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Although the mtDNAs of the representatives of the Klebsormidiales exhibit less important differences in genome size and intron content than their zygnematelean homologs (table 1), they appear to be more fluid at the level of gene order as evidenced by MP analysis of gene pairs (fig. 6) and the inferred scenario of genome rearrangements (supplementary fig. S4, Supplementary Material online).
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This changing view with respect to geographical location of refugia has also had direct implications for the inferred scenarios of recolonization for many widespread species from the Western Palaearctic.
We also simulate two more scenarios to mimic the cases that the incidence assay data imply a different incidence rate: either double the inferred incidence (Scenario II) or half the inferred incidence (Scenario III).
The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events.
This inferred evolutionary scenario resembles that for the NAD-dependent DNA ligase of the NCLDV (Yutin and Koonin 2009).
This follows from the need for the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events to be consistent with the causal hypothesis.
Additionally, we also discussed the introgression pattern based on inferred evolutionary scenario with the goal of understanding the demographic history of silkworm.
We used genome flux as an external criterion to evaluate the accuracy of every inferred evolutionary scenario of genome-level changes.
The main drawback of reconciliation is that the inferred evolutionary scenario is strongly dependent on the considered gene trees, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses.
By "consistent with" we specifically mean that the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events are all consistent with the vicariance hypothesis.
An inferred evolutionary scenario for fungal CYPs along with fungal divergences is generated based on the phylogenetic and taxonomic relationships among fungal CYP families (fig. 4), which helps understanding the current distribution of CYPomes in fungi and their evolutionary adaptation to ecological niches.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com