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 …
Population genomics meets the taxonomy of cyanobacteria
The emergence of cyanobacterial species (speciation) is driven by mutation, selection, gene
flow, and geographical and ecological isolation. Population genomics explores the process …
flow, and geographical and ecological isolation. Population genomics explores the process …
Genomic analysis reveals a cryptic pangolin species
Eight extant species of pangolins are currently recognized. Recent studies found that two
mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to …
mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to …
PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts on targeted lineages accounting for gene tree discordance
An important goal of evolutionary genomics is to identify genomic regions whose substitution
rates differ among lineages. For example, genomic regions experiencing accelerated …
rates differ among lineages. For example, genomic regions experiencing accelerated …
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
In phylogenomics, incongruences between gene trees, resulting from both artifactual and
biological reasons, can decrease the signal-to-noise ratio and complicate species tree …
biological reasons, can decrease the signal-to-noise ratio and complicate species tree …
Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance
MS Hibbins, LC Breithaupt… - Proceedings of the …, 2023 - National Acad Sciences
Phylogenetic comparative methods have long been a mainstay of evolutionary biology,
allowing for the study of trait evolution across species while accounting for their common …
allowing for the study of trait evolution across species while accounting for their common …
Identifying and addressing methodological incongruence in phylogenomics: A review
JF Fleming, A Valero‐Gracia… - Evolutionary …, 2023 - Wiley Online Library
The availability of phylogenetic data has greatly expanded in recent years. As a result, a
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …
Likelihood-based tests of species tree hypotheses
R Adams, M DeGiorgio - Molecular Biology and Evolution, 2023 - academic.oup.com
Likelihood-based tests of phylogenetic trees are a foundation of modern systematics. Over
the past decade, an enormous wealth and diversity of model-based approaches have been …
the past decade, an enormous wealth and diversity of model-based approaches have been …
Weighted ASTRID: fast and accurate species trees from weighted internode distances
Background Species tree estimation is a basic step in many biological research projects, but
is complicated by the fact that gene trees can differ from the species tree due to processes …
is complicated by the fact that gene trees can differ from the species tree due to processes …
Effect of different types of sequence data on palaeognath phylogeny
N Takezaki - Genome Biology and Evolution, 2023 - academic.oup.com
Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four
flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular …
flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular …