Olga Chernomor

• PhD
• PostDoc Position at University of Vienna

For a set of binary unrooted subtrees generating all binary unrooted trees compatible with them, i.e. generating their stand, is one of the classical problems in phylogenetics. Here, we introduce Gentrius – an efficient algorithm to tackle this task. The algorithm has a direct application in practice. Namely, Gentrius generates phylogenetic terrace...

Phylogenetic trees are routinely built from huge and yet incomplete multi-locus datasets often leading to multiple equally scoring trees under many common criteria. As typical tree inference software output only a single tree, identifying all trees with identical score challenges phylogenomics. Here, we introduce Gentrius – an efficient algorithm t...

The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputatio...

Light-dependent and dark-operative protochlorophyllide oxidoreductases (LPORs and DPORs) are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis that LPORs are only present in...

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of p...

IQ-TREE (http://www.iqtree.org) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal wi...

A bstract Terraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled...

The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an eff...

The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an eff...

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Though partition models provide a more comprehensive analysis of supermatrices, miss...

About 20 years ago the concepts of phylogenetic diversity and phylogenetic split networks were separately introduced in conservation biology and evolutionary biology, respectively. While it has been widely recognized that biodiversity assessment should better take into account the phylogenetic tree of life, it has also been widely acknowledged that...

In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not...

Reserve Selection Problems Revisited. Data S2. Data description. Data S3. Additional results and analysis. Table S1. Diet composition matrix for 250 Caribbean species. Table S2. NCBI accession numbers of six genes for Caribbean case study. Table S3. Sequence data collected for Caribbean case study. Table S4. List of taxa in optimal sets SPD, SSD, S...

Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization. Depending on the conservation goal and the information available about species, one can co...

We used Quantum Monte Carlo (QMC) methods to study the polarizability and the quadrupole moment of the ethyne molecule using the Jastrow-Antisymmetrised Geminal Power (JAGP) wave function, a compact and strongly correlated variational ansatz. The compactness of the functional form and the full optimization of all its variational parameters, includi...