Almost all extant plant species have doubled their genomes at least once in their
evolutionary histories, resulting in polyploidy which provided a rich genomic resource for …

Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each
gene, exclusively 1: 1 orthologos. Paralogs are treated as a dangerous nuisance that has to …

Gene duplication plays an important role in plants for diversification and adaptation to new
habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large …

Background Tree reconciliation problems have long been studied in phylogenetics. A
particular variant of the reconciliation problem for a gene tree T and a species tree S …

Background There has been a trend in increasing the phylogenetic scope of genome
sequencing without finishing the sequence of the genome. Increasing numbers of genomes …

Assembling the tree of life is one of the grand challenges in computational biology. A wide
majority of phylogenetic analyses for the tree of life combine genomic sequences, from …

In phylogenetics, reconciliation is an approach to connect the history of two or more
coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree …

Background Gene tree-species tree reconciliation problems infer the patterns and processes
of gene evolution within a species tree. Gene tree parsimony approaches seek the …

With the availability of genomic sequence data, there is increasing interest in using genes
with a possible history of duplication and loss for species tree inference. Here we assess the …

Although dioecy in Actinidia creates difficulties for plant breeders, such as determining the
breeding values for fruit characters of males, there is a counterbalancing huge fecundity …