Papers on current genetics

[Ronalawe]

Impact of patrilocality on contrasting patterns of paternal and maternal heritage in Central-West Africa

8 July 2024

https://pubmed.ncbi.nlm.nih.gov/32890883/

Abstract


Despite their ancient past and high diversity, African populations are the least represented in human population genetic studies. In this study, uniparental markers (mtDNA and Y chromosome) were used to investigate the impact of sociocultural factors on the genetic diversity and inter-ethnolinguistic gene flow in the three major Nigerian groups: Hausa (n = 89), Yoruba (n = 135) and Igbo (n = 134). The results show a distinct history from the maternal and paternal perspectives. The three Nigerian groups present a similar substrate for mtDNA, but not for the Y chromosome. The two Niger–Congo groups, Yoruba and Igbo, are paternally genetically correlated with populations from the same ethnolinguistic affiliation. Meanwhile, the Hausa is paternally closer to other Afro-Asiatic populations and presented a high diversity of lineages from across Africa. When expanding the analyses to other African populations, it is observed that language did not act as a major barrier to female-mediated gene flow and that the differentiation of paternal lineages is better correlated with linguistic than geographic distances. The results obtained demonstrate the impact of patrilocality, a common and well-established practice in populations from Central-West Africa, in the preservation of the patrilineage gene pool and in the affirmation of identity between groups.

link you shared goes to an old 2020 della Rocha Paper
This is the link to paper you posted

https://pubmed.ncbi.nlm.nih.gov/38977763/

Yeah you're right, my bad, thanks!

[RCO]

Marziyeh Afkanpour, Mehri Momeni, Arash Alipour Tabrizi, Hamed Tabesh,
A Haplogroup-based Methodology for Assigning Individuals to Geographical Regions Using Y-STR Data,
Forensic Science International,
2024,
112260,
ISSN 0379-0738,
https://doi.org/10.1016/j.forsciint.2024.112260.
(https://www.sciencedirect.com/science/ar...3824003426)
Abstract: Y chromosome markers are essential tools in forensic genetics, offering valuable insights for genetic identification. This study seeks to develop a forensic prediction model using machine learning techniques to improve the efficiency of genetic identification processes. Specifically, the model aims to predict an individual's nearest geographical area of residence based on Y chromosome marker analysis. The methodology involved four key steps: haplogroup determination, primary branch identification, geographical region assignment, model stratification, and fine-tuning. Once developed, the model can be integrated into decision support systems, providing forensic geneticists with a reliable knowledge source to enhance decision-making during investigations.
Keywords: Y-STR; Haplogroup; Y haplotype; Y Chromosome; prediction model; machine learning; Phylogenetic Tree; Forensic Genetics; Iranian Population
=======
Very nice, but we still need the Iranian detailed Y-DNA SNPs !!!!

[teepean]

Y chromosome sequencing data suggest dual paths of haplogroup N1a1 into Finland

Abstract

The paternally inherited Y chromosome is highly informative of genetic ancestry, therefore making it useful in studies of population history. In Finland, two Y-chromosomal haplogroups reveal the major substructure of the population: N1a1 enriched in the northeast and I1a in the southwest, suggested to reflect eastern and western ancestry contributions to the population. Yet, beyond these major Y-chromosomal lineages, the distribution of finer-scale Y-chromosomal variation has not been assessed in Finland. Here, we provide the most comprehensive Y-chromosomal study among the Finns to date, exploiting sequences for 1802 geographically mapped Finnish Y chromosomes from the FINRISK project. We assessed the distribution of common Y-chromosomal haplogroups (frequency ≥1%) throughout 19 Finnish regions and compared the autosomal genetic backgrounds of the Y-chromosomal haplogroups. With such high-resolution data, we were able to find previously unreported sublineages and resolve phylogenetic relationships within haplogroups N1a1 (64%), I1a (25%), R1a (4.3%), and R1b (4.8%). We further find novel geographical enrichment patterns among these Y-chromosomal haplogroups, most notably observed for haplogroup N1a1 dividing into two lineages with differing distributions. While sublineage N-Z1934 (42%) followed a northeastern enrichment pattern observed for all N1a1 carriers in general, sublineage N-VL29 (22%) displayed an enrichment in the southwest. Further, the carriers of N-VL29 showed a higher proportion of southwestern autosomal ancestry compared to carriers of N-Z1934. Collectively, these results point to distinct demographics within haplogroup N1a1, possibly induced by two distinct arrival routes into Finland. Overall, our study suggests a more complex genetic population history for Finns than previously proposed.

https://www.nature.com/articles/s41431-024-01707-7

[Riverman]

Characterization of Y chromosome diversity in newfoundland and labrador: evidence for a structured founding population

Abstract

The population of Newfoundland and Labrador (NL) is largely derived from settlers who migrated primarily from England and Ireland in the 1700s–1800s. Previously described as an isolated founder population, based on historical and demographic studies, data on the genetic ancestry of this population remains fragmentary. Here we describe the largest investigation of patrilineal ancestry in NL. To determine the paternal genetic structure of the population, 1,110 Y chromosomes from an NL-based cohort were analyzed using 5,761 Y-specific SNPs. We identified 160 distinct terminal haplogroups, the majority of which (71.4%) belong to the R1b haplogroup. When compared with global reference populations, the NL population haplogroup composition and frequencies primarily resemble those observed in English and Irish ancestral source populations. There is also evidence of genetic contributions from Basque, French, Portuguese, and Spanish fishermen and early settlers who frequented NL. Interestingly, the observed population structure shows geographical and religious clustering that can be associated with the settlement of the ancestral source populations from predominantly Protestant, England, and Catholic, Ireland respectively. For example, the R1b-M222 haplogroup, seen in people of Irish descent, is found clustered in the Irish-settled Southeast region of NL. The clustering and expansion of Y haplogroups in conjunction with the geographical and religious clusters illustrate that limited subsequent in-migration, geographic isolation, and societal factors have contributed to the genetic substructure of the NL population and its designation as a founder population.

https://www.nature.com/articles/s41431-0...Q&sfnsn=mo

[Rufus191]

Using Y-DNA to Discover the Scottish Connection Between Two Lineages

Through Y-DNA testing, traditional genealogy, and multiple trips to the Isle of Bute, a connection between a subgroup of Duncan descendants and McConnachie descendants was found on the Isle of Bute in Scotland.

We present to you an investigative case study. A step-by-step genetic genealogy investigation into a developing medieval kin group, its geographical origin, and subsequent migrations.

By: Susan Hedeen and Tim Duncan, March 14, 2024


https://blog.familytreedna.com/y-dna-dun...-scottish/

[Rufus191]

Y-DNA Sheds New Light on the Medieval Genealogies of the Uí Briúin Dynasty of Northwest Ireland

By: Maurice Gleeson and Kyle DePew,  May 24, 2024


"Medieval Irish genealogies are the oldest in Europe, stretching back over 2,000 years. These were transmitted orally (prior to the introduction of the written record) so are likely to be prone to inaccuracies prior to about 600 A.D.
The first compilation of written records is believed to date from the mid-700s. Various versions of the medieval genealogies exist, and inconsistencies in these versions indicate further inaccuracies. Some of these appear to have been innocent transcription errors, whilst others may have been due to deliberate falsifications for social prestige or political gain.
These known examples of inaccuracies have cast doubt on the veracity of the medieval genealogies as a whole, and this has been the subject of ongoing debate since the resurgence of interest in Irish heritage with the Gaelic Revival of the 1800s.

A new scientific article assesses what Y-DNA tells us about the medieval genealogies of the Uí Briúin (pronounced ee brew-in) dynasty of northwest Ireland. The authors are Maurice Gleeson, Kyle DePew and Bart Jaski. Maurice and Kyle authored this blog post and are project administrators of various FamilyTreeDNA Group Projects. "


Part 1

https://blog.familytreedna.com/y-dna-med...n-dynasty/

Part 2

https://blog.familytreedna.com/y-dna-med...ty-part-2/

[RCO]

Genetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan.
Zhabagin, M.; Tashkarayeva, A.; Bukayev, A.; Zhunussova, A.; Ponomarev, G.; Tayshanova, S.; Maxutova, A.; Adamov, D.; Balanovska, E.; Sabitov, Z. Genes 2024, 15, 1501. https://doi.org/10.3390/genes15121501

Abstract
This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating. Subhaplogroups Q1a and Q1b identified in Turkmenistan trace back to ancient Y-chromosome lineages from the Bronze Age. Comparative analyses, including genetic distance (RST), median-joining network, and multidimensional scaling (MDS), highlight the genetic proximity of the Turkmen in Turkmenistan to those in Afghanistan and Iran, while Iraqi Turkmen display unique characteristics, aligning with Near Eastern populations. This study underscores the Central Asian genetic affinity across most Turkmen populations. It demonstrates the value of deep-sequencing Y-chromosome data in tracing the patrilineal history of Central Asia for future studies. These findings contribute to a more comprehensive understanding of Turkmen genetic ancestry and add new data to the ongoing study of Central Asian population genetics.
Keywords: population genetics; Y-chromosome; haplotype; haplogorup; network analysis; Turkmen population; Jochi Ulus; Central Asia

https://www.mdpi.com/2073-4425/15/12/1501

https://www.mdpi.com/article/10.3390/genes15121501/s1
---------------------

One match with my J1 clade, present from modern Turkmenistan to Portugal and Brazil.
Sample 8 Turkmenistan Dashoguz Turkmen Yomut 16 13 20 30 15 10 27 13 11 10 14 18 21 22 11 11 9 13 17,2 12 19 14 10 J1a >> L620>> FGC6064> M365 100% 39.21 [0.61] J1a

[RCO]

Demographic history and genetic variation of the Armenian population
Anahit Hovhannisyan, Pierpaolo Maisano Delser, Anna Hakobyan, Eppie R. Jones, Joshua G. Schraiber, Mariya Antonosyan, Ashot Margaryan, Zhe Xue, Sungwon Jeon, Jong Bhak, Peter Hrechdakian, Hovhannes Sahakyan, Lehti Saag, Zaruhi Khachatryan, Levon Yepiskoposyan, and Andrea Manica.
The American Journal of Human Genetics, Volume 112

https://doi.org/10.1016/j.ajhg.2024.10.022

Summary
We introduce a sizable (n = 34) whole-genome dataset on Armenians, a population inhabiting the region in West Asia known as the Armenian highlands. Equipped with this genetic data, we conducted a whole-genome study of Armenians and deciphered their fine-scale population structure and complex demographic history. We demonstrated that the Armenian populations from western, central, and eastern parts of the highlands are relatively homogeneous. The Sasun, a population in the south that had been argued to have received a major genetic contribution from Assyrians, was instead shown to have derived its slightly divergent genetic profile from a bottleneck that occurred in the recent past. We also investigated the debated question on the genetic origin of Armenians and failed to find any significant support for historical suggestions by Herodotus of their Balkan-related ancestry. We checked the degree of continuity of modern Armenians with ancient inhabitants of the eastern Armenian highlands and detected a genetic input into the region from a source linked to Neolithic Levantine Farmers at some point after the Early Bronze Age. Additionally, we cataloged an abundance of new mutations unique to the population, including a missense mutation predicted to cause familial Mediterranean fever, an autoinflammatory disorder highly prevalent in Armenians. Thus, we highlight the importance of further genetic and medical studies of this population.
Keywords
genetic continuityArmenian highlandsArmeniansBalkan theoryBronze Agewhole-genome study

https://www.cell.com/ajhg/fulltext/S0002...24)00391-4?

-------------

Y-chromosome Haplogroup Y-Marker Study

G2b2b1 FGC5085,Y6224 This study
R1b1a1b1b1 L584 This study
J2b M12 This study
J2a1a1b2a1b PF5427 This study
T1a1a1b2b2b1a1a1 CTS9882 This study
J1a2a1a2d2b2b2c4b2b1a~ BY102 This study
T1a1a1b2b2b1a1a1 CTS9882 This study
J2a1a1b2a1b1b~ Z423 This study
J2a1a1a2a2a1a1~ Y104740 This study
I2a1b1a2b1 CTS2392 This study
I2a1b1a2b1 CTS2392 This study
R1b1a1b1b1 L584 This study
R2a2b1b2b3b2a1a Y17752 This study
J2a1a1a2b2a1a1b~ Y7147 This study
J1a2a2 FGC6064 This study
G2a2b1a1a1a2b BY91399 This study
R2a2b1 FGC12643 This study
G2a2a1a2a3~ FT155546 This study
J2a1a1a2b2a3b1b1~ CTS5965 This study
T1a2a PH141/Y13244 This study
J1a2a1a2d2b~ Z1853 This study
J1a2a1a2d2b2b1~ ZS2518 This study
J2a1a1a2a2b2a~ Y8531 This study
R1b1a1b1b Z2103 This study
R1b1a1b1b1 L584 Mallik, S. et al, 2016
Q2a1a4b~ BZ5070 This study
J1a2a1a2d2b2b2c4d2a2a4~ FGC4415 This study
R1b1a1b1b1 L584 This study
R1b1a1b1b Z2103 This study
R1b1a1b1b Z2103 This study
J2a1a1b2a1a2 FGC9878 Mallik, S. et al, 2016

[Radko]

The Finnic Peoples of Russia: Genetic Structure Inferred from Genome-Wide and Y-Chromosome Data

Abstract
Background: Eastern Finnic populations, including Karelians, Veps, Votes, Ingrians, and Ingrian Finns, are a significant component of the history of Finnic populations, which have developed over ~3 kya. Yet, these groups remain understudied from a genetic point of view. Methods: In this work, we explore the gene pools of Karelians (Northern, Tver, Ludic, and Livvi), Veps, Ingrians, Votes, and Ingrian Finns using Y-chromosome markers (N = 357) and genome-wide autosomes (N = 67) and in comparison with selected Russians populations of the area (N = 763). The data are analyzed using statistical, bioinformatic, and cartographic methods. Results: The autosomal gene pool of Eastern Finnic populations can be divided into two large categories based on the results of the PCA and ADMIXTURE modeling: (a) “Karelia”: Veps, Northern, Ludic, Livvi, and Tver Karelians; (b) “Ingria”: Ingrians, Votes, Ingrian Finns. The Y-chromosomal gene pool of Baltic Finns is more diverse and is composed of four genetic components. The “Northern” component prevails in Northern Karelians and Ingrian Finns, the “Karelian” in Livvi, Ludic, and Tver Karelians, the “Ingrian-Veps” in Ingrians and Veps (a heterogeneous cluster occupying an intermediate position between the “Northern” and the “Karelian” ones), and the “Southern” in Votes. Moreover, our phylogeographic analysis has found that the Y-haplogroup N3a4-Z1927 carriers are frequent among most Eastern Finnic populations, as well as among some Northern Russian and Central Russian populations. Conclusions: The autosomal clustering reflects the major areal groupings of the populations in question, while the Y-chromosomal gene pool correlates with the known history of these groups. The overlap of the four Y-chromosomal patterns may reflect the eastern part of the homeland of the Proto-Finnic gene pool. The carriers of the Y-haplogroup N3a4-Z1927, frequent in the sample, had a common ancestor at ~2.4 kya, but the active spread of N3a4-Z1927 happened only at ~1.7–2 kya, during the “golden” age of the Proto-Finnic culture (the archaeological period of the “typical” Tarand graves). A heterogeneous Y-chromosomal cluster containing Ingrians, Veps, and Northern Russian populations, should be further studied.

https://www.mdpi.com/2073-4425/15/12/1610

[teepean]

The Finnic Peoples of Russia: Genetic Structure Inferred from Genome-Wide and Y-Chromosome Data

Abstract
Background: Eastern Finnic populations, including Karelians, Veps, Votes, Ingrians, and Ingrian Finns, are a significant component of the history of Finnic populations, which have developed over ~3 kya. Yet, these groups remain understudied from a genetic point of view. Methods: In this work, we explore the gene pools of Karelians (Northern, Tver, Ludic, and Livvi), Veps, Ingrians, Votes, and Ingrian Finns using Y-chromosome markers (N = 357) and genome-wide autosomes (N = 67) and in comparison with selected Russians populations of the area (N = 763). The data are analyzed using statistical, bioinformatic, and cartographic methods. Results: The autosomal gene pool of Eastern Finnic populations can be divided into two large categories based on the results of the PCA and ADMIXTURE modeling: (a) “Karelia”: Veps, Northern, Ludic, Livvi, and Tver Karelians; (b) “Ingria”: Ingrians, Votes, Ingrian Finns. The Y-chromosomal gene pool of Baltic Finns is more diverse and is composed of four genetic components. The “Northern” component prevails in Northern Karelians and Ingrian Finns, the “Karelian” in Livvi, Ludic, and Tver Karelians, the “Ingrian-Veps” in Ingrians and Veps (a heterogeneous cluster occupying an intermediate position between the “Northern” and the “Karelian” ones), and the “Southern” in Votes. Moreover, our phylogeographic analysis has found that the Y-haplogroup N3a4-Z1927 carriers are frequent among most Eastern Finnic populations, as well as among some Northern Russian and Central Russian populations. Conclusions: The autosomal clustering reflects the major areal groupings of the populations in question, while the Y-chromosomal gene pool correlates with the known history of these groups. The overlap of the four Y-chromosomal patterns may reflect the eastern part of the homeland of the Proto-Finnic gene pool. The carriers of the Y-haplogroup N3a4-Z1927, frequent in the sample, had a common ancestor at ~2.4 kya, but the active spread of N3a4-Z1927 happened only at ~1.7–2 kya, during the “golden” age of the Proto-Finnic culture (the archaeological period of the “typical” Tarand graves). A heterogeneous Y-chromosomal cluster containing Ingrians, Veps, and Northern Russian populations, should be further studied.

https://www.mdpi.com/2073-4425/15/12/1610

Thank you! I have sent the dataset to David.

[Riverman]

Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum

Abstract
While a broad consensus about the first successful migration modern humans out of Africa seems established, the peopling of Arabia remains somewhat enigmatic. Identifying the ancestral populations that contributed to the gene pool of the current populations inhabiting Arabia and the impact of their contributions remains a challenging task. We investigate the genetic makeup of the current Yemeni population using 46 whole genomes and 169 genotype arrays derived from Yemeni individuals from all geographic regions across Yemen and 351 genotype arrays derived from neighboring populations providing regional context. Principal Component Analysis shows stratification between Yemen districts but also with respect to nearby populations: Yemeni, other Arabian and Bedouin samples form a continuum towards the populations of the Levant, whereas East Africa and India appear strongly differentiated. This finding is further supported by higher Principal Components, admixture and haplogroup analyses, and F-statistics. Moreover, two-reference linkage disequilibrium decay estimates are most significant for Yemeni admixture from an ancient northern influx (up to 5220BP from Palestine) and East Africa (750BP). We show that the initial gene flow into the Yemeni populations of today came from the rest of Arabia and the Levant, and a less substantial and more recent genetic impact into coastal Yemen from East Africa, particularly.

Some fully sequenced yDNA samples:




https://www.nature.com/articles/s41598-024-81615-4

[AimSmall]

Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum

Abstract
While a broad consensus about the first successful migration modern humans out of Africa seems established, the peopling of Arabia remains somewhat enigmatic. Identifying the ancestral populations that contributed to the gene pool of the current populations inhabiting Arabia and the impact of their contributions remains a challenging task. We investigate the genetic makeup of the current Yemeni population using 46 whole genomes and 169 genotype arrays derived from Yemeni individuals from all geographic regions across Yemen and 351 genotype arrays derived from neighboring populations providing regional context. Principal Component Analysis shows stratification between Yemen districts but also with respect to nearby populations: Yemeni, other Arabian and Bedouin samples form a continuum towards the populations of the Levant, whereas East Africa and India appear strongly differentiated. This finding is further supported by higher Principal Components, admixture and haplogroup analyses, and F-statistics. Moreover, two-reference linkage disequilibrium decay estimates are most significant for Yemeni admixture from an ancient northern influx (up to 5220BP from Palestine) and East Africa (750BP). We show that the initial gene flow into the Yemeni populations of today came from the rest of Arabia and the Levant, and a less substantial and more recent genetic impact into coastal Yemen from East Africa, particularly.

Some fully sequenced yDNA samples:




https://www.nature.com/articles/s41598-024-81615-4

I love it.  These researchers used code and techniques from Nganasankhan and what was then Anthrogenica.  Our little citizen scientist community contributes!

Code snippet from the header... noticed the comment.  Eupedia is just a reposter of the original.

Code:

library(admixtools)
library(tidyverse)
library(pheatmap)
library(vegan)
library(colorspace)
# adapted from https://www.eupedia.com/forum/threads/41493-R-scripts-for-ADMIXTOOLS-2-Nganasankhan-from-Anthrogenica

setwd("/mnt/Drive1/ahenschel/SambaShare/YemenGenomeAnalysis_Unused/WGS")

# Selected world populations, Yemen on governorate level
#p = "San Mbuti_Pygmies Bantu Pima Surui Maya Yakut Daur Tu Dai Han Japanese Uygur Balochi Pathan Makrani Bayda Lahij Adygei Druze\tRussian\tOrcadian French Tuscan  Mozabite Abyan Hadramout Bedouin Palestinian\tHudayda\tTaizz Mahwit Amran Dhamar Ibb Maarib Saada YEMEN SAUDI"

# switching to district level
p = "San Mbuti_Pygmies Bantu Pima Surui Maya Yakut Daur Tu Dai Han Japanese Uygur Balochi Pathan Makrani Adygei Druze\tRussian\tOrcadian French Tuscan  Mozabite Bedouin Palestinian Hudayda Aden Aljanad Azal Hadramout Sheba Tahamh"

UPDATE: Interesting observation, the code in GitHub is three years old, the paper was published 30 Dec 2024.

[Average_Reward]

A study of genetic variants associated with skin traits in the Vietnamese population
https://bmcgenomics.biomedcentral.com/ar...23-09932-y

Code:

SCALED

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Data (incl. VCF)
https://www.ncbi.nlm.nih.gov/geo/query/a...=GSE248483

I cannot find any supplementary material about the exact ethnicity.