What are fungal species and how to delineate them?
This is the opening paper in the special issue of Fungal Diversity, which collates the data on
defining species. Defining and recognizing species has long been a controversial issue …
defining species. Defining and recognizing species has long been a controversial issue …
Incongruence in the phylogenomics era
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …
strongly contradictory on certain, contentious relationships. Here, we use a maximum …
[PDF][PDF] The evolutionary emergence of land plants
There can be no doubt that early land plant evolution transformed the planet but, until
recently, how and when this was achieved was unclear. Coincidence in the first appearance …
recently, how and when this was achieved was unclear. Coincidence in the first appearance …
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies
Background Phylogenetic and population genetic studies often deal with multiple sequence
alignments that require manipulation or processing steps such as sequence concatenation …
alignments that require manipulation or processing steps such as sequence concatenation …
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
A Criscuolo, S Gribaldo - BMC evolutionary biology, 2010 - Springer
Background The quality of multiple sequence alignments plays an important role in the
accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned …
accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned …
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Background Next-generation sequencing has provided a wealth of plastid genome
sequence data from an increasingly diverse set of green plants (Viridiplantae). Although …
sequence data from an increasingly diverse set of green plants (Viridiplantae). Although …
Inferring ancient divergences requires genes with strong phylogenetic signals
L Salichos, A Rokas - Nature, 2013 - nature.com
To tackle incongruence, the topological conflict between different gene trees, phylogenomic
studies couple concatenation with practices such as rogue taxon removal or the use of …
studies couple concatenation with practices such as rogue taxon removal or the use of …
Relaxed phylogenetics and dating with confidence
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are
two extremes of a continuum. Despite their dominance in phylogenetic inference, it is …
two extremes of a continuum. Despite their dominance in phylogenetic inference, it is …
Genome‐wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the L ake V ictoria cichlid adaptive radiation
Although population genomic studies using next generation sequencing (NGS) data are
becoming increasingly common, studies focusing on phylogenetic inference using these …
becoming increasingly common, studies focusing on phylogenetic inference using these …