Unexpected hybridization patterns in Near Eastern terrapins (Mauremys caspica,M. rivulata) indicate ancient gene flow across the Fertile Crescent

2016 ◽  
Vol 46 (4) ◽  
pp. 401-413 ◽  
Author(s):  
Melita Vamberger ◽  
Heiko Stuckas ◽  
Mario Vargas-Ramírez ◽  
Christian Kehlmaier ◽  
Dinçer Ayaz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Near Eastern ◽  
Fertile Crescent ◽  
Ancient Gene ◽  
Mauremys Caspica

scholarly journals Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe

2011 ◽  
Vol 278 (1720) ◽  
pp. 2874-2880 ◽  
Author(s):  
Noreen von Cramon-Taubadel ◽  
Ron Pinhasi
Keyword(s):  
Gene Flow ◽  
Cultural Transmission ◽  
Complete Replacement ◽  
Cultural Elements ◽  
Near Eastern ◽  
Farming Communities ◽  
Geographical Regions ◽  
Significant Gene ◽  
Transition To Agriculture ◽  
Outlying Regions

The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter–gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter–gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter–gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter–gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.

scholarly journals Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

2018 ◽  
Author(s):  
Gang Li ◽  
Henrique V. Figueiro ◽  
Eduardo Eizirik ◽  
William J. Murphy
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Selective Sweeps ◽  
A Genome ◽  
Chromosome Recombination ◽  
History Of ◽  
Lineage Divergence ◽  
Recurrent Patterns ◽  
Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

scholarly journals Ancient gene flow from early modern humans into Eastern Neanderthals

Nature ◽  
2016 ◽  
Vol 530 (7591) ◽  
pp. 429-433 ◽  
Author(s):  
Martin Kuhlwilm ◽  
Ilan Gronau ◽  
Melissa J. Hubisz ◽  
Cesare de Filippo ◽  
Javier Prado-Martinez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Early Modern ◽  
Modern Humans ◽  
Early Modern Humans ◽  
Ancient Gene

scholarly journals Divergence and hybridization in sea turtles: inferences from genome data show evidence of ancient gene flow between species

2021 ◽  
Author(s):  
Sibelle Torres Vilaça ◽  
Riccardo Piccinno ◽  
Omar Rota‐Stabelli ◽  
Maëva Gabrielli ◽  
Andrea Benazzo ◽  
...  
Keyword(s):  
Gene Flow ◽  
Sea Turtles ◽  
Genome Data ◽  
Show Evidence ◽  
Ancient Gene

scholarly journals Extensive Female-Mediated Gene Flow from Sub-Saharan Africa into Near Eastern Arab Populations

2003 ◽  
Vol 72 (4) ◽  
pp. 1058-1064 ◽  
Author(s):  
Martin Richards ◽  
Chiara Rengo ◽  
Fulvio Cruciani ◽  
Fiona Gratrix ◽  
James F. Wilson ◽  
...  
Keyword(s):  
Gene Flow ◽  
Sub Saharan Africa ◽  
Near Eastern ◽  
Sub Saharan

scholarly journals Inversions shape the divergence of Drosophila pseudoobscura and D. persimilis on multiple timescales

2019 ◽  
Author(s):  
Katharine L Korunes ◽  
Carlos A Machado ◽  
Mohamed AF Noor
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Drosophila Pseudoobscura ◽  
Ancestral Polymorphism ◽  
Chromosomal Inversions ◽  
History Of ◽  
Ancient Gene

AbstractBy shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.

scholarly journals Episodes of gene flow and selection during the evolutionary history of domesticated barley

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peter Civáň ◽  
Konstantina Drosou ◽  
David Armisen-Gimenez ◽  
Wandrille Duchemin ◽  
Jérôme Salse ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Interaction ◽  
Seedling Emergence ◽  
Genetic Selection ◽  
Pathogen Resistance ◽  
Population History ◽  
Founding Population ◽  
Fertile Crescent ◽  
History Of ◽  
Cultivated Barley

Abstract Background Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop. Results We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups. Conclusions Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as ‘domestication traits’. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin.

Ancient Gene Duplication and Differential Gene Flow in Plastid Lineages: The GroEL/Cpn60 Example

1999 ◽  
Vol 48 (1) ◽  
pp. 112-117 ◽  
Author(s):  
Jürgen Wastl ◽  
Martin Fraunholz ◽  
Stefan Zauner ◽  
Susan Douglas ◽  
Uwe-G. Maier
Keyword(s):  
Gene Flow ◽  
Gene Duplication ◽  
Differential Gene ◽  
Ancient Gene ◽  
Ancient Gene Duplication
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