly Conquerors), which arrived to the Carpathian Basin from the Eastern European steppe at the end of the 9th century AD as an alliance of seven tribes. Leaders of the alliance, Álmos and his son Árpád founded a steppe state upon the ashes of the Avar Khaganate, and their descendants later established the Hungarian Kingdom. The archeological legacy of the Conquerors is well defined, especially the 10th century small cemeteries of the military leader strata whose grave finds included precious metal jewels, costume ornaments as well as decorated horse riding- and weapon-related grave goods. Most of the larger cemeteries attributed to the common people are dated somewhat later, to the 10-12th centuries. People in these so called village cemeteries were buried with simpler jewels and grave goods, with sporadic appearance of weapons or harness accessories. There is a general agreement that elite graves with typical grave goods represent first or second generation immigrant Conquerors, but affiliation of people in the village cemeteries is far less clear. The several hypothesis presumed among others Slavic ethnicity, immigrant commoner strata of the conquering Hungarians, and local inhabitants from the previous Avar period. Origin of the commoner strata considerably determines the historical interpretation of the conquer and subsequent events in the Carpathian Basin and genetic data may contribute to clarify this issue.

We set out to implement a comprehensive study in this matter and for this end selected 8 cemeteries archaeologically evaluated as belonging to the 10-11th century commoners, from which we determined altogether 202 whole mitogenome sequences. Phylogenetic analysis was performed to illuminate the origin of each maternal sub-lineages of the studied remains. We compared the mitochondrial haplogroup composition of the commoner and elite population to find out their genetic relations and applied different population genetic methods to elucidate the relationship of the commoners with other ancient Eurasian populations.

First, we compared the major Hg distribution of the conqueror period elite and commoner populations. The heterogeneity of major-Hg distribution of ConqElite is comparable to that of ConqCommoner, however the Hg composition of the two groups shows considerable differences. The ratio of east Eurasian major-Hgs in the commoners is 7.69% contrary to the 19.64% of the elite, besides the elite contains a broad spectrum of these; A, B, C, D, F, G, and Y, while only C and D occur with notable frequencies in the commoners, with single appearance of B. West Eurasian Hgs of ConqC and ConqE also show notable differences: Hgs HV, I, M, R, U1, U8 and W occur with moderate frequencies in commoners, while these are completely absent from the elite. Three Hgs N, T1 and X, typically widespread both in east and west Eurasia, show much higher ratio in the elite than in commoners: N 11.61% in elite, 3.85% in commoners; T1 11.61% in elite, 2.75% in commoners; X 4.46% in elite and 0.55% in commoners. The opposite is true for Hgs H and T2; among commoners H is the most prevalent Hg with 33.52% frequency, while in the elite group its proportion is significantly lower 19.64%; T2 has 6.59% proportion in the commoners and 1.79% in the elite.

The ConqC clustered in the eastern side of the European aggregation, with closest genetic affinity to Baltic Bronze Age, Baltic Iron Age, Baltic Medieval, Bell Baker Germany and Great Britain Bronze Age populations and is not far away from the Steppe Early-Middle Bronze Age (Steppe_EMBA). In contrast the Conqueror Elite is located between ancient European and Asian populations and its closest clusters are Sarmatian Iron Age, Tien Shan Iron Age, Karasuk late Bronze Age and the two groups suggested to be in connection with the Conquerors: the Cis-Ural Medieval and Uyelgi trans-Ural Medieval.

https://www.biorxiv.org/content/biorxiv/early/2021/01/27/2021.01.26.428268/F4.large.jpg?width=800&height=600&carousel=1

The overall Hg composition of the commoner population proved to be significantly dissimilar from the elite in respect to both east and West Eurasian Hgs, indicating that these two groups had highly different origin. Population genetic analysis definitely clustered ConqC primarily with European and Near Eastern populations, well separating them from the elite, suggesting that people with local European origin dominated the ConqC population. On the other hand, ConqC had smallest SHD distance from ConqE suggesting that in spite of their dissimilarity, out of the studied ancient populations ConqE shared highest proportion of identical terminal Hgs with ConqC, which can be best explained by admixture between these groups.

Reciprocal gene flow from ConqC to ConqE is indicated by their shared Hgs; H7, K1c1, T2b and V7a which are absent from east Eurasia but had been present in the Carpathian Basin from the Neolithic-Bronze Age. On the whole above data imply that the proportion of immigrant Conquerors did not exceed 14% of the local population, but the more realistic value must be far smaller."

https://www.biorxiv.org/content/10.1101/2021.01.26.428268v1.full

[Dunai]

It's very interesting to see that the Hungarians Conqueror elite was 20% East Eurasian, and most similar to ancient steppe populations of the area between the Ural and Altai Mountains. Also even if the Hungarian Commoner population was mostly West Eurasian based and overall they had a different set of maternal haplogroups from the conquering elite, they still were around 8% East Eurasian, meaning the Late-Avar population that the conquerors found in the Carpathian Basin was already quite mixed with previous Asiatic migratory people, like the Avars most probably. Now what future research will have to reflect more is to give us a better explanation if the Magyar Conquerors, besides the elite and their families, did they also bring a commoner population with them? Or were they very few in numbers while the conquered people of the Carpathian Basin became the commoner population under a very short time, who adopted the Magyar language of the elite? There might be some issues of logic if we have to accept that the small elite, probably outnumbered 1 to 10 by the locals, still managed to Magyarize them, especially knowing how many raids all over Europe did mostly members of the elite accomplish during the vital 10th century. From who could the locals have learned the Hungarian language, if we must accept that the Conqueror Elite were the ones who brought Hungarian here first, while they were often away from their residence in the 10th century, plus if they were so few?

[Dunai]

Just to present a counterargument for my previous questioning if were the Conqueror Elite indeed the bearers of Hungarian language or not, here is an overlooked study from last year about both maternal and paternal continuity between Hungarian Conquerors and the various Uralic cultures from where they migrated. This was done by another Hungarian archeogenetic team than the one I posted in OP (Neparáczki), and both teams have somewhat differing interpretations of the raw results.

"The ancient Hungarians originated from the Ural region of Russia, and migrated through the Middle-Volga region and the Eastern European steppe into the Carpathian Basin during the ninth century AD. Their Homeland was probably in the southern Trans-Ural region, where the Kushnarenkovo culture was disseminated. In the Cis-Ural region Lomovatovo and Nevolino cultures are archaeologically related to ancient Hungarians. In this study we describe maternal and paternal lineages of 36 individuals from these regions and nine Hungarian Conquest period individuals from today’s Hungary, as well as shallow shotgun genome data from the Trans-Uralic Uyelgi cemetery. We point out the genetic continuity between the three chronological horizons of Uyelgi cemetery, which was a burial place of a rather endogamous population. Using phylogenetic and population genetic analyses we demonstrate the genetic connection between Trans-, Cis-Ural and the Carpathian Basin on various levels.

Based on linguistic evidences, the Hungarian language, belonging to the Ugric branch of the Uralic language family, was developed at the eastern side of Ural Mountains between 1000 and 500 BC. According to the written and linguistic sources and archaeological arguments, after the sixth century AD, part of the predecessors of Hungarians moved to the Western Urals (Cis-Ural region) from their ancient homeland. Around the first third of ninth century AD a part of this Cis-Uralic population crossed the Volga River and settled near to the Khazarian Khaganate in the Dnieper-Dniester region. Early Hungarians lived in Eastern Europe (forming the so-called Subbotsy archaeological horizon) until the conquest of the Carpathian Basin that took place in 895 AD.

https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41598-020-75910-z/MediaObjects/41598_2020_75910_Fig1_HTML.png?as=webp

Genetic history of prehistoric to medieval populations of the Ural region have been scarcely investigated to date. On the other side, the populations of the medieval Carpathian Basin have been intensively studied from the perspective of uniparental markers. Recently, Neparáczki et al. have published 102 whole mitogenomes from early Conquest period cemeteries in Hungary. Authors have suggested that the mixed population of steppe nomads (Central Asian Scythians) and descendants of the East European Srubnaya culture’s population—among other undescribed populations—could have been the basis of genetic makeup of Hungarian conquerors. Their results furthermore assume Asian Hunnic-Hungarian conqueror genetic connections. It is important to note, that the investigated medieval sample set does not represent the conqueror population as a whole, hence 76% of the samples originated from a special site complex Karos-Eperjesszög from northeast Hungary, which is one of the most important sites of the Hungarian Conquest period with many findings of eastern characteristics as well. The conclusions are large-scale, but the most highlighted connection with the population of the Srubnaya culture is vague, because it existed more than 2000 years before the appearance of the first traces of ancient Hungarians’ archaeological heritage. Additionally, further mentioned relations such as the Xiongnu (Hunnic) genetic dataset is bare from Eurasia, and Huns’ genetic heritage is yet uncharacterised.

Two recent articles have investigated the Y-haplogroup variability of Hungarian conquerors describing the conqueror’s elite population as heterogenous, with significant proportion of European, Finno-Permic, Caucasian and Siberian (or East Eurasian) paternal lineages. Fóthi et al. have claimed that the Hungarian conquerors originated from three distant sources: Inner Asia (Lake Baikal—Altai Mountains), Western Siberia—Southern Urals (Finno-Ugric peoples) and the Black Sea—Northern Caucasus (Northern Caucasian Turks, Alans, and Eastern Europeans). Both studies pointed out the presence of the Y-haplogroup N-Z1936 (also known as N3a4-Z1936 under N-Tat/M46), which is frequent among Finno-Ugric speaking peoples. This lineage also occurs among modern Hungarians in a frequency up to 4%. Post et al. have reconstructed the detailed phylogeny of N-Z1936 Y-haplogroup showing that specific sublineages are shared by certain ethnic groups, e.g. N-Y24365/B545 by Tatars, Bashkirs and Hungarians, which connect modern-day Hungarians to the people living in the Volga-Ural region.

The sampled Uyelgi cemetery from Trans-Ural region presented the greatest similarity to the archaeological traits of the tenth-century Carpathian Basin. This cemetery of the late Kushnarenkovo culture was used from the end of eighth century to the eleventh century. As the archaeological and historical theories are slightly diverse, we aimed to cover a wide range of early medieval archaeological cultures located in the middle course of the Kama River in the west side of the Ural Mountains (Cis-Ural region). Scholars connect the termination of the Nevolino Culture in eighth–ninth centuries AD to the westward migration of ancestors of Hungarians.

The genetic distances of Hungarian conquerors and the investigated two populations from the Ural region does not correlate with their geographic distances. The genetic distance between Uyelgi and Hungarian conquerors is lower than between Uyelgi and geographical closer Cis-Ural population. The genetic connection of Cis-Ural population and Hungarian conquerors is obvious based on pairwise FST calculation and is visible on the PCA and MDS plots as well, where they are the closest, although direct phylogenetic connections are scarce. This indicates geographical proximity of their former settlement area, rather than a direct connection. Neparáczki et al. have described the Hungarian conqueror mitogenome diversity in essence as a mixture of Srubnaya culture associated and Asian nomadic populations. Their analyses and interpretation were restricted by the lack of ancient samples from the Ural region, whereas new data now refine such previous conclusions.

The genetic connection of Uyelgi cemetery in the Trans-Ural and tenth century Hungarian conquerors in the Carpathian Basin is supposed by close maternal relationships of the following individuals: Uyelgi3 and three Hungarian conquerors from Karos II cemetery have identical U4d2 mitogenome haplotype. The D4j phylogenetic tree shows one interesting phenomenon: Uyelgi21 clusters with one modern-day Hungarian. The findings of this Kurgan 11 (belonging to the Srostki culture) show similarities to the typical findings of the Hungarian conquerors from the Carpathian Basin as well.

Majority of Uyelgi males belong to Y chromosome haplogroup N, and according to combined STR, SNP and network analyses they belong to the same subclade within N-M46 (also known as N-Tat and N1a1-M46 in ISOGG 14.255). N-M46 is geographically widely distributed from East of Siberia to Scandinavia. One of its subclades is N-Z1936 (also known as N3a4 and N1a1a1a1a2 in ISOGG 14.255), which is prominent among Uralic speaking populations, probably originated from the Ural region as well and mainly distributed from the west of Ural Mountains to Scandinavia (Finland). Seven samples of Uyelgi site most probably belong to N-Y24365 (also known as N-B545 and N1a1a1a1a2a1c2 in ISOGG 14.255) under N-Z1936, a specific subclade that can be found almost exclusively in todays’ Tatarstan, Bashkortostan and Hungary."

https://www.nature.com/articles/s41598-020-75910-z

[vbnetkhio]

A very exhaustive study was done by Hungarian archeogeneticists regarding the maternal ancestry of the commoner population in Hungary, which haven't been done on this scale thus far on this very important group, only on the elite population. I will quote some of the most important finds, but the whole study should be read since it provides further explanations.


could you make a list of all studies on Hungarian conquerors?
I think there were 3 already. one with Huns, Avars and Hungarians, one about the Arpad dinasty, and this.

[Dunai]

could you make a list of all studies on Hungarian conquerors?
I think there were 3 already. one with Huns, Avars and Hungarians, one about the Arpad dinasty, and this.

You will find them among my created threads, I try to bring to attention every time I read about a new study, even if there doesn't seem to be too much interest here.

[vbnetkhio]

You will find them among my created threads, I try to bring to attention every time I read about a new study, even if there doesn't seem to be too much interest here.

it seems autosomal data files are available for these 4:

Maternal lineages from 10-11th century commoner cemeteries of the Carpathian Basin(this one)
Determination of the phylogenetic origins of the Arpad Dynasty based on Y chromosome sequencing of Bela the Third
Y-chromosome haplogroups from Hun, Avar and conquering Hungarian nomadic people of the Carpathian Basin
Mitogenomic data indicate admixture components of Central-Inner Asian and Srubnaya origin in the conquering Hungarians

for some it could just be yDNA/mtDNA data, I'll have to check. but some definitely have autosomal files too.

do you know of any study besides these 4?

edit:
found one more:
Early medieval genetic data from Ural region evaluated in the light of archaeological evidence of ancient Hungarians
https://www.nature.com/articles/s41598-020-75910-z#Sec18
https://www.ebi.ac.uk/ena/browser/view/PRJEB39054

[vbnetkhio]

I checked this one first: "Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third"

https://www.ebi.ac.uk/ena/browser/view/PRJNA490697
first 9 entries here are the samples of the Hungarian king Bela III and 8 other Hungarian royals.
I can't convert them, I get this error:

[E::main_mem] fail to open file `SRR11727888_2.fa.fastq'.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

there is also 200 modern samples from these populations:
Abazin
Abkhaz
Afghan
Andi
Balkar
Bashkir
Bashkirs
Chechen
Cherkes
Chuvas
Iraqi
Kabardin
Karachay
Karanogay
Kumyk
Ossetin
Pakistani
Tatar
Unknown(Serb/Hungarian from Serbia?)

[Kaspias]

it seems autosomal data files are available for these 4:

Maternal lineages from 10-11th century commoner cemeteries of the Carpathian Basin(this one)
Determination of the phylogenetic origins of the Arpad Dynasty based on Y chromosome sequencing of Bela the Third
Y-chromosome haplogroups from Hun, Avar and conquering Hungarian nomadic people of the Carpathian Basin
Mitogenomic data indicate admixture components of Central-Inner Asian and Srubnaya origin in the conquering Hungarians

for some it could just be yDNA/mtDNA data, I'll have to check. but some definitely have autosomal files too.

do you know of any study besides these 4?

Files of Maternal lineages from 10-11th century commoner cemeteries of the Carpathian Basin are lacking for autosomal and y snps. Only mt snps are present in the complete genome file. This is the filtered data for MHper1, for example:


rsid chromosome position allele1 allele2
M 146 T R S
4 44399 T/T 0 0
20 79303 C/C 0 0
2 87004 A/A 0 0
12 92646 T/T 0 0
9 97178 G/G 0 0
17 125587 C/C 0 0
16 137307 T/T 0 0
18 142395 G/G 0 0
5 326910 A/A 0 0
X 341357 C/C 0 0
8 406278 T/T 0 0
3 430024 A/A 0 0
6 444400 A/A 0 0
11 468798 T/T 0 0
7 470519 A/A 0 0
10 515385 T/T 0 0
19 546469 A/A 0 0
1 564578 T/T 0 0
Y 3612393 A 0 0
21 10421794 C/C 0 0
22 16851455 T/T 0 0
14 19009106 T/T 0 0
15 20092079 T/T 0 0
13 20152344 A/A 0 0

And when run for y snps:


Z14734-, CTS2560-, Z1634-, M8627-, CTS10152-, M1989-, Z6186-

For mt, gives accurate assignment:


73G, 152C, 199C, 204C, 228A, 263G, 669C, 750G, 1438G, 1719A, 2706G, 3336C, 5315G, 8901G, 9300A, 10238C, 10398G, 11719A, 12501A, 13780G, 14766T, 15043A, 15326G, 16519C

[vbnetkhio]

Files of Maternal lineages from 10-11th century commoner cemeteries of the Carpathian Basin are lacking for autosomal and y snps. Only mt snps are present in the complete genome file. This is the filtered data for MHper1, for example:


rsid chromosome position allele1 allele2
M 146 T R S
4 44399 T/T 0 0
20 79303 C/C 0 0
2 87004 A/A 0 0
12 92646 T/T 0 0
9 97178 G/G 0 0
17 125587 C/C 0 0
16 137307 T/T 0 0
18 142395 G/G 0 0
5 326910 A/A 0 0
X 341357 C/C 0 0
8 406278 T/T 0 0
3 430024 A/A 0 0
6 444400 A/A 0 0
11 468798 T/T 0 0
7 470519 A/A 0 0
10 515385 T/T 0 0
19 546469 A/A 0 0
1 564578 T/T 0 0
Y 3612393 A 0 0
21 10421794 C/C 0 0
22 16851455 T/T 0 0
14 19009106 T/T 0 0
15 20092079 T/T 0 0
13 20152344 A/A 0 0

And when run for y snps:


Z14734-, CTS2560-, Z1634-, M8627-, CTS10152-, M1989-, Z6186-

For mt, gives accurate assignment:


73G, 152C, 199C, 204C, 228A, 263G, 669C, 750G, 1438G, 1719A, 2706G, 3336C, 5315G, 8901G, 9300A, 10238C, 10398G, 11719A, 12501A, 13780G, 14766T, 15043A, 15326G, 16519C

are you sure? is this from the BAM file? i'm running the BAM of the sample with the most reads (SHper267) and it looks like the converter is detecting something on the autosomal chromosomes. but maybe it's a very small number of SNPs, we'll see when it finishes.

you can see the number of reads here, in the S2 table:
https://www.biorxiv.org/content/10.1101/2021.01.26.428268v1.supplementary-material

[Kaspias]

are you sure? is this from the BAM file? i'm running the BAM of the sample with the most reads (SHper267) and it looks like the converter is detecting something on the autosomal chromosomes.

Well, I did not check how many reads MHper1 had and just picked it randomly to test. It might be about it, too. Anyway, this is an output from .bam extracted by teepan's bam kit. During the process, it also showed me it detects something but resulted in no significant outcome. Wait for yours conclusion, so we can see the situation.

[vbnetkhio]

Well, I did not check how many reads MHper1 had and just picked it randomly to test. It might be about it, too. Anyway, this is an output from .bam extracted by teepan's bam kit. During the process, it also showed me it detects something but resulted in no significant outcome. Wait for yours conclusion, so we can see the situation.

maybe we could get more SNPs by converting the fastq to BAM? I can send you the fastq converter if you don't have it.

[Kaspias]

maybe we could get more SNPs by converting the fastq to BAM? I can send you the fastq converter if you don't have it.

I can try if you send it. I did not have.

[vbnetkhio]

I can try if you send it. I did not have.

here is what I managed to get.

https://i.imgur.com/SOBb18I.png

only 1% K13 snps are present, it still detects a vague European/Siberian mix.

[Kaspias]

here is what I managed to get.

https://i.imgur.com/SOBb18I.png

only 1% K13 snps are present, it still detects a vague European/Siberian mix.

How did you manage to reach snp number that admixture studio needs?

I tried to convert fasta to bam and it ended up with literally 0 snps in autosomal data. I tried with another sample, using directly the bam shared, and see such ratio:

-----------------------------------------------------------
12 ancestral populations
166770 total SNPs
1 flipped SNPs
0 heterozygous SNPs
0 no-calls
166764 absent SNPs
0.000036 genotype rate
Fewer than 100 usable SNPs!

[vbnetkhio]

How did you manage to reach snp number that admixture studio needs?

I tried to convert fasta to bam and it ended up with literally 0 snps in autosomal data. I tried with another sample, using directly the bam shared, and see such ratio:

-----------------------------------------------------------
12 ancestral populations
166770 total SNPs
1 flipped SNPs
0 heterozygous SNPs
0 no-calls
166764 absent SNPs
0.000036 genotype rate
Fewer than 100 usable SNPs!

this is the sample with the most reads, SHper267. maybe that's why.
although more reads doesn't necesarily mean more k13 SNPs. maybe some of the samples with less reads have more k13 SNPs.

[Jana]

here is what I managed to get.

https://i.imgur.com/SOBb18I.png

only 1% K13 snps are present, it still detects a vague European/Siberian mix.

Do you know to whom this sample belongs, some conqueror?

[vbnetkhio]

Do you know to whom this sample belongs, some conqueror?

SHper267 (Sárrétudvari-Hízóföld/267) from this study. So it's actually a commoner?

mtdna : D4b1
closest mtdna matches in: Kazakhstan, Mongolia
burrial info: sub-adult infantia silver penannular hair ring, string of beads (withs shells), braid ornaments, silver braclet 10.

Sárrétudvari-Hízóföld (Hajdú-Bihar County)
The site was excavated between 1980 and 1985 under the leadership of Ibolya M. Nepper [18].
The site with 262 graves is considered the largest 10th
-century cemetery in Hungary. The
cemetery contains very high proportion of burials with weapon- (archery equipment, sabers,
ax) and horse riding-related (eg: pear-shaped stirrups) grave-goods, and the archeological
findings consist of jewelry - hoops around the head (penannular hair rings), neck jewelry
(neckrings, beads), arm jewelry (e.g., bracelets, beads), - dress fittings, and implements (e.g.,
knives, fire-lightning equipment). Based on the composition of the findings and the lack of
coins and grave-goods dated to the reign of the kings of the Árpád dynasty, the cemetery can
be dated to the 10th century. Formerly it was classified as a commoner cemetery, and in the new
classification it belongs to the 10th
-century village cemeteries.
The skeletal remains are of good / medium preservation. During the extensive anthropological
analysis (e.g., [21]), 265 individuals were determined, of whom 98 belonged to sub-adult- and
162 skeletons to adult categories. Based on the skulls suitable for taxonomic studies, the series
shows European characteristics with the presence of cromagnoid and nordoid elements.

[vbnetkhio]

How did you manage to reach snp number that admixture studio needs?

I tried to convert fasta to bam and it ended up with literally 0 snps in autosomal data. I tried with another sample, using directly the bam shared, and see such ratio:

-----------------------------------------------------------
12 ancestral populations
166770 total SNPs
1 flipped SNPs
0 heterozygous SNPs
0 no-calls
166764 absent SNPs
0.000036 genotype rate
Fewer than 100 usable SNPs!

btw, here is the code I used:


plink2 --vcf bam_chr1.vcf.gz --make-bed --out chr1 --set-missing-var-ids @:#
plink2 --vcf bam_chr10.vcf.gz --make-bed --out chr10 --set-missing-var-ids @:#
plink2 --vcf bam_chr11.vcf.gz --make-bed --out chr11 --set-missing-var-ids @:#
plink2 --vcf bam_chr12.vcf.gz --make-bed --out chr12 --set-missing-var-ids @:#
plink2 --vcf bam_chr13.vcf.gz --make-bed --out chr13 --set-missing-var-ids @:#
plink2 --vcf bam_chr14.vcf.gz --make-bed --out chr14 --set-missing-var-ids @:#
plink2 --vcf bam_chr15.vcf.gz --make-bed --out chr15 --set-missing-var-ids @:#
plink2 --vcf bam_chr16.vcf.gz --make-bed --out chr16 --set-missing-var-ids @:#
plink2 --vcf bam_chr17.vcf.gz --make-bed --out chr17 --set-missing-var-ids @:#
plink2 --vcf bam_chr18.vcf.gz --make-bed --out chr18 --set-missing-var-ids @:#
plink2 --vcf bam_chr19.vcf.gz --make-bed --out chr19 --set-missing-var-ids @:#
plink2 --vcf bam_chr2.vcf.gz --make-bed --out chr2 --set-missing-var-ids @:#
plink2 --vcf bam_chr20.vcf.gz --make-bed --out chr20 --set-missing-var-ids @:#
plink2 --vcf bam_chr21.vcf.gz --make-bed --out chr21 --set-missing-var-ids @:#
plink2 --vcf bam_chr22.vcf.gz --make-bed --out chr22 --set-missing-var-ids @:#

plink2 --bfile chr1 --extract snps.txt --make-bed --out chr1_filtered
plink2 --bfile chr10 --extract snps.txt --make-bed --out chr10_filtered
plink2 --bfile chr11 --extract snps.txt --make-bed --out chr11_filtered
plink2 --bfile chr12 --extract snps.txt --make-bed --out chr12_filtered
plink2 --bfile chr13 --extract snps.txt --make-bed --out chr13_filtered
plink2 --bfile chr14 --extract snps.txt --make-bed --out chr14_filtered
plink2 --bfile chr15 --extract snps.txt --make-bed --out chr15_filtered
plink2 --bfile chr16 --extract snps.txt --make-bed --out chr16_filtered
plink2 --bfile chr17 --extract snps.txt --make-bed --out chr17_filtered
plink2 --bfile chr18 --extract snps.txt --make-bed --out chr18_filtered
plink2 --bfile chr19 --extract snps.txt --make-bed --out chr19_filtered
plink2 --bfile chr2 --extract snps.txt --make-bed --out chr2_filtered
plink2 --bfile chr20 --extract snps.txt --make-bed --out chr20_filtered
plink2 --bfile chr21 --extract snps.txt --make-bed --out chr21_filtered
plink2 --bfile chr22 --extract snps.txt --make-bed --out chr22_filtered

plink --bfile chr1_filtered --merge-list list.txt --make-bed --out SHper267
plink2 --bfile SHper267 --export vcf


files used in the code: (snps.txt is a list of ftdna v1 and 23andme v3 snps, because the files are too large otherwise)
https://filebin.net/hpcyzve5pkf77rnr

and then I converted the resulting vcf to 23andme with dnakitstudio.
I used the ft_23 template, it's also there in the filebin.

did you use "--set-missing-var-ids @:#"? otherwise there are no rsids in the output.