scholarly journals Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

2020 ◽  
Vol 6 (11) ◽  
pp. eaay0456
Author(s):  
Michael V. Westbury ◽  
Stefanie Hartmann ◽  
Axel Barlow ◽  
Michaela Preick ◽  
Bogdan Ridush ◽  
...  
Keyword(s):  
Gene Flow ◽  
Late Pleistocene ◽  
Evolutionary History ◽  
Population Level ◽  
Evolutionary Relationships ◽  
Spotted Hyena ◽  
High Frequencies ◽  
History Of ◽  
The Cross ◽  
Complex Evolutionary History

The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events

2019 ◽  
Vol 28 (24) ◽  
pp. 5299-5314 ◽  
Author(s):  
Shuo Liu ◽  
Amandine Cornille ◽  
Stéphane Decroocq ◽  
David Tricon ◽  
Aurélie Chague ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Species Divergence ◽  
History Of ◽  
Complex Evolutionary History

Human Evolution in Asia: Taking Stock and Looking Forward

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Sang-Hee Lee ◽  
Autumn Hudock
Keyword(s):  
Gene Flow ◽  
Fossil Record ◽  
Evolutionary History ◽  
Annual Review ◽  
Publication Date ◽  
History Of ◽  
Different Populations ◽  
Critical Understanding ◽  
New Research ◽  
Complex Evolutionary History

We review the state of paleoanthropology research in Asia. We survey the fossil record, articulate the current understanding, and delineate the points of contention. Although Asia received less attention than Europe and Africa did in the second half of the twentieth century, an increase in reliably dated fossil materials and the advances in genetics have fueled new research. The long and complex evolutionary history of humans in Asia throughout the Pleistocene can be explained by a balance of mechanisms, between gene flow among different populations and continuity of regional ancestry. This pattern is reflected in fossil morphology and paleogenomics. Critical understanding of the sociocultural forces that shaped the history of hominin fossil research in Asia is important in charting the way forward. Expected final online publication date for the Annual Review of Anthropology, Volume 50 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

Rhizobial plasmids — replication, structure and biological role

2012 ◽  
Vol 7 (4) ◽  
pp. 571-586 ◽  
Author(s):  
Andrzej Mazur ◽  
Piotr Koper
Keyword(s):  
Genome Organization ◽  
Soil Bacteria ◽  
Evolutionary History ◽  
Bacterial Genome ◽  
Biological Role ◽  
Genome Architecture ◽  
Genomic Knowledge ◽  
History Of ◽  
Cryptic Plasmids ◽  
Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

A total evidence approach using palynological characters to infer the complex evolutionary history of the Asian Impatiens (Balsaminaceae)

Taxon ◽  
2012 ◽  
Vol 61 (2) ◽  
pp. 355-367 ◽  
Author(s):  
Steven B. Janssens ◽  
Yi Song Wilson ◽  
Yong-Ming Yuan ◽  
Anne Nagels ◽  
Erik F. Smets ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Total Evidence ◽  
History Of ◽  
Complex Evolutionary History

scholarly journals Evolutionary history of the Pectoral Sparrow Arremon taciturnus : evidence for diversification during the Late Pleistocene

Ibis ◽  
2020 ◽  
Vol 162 (4) ◽  
pp. 1198-1210
Author(s):  
Carina Carneiro de Melo Moura ◽  
Alexandre M. Fernandes ◽  
Alexandre Aleixo ◽  
Helder Farias Pereira de Araújo ◽  
Erich de Freitas Mariano ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Evolutionary History ◽  
History Of

scholarly journals Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

2019 ◽  
Vol 11 (9) ◽  
pp. 2531-2541 ◽  
Author(s):  
Valeria Mateo-Estrada ◽  
Lucía Graña-Miraglia ◽  
Gamaliel López-Leal ◽  
Santiago Castillo-Ramírez
Keyword(s):  
Evolutionary History ◽  
Ad Hoc ◽  
Acinetobacter Calcoaceticus ◽  
Recent Attempt ◽  
Evolutionary Relationships ◽  
Closely Related Species ◽  
Acinetobacter Baumannii Complex ◽  
History Of ◽  
To Come ◽  
Clear Cases

Abstract The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.

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