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On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer
Reconciling a non-binary gene tree with a binary species tree can be done efficiently in the absence of horizontal gene transfers, but becomes...
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Rooting Species Trees Using Gene Tree-Species Tree Reconciliation
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But...
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Exact median-tree inference for unrooted reconciliation costs
BackgroundSolving median tree problems under tree reconciliation costs is a classic and well-studied approach for inferring species trees from...
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Maximum parsimony reconciliation in the DTLOR model
BackgroundAnalyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not...
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Greengenes2 unifies microbial data in a single reference tree
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce...
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xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers....
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Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL
Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of...
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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation
We present Seaview version 5, a multiplatform program to perform multiple alignment and phylogenetic tree building from molecular sequence data....
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Evolution through segmental duplications and losses: a Super-Reconciliation approach
The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families,...
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The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we...
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Characterizing prediction errors of a new tree height model for cut-to-length Pinus radiata stems through the Burr Type XII distribution
Unlike height-diameter equations for standing trees commonly used in forest resources modelling, tree height models for cut-to-length (CTL) stems...
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Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota
The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to...
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Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt...
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WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events
BackgroundMultiple processes impact the probability of retention of individual genes following whole genome duplication (WGD) events. In analyzing...
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Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies
BackgroundAn orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with...
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One Size Does not Fit all: Constraints and Opportunities for Small-Scale Forestry in British Columbia, Canada
Forestry in British Columbia, Canada, is in transition. Social and environmental concerns, such as the conservation of old growth forests,...
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The nature of the last universal common ancestor and its impact on the early Earth system
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across...
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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea
BackgroundThe recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life....
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Impact of Increasing CO2, and Air Pollutants (NOx, SO2, O3) on the Stable Isotope Ratios in Tree Rings
AnthropogenicAnthropogenic activities such as industrializationIndustrial revolution (Industrialization), land use change and intensification of...
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Reconciling East-African Wetland Conservation with Human Needs: Managing Uncertainties in Environmental Policy Design
Rapidly develo** societies in East-Africa impose increasing pressures on wetlands due to rising food demand and degradation of upland soils....
