Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA
▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic
in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one …
in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one …
Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae sl
DF Morales-Briones, G Kadereit, DT Tefarikis… - Systematic …, 2021 - academic.oup.com
Gene tree discordance in large genomic data sets can be caused by evolutionary processes
such as incomplete lineage sorting and hybridization, as well as model violation, and errors …
such as incomplete lineage sorting and hybridization, as well as model violation, and errors …
The influence of gene flow on species tree estimation: a simulation study
Gene flow among populations or species and incomplete lineage sorting (ILS) are two
evolutionary processes responsible for generating gene tree discordance and therefore …
evolutionary processes responsible for generating gene tree discordance and therefore …
Detection and polarization of introgression in a five-taxon phylogeny
When multiple speciation events occur rapidly in succession, discordant genealogies due to
incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of …
incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of …
A statistical approach for distinguishing hybridization and incomplete lineage sorting
S Joly, PA McLenachan… - The American …, 2009 - journals.uchicago.edu
The extent and evolutionary significance of hybridization is difficult to evaluate because of
the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present …
the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present …
Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies
One of the longstanding questions in phylogenetic systematics is how to address
incongruence among phylogenies obtained from multiple markers and how to determine the …
incongruence among phylogenies obtained from multiple markers and how to determine the …
Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”
AR Dunz, UK Schliewen - Molecular Phylogenetics and Evolution, 2013 - Elsevier
African cichlids formerly referred to as” Tilapia” represent a paraphyletic species
assemblage belonging to the so called haplotilapiine lineage which gave rise to the …
assemblage belonging to the so called haplotilapiine lineage which gave rise to the …
Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model
C Meng, LS Kubatko - Theoretical population biology, 2009 - Elsevier
The application of phylogenetic inference methods, to data for a set of independent genes
sampled randomly throughout the genome, often results in substantial incongruence in the …
sampled randomly throughout the genome, often results in substantial incongruence in the …
Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement
W Wang, HL Li, ZD Chen - Science China Life Sciences, 2014 - Springer
Correct combination of plastid (cp) and nuclear (nr) DNA data for plant phylogenetic
reconstructions is not a new issue, but with an increasing number of nrDNA loci being used …
reconstructions is not a new issue, but with an increasing number of nrDNA loci being used …
Deep phylogenetic incongruence in the angiosperm clade Rosidae
Abstract Analysis of large data sets can help resolve difficult nodes in the tree of life and also
reveal complex evolutionary histories. The placement of the Celastrales–Oxalidales …
reveal complex evolutionary histories. The placement of the Celastrales–Oxalidales …