Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

AbstractThe date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies.We addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species.The ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris.Our study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species.

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Genetic analysis of Sephardic ancestry in the Iberian Peninsula

10.1101/325779 ◽

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.

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Multilocus approach reveals discordant molecular markers and corridors for gene flow between North African populations of Fasciola hepatica

Veterinary Parasitology ◽

10.1016/j.vetpar.2020.109035 ◽

2020 ◽

Vol 278 ◽

pp. 109035 ◽

Cited By ~ 2

Author(s):

Nabil Amor ◽

Sarra Farjallah ◽

Paolo Merella ◽

Abdulaziz N Alagaili ◽

Osama B. Mohammed

Keyword(s):

Molecular Markers ◽

Gene Flow ◽

Fasciola Hepatica ◽

North African ◽

African Populations ◽

Multilocus Approach

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.0471 ◽

2019 ◽

Vol 286 (1902) ◽

pp. 20190471 ◽

Cited By ~ 1

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.

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mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow

Genome Biology and Evolution ◽

10.1093/gbe/evaa087 ◽

2020 ◽

Vol 12 (5) ◽

pp. 715-719

Author(s):

Junfeng Liu ◽

Qiao Liu ◽

Qingzhu Yang

Keyword(s):

Gene Flow ◽

Divergence Time ◽

Ancestral Population ◽

Migration Model ◽

Isolation With Migration ◽

Multispecies Coalescent ◽

Coalescent Approach ◽

Population Sizes ◽

And Migration ◽

The Relationship

Abstract Gene flow between species may cause variations in branch length and topology of gene tree, which are beyond the expected variations from ancestral processes. These additional variations make it difficult to estimate parameters during speciation with gene flow, as the pattern of these additional variations differs with the relationship between isolation and migration. As far as we know, most methods rely on the assumption about the relationship between isolation and migration by a given model, such as the isolation-with-migration model, when estimating parameters during speciation with gene flow. In this article, we develop a multispecies coalescent approach which does not rely on any assumption about the relationship between isolation and migration when estimating parameters and is called mstree. mstree is available at https://github.com/liujunfengtop/MStree/ and uses some mathematical inequalities among several factors, which include the species divergence time, the ancestral population size, and the number of gene trees, to estimate parameters during speciation with gene flow. Using simulations, we show that the estimated values of ancestral population sizes and species divergence times are close to the true values when analyzing the simulation data sets, which are generated based on the isolation-with-initial-migration model, secondary contact model, and isolation-with-migration model. Therefore, our method is able to estimate ancestral population sizes and speciation times in the presence of different modes of gene flow and may be helpful to test different theories of speciation.

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