scholarly journals Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
History Of ◽  
Genome Scale

scholarly journals Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16751 ◽  
Author(s):  
Adam C. Silver ◽  
David Williams ◽  
Joshua Faucher ◽  
Amy J. Horneman ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Aeromonas Veronii ◽  
Host Interaction ◽  
History Of ◽  
Complex Evolutionary History

scholarly journals Early history of Neanderthals and Denisovans

2017 ◽  
Vol 114 (37) ◽  
pp. 9859-9863 ◽  
Author(s):  
Alan R. Rogers ◽  
Ryan J. Bohlender ◽  
Chad D. Huff
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Early History ◽  
Middle Pleistocene ◽  
Dna Sequence Data ◽  
The Past ◽  
History Of

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

scholarly journals Widespread introgression across a phylogeny of 155 Drosophila genomes

2020 ◽  
Author(s):  
Anton Suvorov ◽  
Bernard Y. Kim ◽  
Jeremy Wang ◽  
Ellie E. Armstrong ◽  
David Peede ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Gene Tree ◽  
History Of ◽  
Mapping Gene ◽  
Gene Tree Discordance ◽  
Evolutionary Consequences ◽  
Genome Assemblies ◽  
Genome Scale ◽  
Hybridization And Introgression

Genome-scale sequence data has invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred, with introgression at the base of species radiations being particularly common. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

scholarly journals Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?

2019 ◽  
Vol 69 (4) ◽  
pp. 708-721 ◽  
Author(s):  
Luke C Campillo ◽  
Anthony J Barley ◽  
Robert C Thomson
Keyword(s):  
Reproductive Isolation ◽  
Dna Sequence ◽  
Sequence Data ◽  
Species Recognition ◽  
Species Boundaries ◽  
Simultaneous Estimation ◽  
Dna Sequence Data ◽  
Multispecies Coalescent ◽  
Species Pairs ◽  
History Of

Abstract A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]

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