Papers on current genetics

[dilettante layman]

Nuclear genetic diversity of head lice sheds light on human dispersal around the world

Abstract
The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.

https://journals.plos.org/plosone/articl...ne.0293409

[VladMC]

Paternal genomic resources from the YanHuang cohort suggested a Weakly-Differentiated Multi-source Admixture model for the formation of Han’s founding ancestral lineages

Abstract
The large-scale human genome revolution and rapidly advanced statistical innovation have updated our understanding of the fine-scale and complex genetic structure, the entire landscape of genetic diversity and the evolutionary trajectories of spatiotemporally different ancients and ethnolinguistically diverse modern populations. Recent ancient DNA research provided a detailed and complex admixture picture of ancient Europeans but limited insights into East Asians as the few available genomes. Y-chromosome variations in the male-specific regions, served as molecular archaeological tool, have unique evolutionary features that can be utilized to reconstruct the origin and subsequent interaction of ancient East Asian paternal lineages. We launched the YanHuang cohort using our designed highest-resolution capture sequencing panel to explore the detailed evolutionary trajectory of the Han Chinese, one of the largest ethnic groups in the world. We reported one of the largest uniparental genomic resources and observed multiple founding paternal lineages dominant in ancient western Eurasian, Siberian and East Asian participating in the formation of the gene pool of the Han Chinese. We identified fine-scale paternal genetic structure correlated with different patterns of ancient population interaction and geographical mountain barriers (Qinling-Huaihe line and Nanling Mountains), suggesting isolation-enhanced and admixture-introduced genetic differentiation enhanced the complexity of the Han Chinese genomic diversity. We observed a strong direct correlation between the frequency of multiple founding lineages of the Han Chinese and the proportion of subsistence-related ancestry sources related to western pastoralists, Holocene Mongolian Plateau people and ancient East Asians, reflecting the ancient migration events contributed to our identified patterns of Chinese paternal genomic diversity. We finally provided one novel and the most plausible admixture-by-admixture model, the Weakly-Differentiated Multi-Source Admixture model, as the major genetic mechanism to illuminate our observed pattern of complex interactions of multiple ancestral sources and landscape of the Han Chinese paternal genetic diversity. Generally, we presented one large-scale uniparental genomic resource from the YanHuang cohort, portrayed one novel admixture formation model and presented the entire genomic landscape with multiple ancestral sources related to ancient herders, hunter-gatherers and farmers who participated in the ancestral formation of the Han Chinese.

https://www.biorxiv.org/content/10.1101/...8.566335v1

[RCO]

The genomic echoes of the last Green Sahara on the Fulani and Sahelian people
Author links open overlay panel Eugenia D’Atanasio et al
Current Biology - REPORT
Published:November 22, 2023DOI: https://doi.org/10.1016/j.cub.2023.10.075

Highlights
• 43 new modern 30× genomes mostly from Africa, focusing on the Sahelian Fulani herders
• Non-sub-Saharan ancestry component in Fulani similar to the Late Neolithic Moroccans
• The last Green Sahara as a major event for the Fulani/Sahelian genetic composition
• Two Fulani subgroups, with one experiencing higher admixture with neighboring peoples
Summary
The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics. 1 ,2 ,3 ,4 ,5 ,6 ,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world, 8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans. 1 ,2 ,5 ,6 ,7 ,9 ,10 ,11 ,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000–5,000 years before present [BP]). 13 ,14 ,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes 2 ,16 ,17 ,18 and with relevant published ancient sequences (> 1,800 samples). 19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events, 1 ,5 ,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.

Keywords whole genomes Green Sahara population genomics evolutionary genetics
Africa Sahel Fulani Fulbe

https://www.cell.com/current-biology/ful...23)01513-0

[AimSmall]

Ugggh... paywall. Any idea if the raw data is available?

[RCO]

Ugggh... paywall.  Any idea if the raw data is available?

Deposited data 43 whole genome sequences This study EGA: EGAD00001011812

[G-Man]

Indigenous Australian genomes show deep structure and rich novel variation

The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama–Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000–35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.

https://www.nature.com/articles/s41586-023-06831-w

[RCO]

A comprehensive review of HVS-I mitochondrial DNA variation of 19 Iranian populations
Motahareh Amjadi, Zahra Hayatmehr, Balázs Egyed, Mahmood Tavallaei, Anna Szécsényi-Nagy
First published: 31 December 2023 https://doi.org/10.1111/ahg.12544

Abstract
Iran is located along the Central Asian corridor, a natural artery that has served as a cross-continental route since the first anatomically modern human populations migrated out of Africa. We compiled and reanalyzed the HVS-I (hypervariable segment-I) of 3840 mitochondrial DNA (mtDNA) sequences from 19 Iranian populations and from 26 groups from adjacent countries to give a comprehensive review of the maternal genetic variation and investigate the impact of historical events and cultural factors on the maternal genetic structure of modern Iranians. We conclude that Iranians have a high level of genetic diversity. Thirty-six haplogroups were observed in Iran's populations, and most of them belong to widespread West-Eurasian haplogroups, such as H, HV, J, N, T, and U. In contrast, the predominant haplogroups observed in most of the adjacent countries studied here are H, M, D, R, U, and C haplogroups. Using principal component analysis, clustering, and genetic distance-based calculations, we estimated moderate genetic relationships between Iranian and other Eurasian groups. Further, analyses of molecular variance and comparing geographic and genetic structures indicate that mtDNA HVS-I sequence diversity does not exhibit any sharp geographic structure in the country. Barring a few from some culturally distinct and naturally separated minorities, most Iranian populations have a homogenous maternal genetic structure.

https://onlinelibrary.wiley.com/doi/10.1111/ahg.12544

I hope the next article will be about Iranian Y-DNA full sequences or detailed SNPs after more than 10 years !

[Jalisciense]

Someone know when we'll have it for G25? It's very important to us who descend from Nahua, Yuto-Aztec and Yuto-Nahua people because those samples seem to be candidates for spreading Uto-Aztecan languages before they arrived here to Mexico and Central America.

Project: PRJEB66319
The study data: https://www.ebi.ac.uk/ena/browser/view/PRJEB66319

Genetic continuity and change among the Indigenous peoples of California

Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.


https://pubmed.ncbi.nlm.nih.gov/37993721...of%20maize

[Rodoorn]

100 ancient genomes show repeated population turnovers in Neolithic Denmark

Morten E. Allentoft, Martin Sikora, Anders Fischer, Karl-Göran Sjögren, Andrés Ingason, Ruairidh Macleod, Anders Rosengren, Bettina Schulz Paulsson, Marie Louise Schjellerup Jørkov, Maria Novosolov, Jesper Stenderup, T. Douglas Price, Morten Fischer Mortensen, Anne Birgitte Nielsen, Mikkel Ulfeldt Hede, Lasse Sørensen, Poul Otto Nielsen, Peter Rasmussen, Theis Zetner Trolle Jensen, Alba Refoyo-Martínez, Evan K. Irving-Pease, William Barrie, Alice Pearson, Bárbara Sousa da Mota, …Eske Willerslev Show authors
Nature volume 625, pages 329–337 (2024)Cite this article


Abstract
Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1,2,3,4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5,6,7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

https://www.nature.com/articles/s41586-023-06862-3

[Kaltmeister]

Effect of iris pigmentation of blue and brown eyed individuals with European ancestry on ability to see in low light conditions after a short-term dark adaption period


Abstract

The effect of iris depigmentation on ability to see in low light conditions has not been thoroughly investigated as an adaptive advantage that could have contributed to the evolution and persistence of blue eyes in Europe. In this study 40 participants took part in a simple eye test in increasing luminance to examine if there was a difference in capacity to see in low light conditions between blue and brown-eyed individuals after a brief adaptation period. Blue eyed individuals were identified to have significantly better ability to see in lower lighting after a short adaption period than brown eyed individuals making it likely depigmented irises provide an adaptive advantage (p=0.046). Superior ability to see in low light conditions could be the result of increased straylight in depigmented irises, which in light luminance is disadvantageous but in low light conditions may provide an advantage. More research is needed to determine the specific association between melanin content and low-light visual acuity. Furthermore, more research is needed to establish that the improved capacity of blue-eyed individuals to see in low light settings seen in this study is attributable to iris pigmentation rather than corresponding pigmentation elsewhere.

https://www.biorxiv.org/content/10.1101/...7.576074v1

[parasar]

https://www.biorxiv.org/content/10.1101/...5.580575v1
50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences
Elise Kerdoncuff, Laurits Skov, Nick Patterson, Wei Zhao, Yuk Yee Lueng, Gerard D Schellenberg, Jennifer A Smith, Sharmistha Dey, Andrea Ganna, AB Dey, Sharon L.R Kardia, Jinkook Lee, Priya Moorjani
"India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India - including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups - providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe."