scholarly journals Genetic analysis of Sephardic ancestry in the Iberian Peninsula

2018 ◽  
Author(s):  
Miguel Martín Álvarez-Álvarez ◽  
Neil Risch ◽  
Christopher R. Gignoux ◽  
Scott Huntsman ◽  
Elad Ziv ◽  
...  
Keyword(s):  
Gene Flow ◽  
Iberian Peninsula ◽  
Eastern Mediterranean ◽  
Genetic Data ◽  
North African ◽  
Religious Persecution ◽  
South Italy ◽  
Target Populations ◽  
Snp Data ◽  
Genome Wide

AbstractThe Sephardim are a major Jewish ethnic division whose origins can be traced back to the Iberian Peninsula. We used genome-wide SNP data to investigate the degree of Sephardic admixture in seven populations from the Iberian Peninsula and surrounding regions in the aftermath of their religious persecution starting in the late 14th century. To this end, we used Eastern Mediterranean (from South Italy, Greece and Israel) and North African (Tunisian and Moroccan) populations as proxies for the major ancestral components found in the target populations and carried out unlinked- and linked-marker analyses on the available genetic data. We report evidence of Sephardic ancestry in some of our Iberian samples, as well as in North Italy and Tunisia. We find the Sephardic admixture to be more recent relative to the Berber admixture following an out-of-Iberia geographic dispersal, suggesting Sephardic gene flow from Spain outwards. We also report some of the challenges in assigning Sephardic ancestry to potentially admixed individuals due to the lack of a clear genetic signature.

scholarly journals The genomic history of the Iberian Peninsula over the past 8000 years

Science ◽  
2019 ◽  
Vol 363 (6432) ◽  
pp. 1230-1234 ◽  
Author(s):  
Iñigo Olalde ◽  
Swapan Mallick ◽  
Nick Patterson ◽  
Nadin Rohland ◽  
Vanessa Villalba-Mouco ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
Iron Age ◽  
North Africa ◽  
Eastern Mediterranean ◽  
Hunter Gatherers ◽  
Y Chromosomes ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Genetic Substructure

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

2020 ◽  
Vol 29 (7) ◽  
pp. 1235-1249 ◽  
Author(s):  
Nathan K. Lujan ◽  
Jason T. Weir ◽  
Brice P. Noonan ◽  
Nathan R. Lovejoy ◽  
Nicholas E. Mandrak
Keyword(s):  
Gene Flow ◽  
Native Species ◽  
Niagara Falls ◽  
Snp Data ◽  
Genome Wide

scholarly journals Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime

2021 ◽  
Author(s):  
Naoko Kurata ◽  
Michael Hickerson ◽  
Sandra Hoffberg ◽  
Ned Gardiner ◽  
Melanie L.J. Stiassny ◽  
...  
Keyword(s):  
Gene Flow ◽  
Spatial Scales ◽  
Hydrological Regime ◽  
High Energy ◽  
Ecological Specialization ◽  
Cichlid Fishes ◽  
Heterogeneous Habitats ◽  
Snp Data ◽  
Genome Wide ◽  
Physical Barriers

Rivers provide excellent models to understand how species diversity is generated and maintained across heterogeneous habitats. The lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, and generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. In this study, we examined four species of lamprologine cichlids endemic to the LCR, of which three are sequentially distributed along the LCR without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that the rapids sometimes serve to reduce gene flow, but also suggest that at certain temporal and spatial scales, they may also act as promoters of gene flow. Furthermore, we detected both upstream and downstream gene flow between some populations of Lamprologus tigripictilis as well as hybridization between congeneric species. These results suggest that powerful high-energy rapids may therefore provide occasional multidirectional dispersal opportunities for riverine cichlid fishes, highlighting the complexity of factors driving evolutionary processes in the LCR.

scholarly journals Dissecting human North African gene-flow into its western coastal surroundings

2019 ◽  
Vol 286 (1902) ◽  
pp. 20190471 ◽  
Author(s):  
Lara R. Arauna ◽  
Garrett Hellenthal ◽  
David Comas
Keyword(s):  
Roman Empire ◽  
Gene Flow ◽  
Iberian Peninsula ◽  
Canary Islands ◽  
North Africa ◽  
Mediterranean Coast ◽  
North African ◽  
The North ◽  
Geographical Regions ◽  
The Impact

North African history and populations have exerted a pivotal influence on surrounding geographical regions, although scant genetic studies have addressed this issue. Our aim is to understand human historical migrations in the coastal surroundings of North Africa. We built a refined genome-wide dataset of North African populations to unearth the fine-scale genetic structure of the region, using haplotype information. The results suggest that the gene-flow from North Africa into the European Mediterranean coast (Tuscany and the Iberian Peninsula) arrived mainly from the Mediterranean coast of North Africa. In Tuscany, this North African admixture date estimate suggests the movement of peoples during the fall of the Roman Empire around the fourth century. In the Iberian Peninsula, the North African component probably reflects the impact of the Arab expansion since the seventh century and the subsequent expansion of the Christian Kingdoms. By contrast, the North African component in the Canary Islands has a source genetically related to present-day people from the Atlantic North African coast. We also find sub-Saharan gene-flow from the Senegambia region in the Canary Islands. Specifically, we detect a complex signal of admixture involving Atlantic, Senegambian and European sources intermixing around the fifteenth century, soon after the Castilian conquest. Our results highlight the differential genetic influence of North Africa into the surrounding coast and show that specific historical events have not only had a socio-cultural impact but additionally modified the gene pool of the populations.

scholarly journals Denisovan Ancestry in East Eurasian and Native American Populations.

2015 ◽  
Author(s):  
Pengfei Qin ◽  
Mark Stoneking
Keyword(s):  
Native American ◽  
Gene Flow ◽  
New Guinea ◽  
Modern Human ◽  
Common Source ◽  
Human Populations ◽  
Snp Data ◽  
Genome Wide ◽  
Or Gene ◽  
The Relationship

Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.

scholarly journals Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations

2020 ◽  
Author(s):  
Alba Rey-Iglesia ◽  
Philippe Gaubert ◽  
Gonçalo Espregueira Themudo ◽  
Rosa Pires ◽  
Constanza De La Fuente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North Atlantic ◽  
Marine Mammals ◽  
Eastern Mediterranean ◽  
The Black Sea ◽  
Mediterranean Populations ◽  
Geographic Ranges ◽  
Western Sahara ◽  
The Mediterranean

Abstract The Mediterranean monk seal Monachus monachus is one of the most threatened marine mammals, with only 600–700 individuals restricted to three populations off the coast of Western Sahara and Madeira (North Atlantic) and between Greece and Turkey (eastern Mediterranean). Its original range was from the Black Sea (eastern Mediterranean) to Gambia (western African coast), but was drastically reduced by commercial hunting and human persecution since the early stages of marine exploitation. We here analyse 42 mitogenomes of Mediterranean monk seals, from across their present and historical geographic ranges to assess the species population dynamics over time. Our data show a decrease in genetic diversity in the last 200 years. Extant individuals presented an almost four-fold reduction in genetic diversity when compared to historical specimens. We also detect, for the first time, a clear segregation between the two North Atlantic populations, Madeira and Cabo Blanco, regardless of their geographical proximity. Moreover, we show the presence of historical gene-flow between the two water basins, the Atlantic Ocean and the Mediterranean Sea, and the presence of at least one extinct maternal lineage in the Mediterranean. Our work demonstrates the advantages of using full mitogenomes in phylogeographic and conservation genomic studies of threatened species.

scholarly journals Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Athea Vichas ◽  
Amanda K. Riley ◽  
Naomi T. Nkinsi ◽  
Shriya Kamlapurkar ◽  
Phoebe C. R. Parrish ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Spindle Assembly Checkpoint ◽  
Spindle Assembly ◽  
Genetic Data ◽  
Multiple Models ◽  
Ras Pathway ◽  
Functional Interactions ◽  
Genome Wide ◽  
A Genome ◽  
Mutant Cells

AbstractCRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1-mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional interactions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

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