scholarly journals On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

2015 ◽  
Vol 282 (1820) ◽  
pp. 20152189 ◽  
Author(s):  
Małgorzata Pilot ◽  
Tadeusz Malewski ◽  
Andre E. Moura ◽  
Tomasz Grzybowski ◽  
Kamil Oleński ◽  
...  
Keyword(s):  
East Asian ◽  
Domestic Dog ◽  
Indigenous Status ◽  
Westward Expansion ◽  
Pure Breed ◽  
Archaeological Data ◽  
Genome Wide ◽  
History Of ◽  
Western Eurasia ◽  
Free Ranging

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.

scholarly journals Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

2019 ◽  
Author(s):  
Haige Han ◽  
Kenneth Bryan ◽  
Wunierfu Shiraigol ◽  
Dongyi Bai ◽  
Yiping Zhao ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genomic Diversity ◽  
Data Sets ◽  
Domestic Horse ◽  
Snp Data ◽  
Genome Wide ◽  
History Of ◽  
Genomic Characterization ◽  
Mongolian Horse ◽  
Free Ranging

Abstract The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

scholarly journals The genomic landscape of contemporary western Remote Oceanians

2022 ◽  
Author(s):  
Lara R. Arauna ◽  
Jacob Bergstedt ◽  
Jeremy Choin ◽  
Javier Mendoza-Revilla ◽  
Christine Harmant ◽  
...  
Keyword(s):  
East Asian ◽  
Genomic Diversity ◽  
Sociocultural Factors ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Population Turnover ◽  
Genome Wide Data ◽  
History Of ◽  
Source Populations ◽  
Sociocultural Processes

The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands around 3,200 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet, there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous admixture events that occurred around 1,700-2,300 years ago, indicating a peopling history common to all the archipelago. However, our analyses reveal that the Papuan population turnover was geographically uneven, and that the genetic contribution of Papuan-related peoples was male-biased. Furthermore, we detect Polynesian ancestry arriving around 600-1,000 years ago to South Vanuatu, and map its distribution to both Polynesian- and non-Polynesian-speaking islands. Lastly, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.

scholarly journals Variation in VKORC1 Is Associated with Vascular Dementia

2021 ◽  
Vol 80 (3) ◽  
pp. 1329-1337
Author(s):  
Jure Mur ◽  
Daniel L. McCartney ◽  
Daniel I. Chasman ◽  
Peter M. Visscher ◽  
Graciela Muniz-Terrera ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Vascular Dementia ◽  
Genetic Variant ◽  
Warfarin Dose ◽  
Uk Biobank ◽  
Parental History ◽  
Genome Wide ◽  
History Of ◽  
First Time ◽  
The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

scholarly journals Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Todd R. Robeck ◽  
Zhe Fei ◽  
Ake T. Lu ◽  
Amin Haghani ◽  
Eve Jourdain ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Age Estimation ◽  
Species Conservation ◽  
Genome Wide ◽  
Epigenetic Aging ◽  
Highly Correlated ◽  
Methylation Patterns ◽  
Cg Dinucleotides ◽  
Free Ranging ◽  
Unique Species

AbstractThe development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

scholarly journals Multitemporal–Multispectral UAS Surveys for Archaeological Research: The Case Study of San Vincenzo Al Volturno (Molise, Italy)

2021 ◽  
Vol 13 (14) ◽  
pp. 2719
Author(s):  
Nicodemo Abate ◽  
Alessia Frisetti ◽  
Federico Marazzi ◽  
Nicola Masini ◽  
Rosa Lasaponara
Keyword(s):  
Middle Ages ◽  
Principal Component ◽  
Archaeological Site ◽  
Archaeological Sites ◽  
Medieval Art ◽  
Archaeological Data ◽  
History Of ◽  
Close Range ◽  
Low Altitude

Unmanned aerial vehicles are currently the most used solution for cultural heritage in the field of close range and low altitude acquisitions. This work shows data acquired by multitemporal and multispectral aerial surveys in the archaeological site of San Vincenzo al Volturno (Molise, Italy). The site is one of the most important medieval archaeological sites in the world. It is a monastic settlement that was particularly rich during the early Middle Ages, and is famous for its two full-frescoed crypts which represent a milestone in the history of medieval art. Thanks to the use of multispectral aerial photography at different times of the year, an area not accessible to archaeological excavation has been investigated. To avoid redundancy of information and reduce the number of data to be analysed, a method based on spectral and radiometric enhancement techniques combined with a selective principal component analysis was used for the identification of useful information. The combination of already published archaeological data and new remote sensing discoveries, has allowed to better define the situation of the abbey during the building phases of the 8th/9th century and 11th century, confirming and adding new data to the assumptions made by archaeologists.

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