[PDF] apex: phylogenetics with multiple genes | Semantic Scholar (2024)

The approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low‐dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group‐specific consensus phylogenies.

It is shown that ANI-based groups are in agreement with the International Committee on Taxonomy of Viruses (ICTV) classification and already established dot-plot groups, which are occasionally further refined owing to higher resolution of ANI analysis.

Diversity in a set of 90 accessions comprising most of Vitis species and some putative hybrids was analyzed and single nucleotide polymorphisms (SNPs) in SANGER sequences of twelve loci and genotyped accessions at a larger number of SNPs were discovered using a previously developed SNP array.

Comparison and species delimitation using universally conserved orthologs and protein-coding mitochondrial genes revealed that the canine and feline isolates are different species, building a base for future integrative taxonomy.

Comparison and species delimitation using universally conserved orthologs and protein coding mitochondrial genes revealed that the canine and feline isolates are different species, building a base for future integrative taxonomy.

Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents, and molecular markers used to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia revealed the existence of three mycobiont lineages.

Assessment of mitochondrial genomes from Australasian snapper sampled in New Zealand demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to the growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.

Results suggest that identification of Fon isolates by race determination alone may fail to detect economically important phenotypic characteristics such as aggressiveness leading to inaccurate risk assessment, and justification for future whole genome sequencing efforts whose more robust genomic comparisons will provide higher resolution of intra-species genetic distinctions.

...

...

Ape's repertoire for phylogenetic inference from complete distances is extended, several methods from the literature for phylogenetic inference from incomplete distance matrices are incorporated, and a new object class is added to efficiently encode sets of splits of taxa.

The effect of various factors that cause incongruence in molecular phylogenies are reviewed, the advances in the field that resolved some factors are explored, and unresolved factors that are still unresolved are explored along with possible ways for tackling them.

The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life.

The field of systematic biology has been revitalized and transformed during the last few decades by the confluence of phylogenetic thinking with ready access to the tools of molecular biology and a growing awareness that reliance on a single data set may often result in insufficient phylogenetic resolution or misleading inferences.

This work provides the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method for identifying clonal complexes within a species and displaying the overall structure of the population.

New phylogenetic approaches explicitly consider the relationships between gene trees and the underlying history of species divergence, providing direct estimates of species trees (Fig. 1).

Adephylo implements tests of phylogenetic signal, phylogenetic distances and proximities, and novel methods for describing further univariate and multivariate phylogenetic structures, which open up new perspectives in the analysis of evolutionary comparative data.

It is concluded that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting, which will likely cause phylogeneticincongruences in many comparative genomics datasets.

Phangorn is a package for phylogenetic reconstruction and analysis in the R language that offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation.

...

...