A Framework for Representing Reticulate Evolution [PDF]
Annals of Combinatorics, 2005 In biology it is a very important task representing the evolution of the living world. Generally rooted trees are used to display the evolutionary relations. It is well known, however, that the real-world evolution is ``reticulate'' (= non-tree like) as a consequence of ``hybridizations'' and ``horizontal gene transfers''.
Baroni, M., Semple, C., Steel, M.
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Reticulate Evolution of the Rye Genome [PDF]
The Plant Cell, 2013 Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes ...
Mihaela M. Martis +15 more
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Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era
bioRxiv, 2023 Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments.
Zetao Jin +11 more
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Phylogeny reconstruction and hybrid analysis of populus (Salicaceae) based on nucleotide sequences of multiple single-copy nuclear genes and plastid fragments. [PDF]
PLoS ONE, 2014 Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of
Zhaoshan Wang +5 more
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A Molecular Phylogeny of Stylodipus (Dipodidae, Mammalia): A Small Genus with a Complex History
Diversity, 2023 A range-wide phylogenetic/phylogeographic study of the three-toed jerboas of the genus Stylodipus is conducted using the mitochondrial cytb gene and fragments of several nuclear genes. The genus has been believed to include three species: S.
Vladimir S. Lebedev +10 more
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Reticulate evolution is favored in influenza niche switching. [PDF]
Proc Natl Acad Sci U S A, 2016 Significance Are the processes that result in the exchange of genes between microbes quantitatively advantageous for those microbes when switching between ecological niches? To address this question, we consider the influenza A virus as a model microbe, with its ability to infect multiple host species (ecological niches) and undergo ...
Ma EJ +4 more
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Taxonomy of the Crematogaster degeeri-species-assemblage in the Malagasy region (Hymenoptera: Formicidae) [PDF]
, 2013 We revise the species-level taxonomy of the Crematogaster (Crematogaster) degeerispecies-assemblage, a group of related ants occuring in Madagascar and the wider Malagasy region, and further provide an identification key to all species-groups of the ...
Blaimer, Bonnie B., Fisher, Brian L.
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QS-Net: Reconstructing Phylogenetic Networks Based on Quartet and Sextet
Frontiers in Genetics, 2019 Phylogenetic networks are used to estimate evolutionary relationships among biological entities or taxa involving reticulate events such as horizontal gene transfer, hybridization, recombination, and reassortment.
Ming Tan +9 more
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Which phylogenetic networks are merely trees with additional arcs? [PDF]
, 2015 A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines whether or not any ...
Francis, Andrew R., Steel, Mike
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Reconstructible phylogenetic networks: do not distinguish the indistinguishable. [PDF]
PLoS Computational Biology, 2015 Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays,
Fabio Pardi, Celine Scornavacca
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