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 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

WHEAT EVOLUTION

1995 ◽  
Vol 43 (2) ◽  
pp. 85-98 ◽  
Author(s):  
Adina Breiman ◽  
Dan Graur
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Wild Relatives ◽  
Wheat Species ◽  
Polyploid Species ◽  
Wheat Evolution ◽  
History Of ◽  
Nuclear Genomes ◽  
Evolutionary Consequences ◽  
Independent Evolutionary History

Many wild and cultivated wheat species are amphidiploid, i.e., they are polyploid species containing two or more distinct nuclear genomes, each with its own independent evolutionary history, but whose genetic behavior resembles that of diploids. Amphidiploidy has important evolutionary consequences in wheat. Since the beginning of this century different methods have been employed to identify the diploid donors of the coexisting genomes in the polyploids. To date, several of the genomic donors have been identified, and the search for the others has been narrowed down considerably. Molecular methodologies that are being increasingly used in studies aimed at reconstructing the evolutionary history of wheat species and their wild relatives have resolved many of the phylogenetic relationships among the various taxa.

scholarly journals Approximating the coalescent under facultative sex

2019 ◽  
Author(s):  
Matthew Hartfield
Keyword(s):  
Population Size ◽  
Evolutionary History ◽  
Sampling Strategies ◽  
Effective Population ◽  
Sexual Species ◽  
History Of ◽  
Mitotic Gene Conversion ◽  
Evolutionary Consequences ◽  
Insight Into ◽  
Coalescent Time

AbstractGenome studies of facultative sexual species, which can either reproduce sexually or asexually, are providing insight into the evolutionary consequences of mixed reproductive modes. It is currently unclear to what extent the evolutionary history of facultative sexuals’ genomes can be approximated by the standard coalescent, and if a coalescent effective population size Ne exists. Here, I determine if and when these approximations can be made. When sex is frequent (occurring at a frequency much greater than 1/N per reproduction per generation, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent, with a coalescent Ne ≈ N. When sex is very rare (at frequency much lower than 1/N), approximations for the pairwise coalescent time can be obtained, which is strongly influenced by the frequencies of sex and mitotic gene conversion, rather than N. However, these terms do not translate into a coalescent Ne. These results are used to discuss the best sampling strategies for investigating the evolutionary history of facultative sexual species.

Defining and Disrupting Species Boundaries in Saccharomyces

2020 ◽  
Vol 74 (1) ◽  
pp. 477-495
Author(s):  
Jasmine Ono ◽  
Duncan Greig ◽  
Primrose J. Boynton
Keyword(s):  
Reproductive Isolation ◽  
Evolutionary History ◽  
Life Cycles ◽  
Sexual Life ◽  
Evolutionary Mechanisms ◽  
History Of ◽  
The One ◽  
Reproductive Isolation Mechanisms ◽  
Evolutionary Consequences ◽  
Isolation Mechanisms

The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evolution of diverse Saccharomyces species and hybrids, which occupy a variety of wild and domesticated habitats. In this article, we introduce readers to the mechanisms isolating Saccharomyces species, the circumstances in which reproductive isolation mechanisms are effective and ineffective, and the evolutionary consequences of partial reproductive isolation. We discuss both the evolutionary history of the genus Saccharomyces and the human history of taxonomists and biologists struggling with species concepts in this fascinating genus.

scholarly journals A Linear-Time Algorithm for the Isometric Reconciliation of Unrooted Trees

Algorithms ◽  
2020 ◽  
Vol 13 (9) ◽  
pp. 225
Author(s):  
Broňa Brejová ◽  
Rastislav Královič
Keyword(s):  
Family History ◽  
Gene Family ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Linear Time ◽  
Gene Tree ◽  
Time Algorithm ◽  
Species Tree ◽  
Linear Time Algorithm ◽  
History Of

In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps nodes of the gene tree to the corresponding points of the species tree, and thus helps to interpret the gene family history. In this paper, we study the case when both trees are unrooted and their edge lengths are known exactly. The goal is to root them and to find a reconciliation that agrees with the edge lengths. We show a linear-time algorithm for finding the set of all possible root locations, which is a significant improvement compared to the previous O(N3logN) algorithm.

scholarly journals A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

2019 ◽  
Vol 286 (1898) ◽  
pp. 20182524 ◽  
Author(s):  
Eduardo E. Zattara ◽  
Fernando A. Fernández-Álvarez ◽  
Terra C. Hiebert ◽  
Alexandra E. Bely ◽  
Jon L. Norenburg
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Ability To Regenerate ◽  
History Of ◽  
Phylogenetic Framework ◽  
Regenerative Ability ◽  
Head Regeneration

Animals vary widely in their ability to regenerate, suggesting that regenerative ability has a rich evolutionary history. However, our understanding of this history remains limited because regenerative ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We assessed ability to regenerate heads and tails either through our own experiments or from literature reports for 35 species of Nemertea spanning the diversity of the phylum, including representatives of 10 families and all three orders. We generated a phylogenetic framework using sequence data to reconstruct the evolutionary history of head and tail regenerative ability across the phylum and found that all evaluated species can remake a posterior end but surprisingly few could regenerate a complete head. Our analysis reconstructs a nemertean ancestor unable to regenerate a head and indicates independent gains of head regenerative ability in at least four separate lineages, with one of these gains taking place as recently as the last 10–15 Myr. Our study highlights nemerteans as a valuable group for studying evolution of regeneration and identifying mechanisms associated with repeated gains of regenerative ability.

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 411-416 ◽  
Author(s):  
Hikmet Budak ◽  
Robert C Shearman ◽  
Ismail Dweikat
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
Specific Marker ◽  
Buchloe Dactyloides ◽  
A Genome ◽  
Organelle Genomes ◽  
History Of

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalograss evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.Key words: buffalograss, evolution, organelle genomes, turfgrass.

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