[HTML][HTML] NANUQ: a method for inferring species networks from gene trees under the coalescent model

ES Allman, H Baños, JA Rhodes - Algorithms for Molecular Biology, 2019 - Springer
Species networks generalize the notion of species trees to allow for hybridization or other
lateral gene transfer. Under the network multispecies coalescent model, individual gene …

An evolving view of phylogenetic support

C Simon - Systematic Biology, 2022 - academic.oup.com
If all nucleotide sites evolved at the same rate within molecules and throughout the history of
lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved …

Detectability of varied hybridization scenarios using genome-scale hybrid detection methods

M Bjorner, EK Molloy, CN Dewey… - arXiv preprint arXiv …, 2022 - arxiv.org
Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to
patterns of genetic heritability that are unexpected under traditional, bifurcating models of …

PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow

J Fogg, ES Allman, C Ané - Systematic Biology, 2023 - academic.oup.com
We consider the evolution of phylogenetic gene trees along phylogenetic species networks,
according to the network multispecies coalescent process, and introduce a new network …

MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R

JA Rhodes, H Baños, JD Mitchell, ES Allman - Bioinformatics, 2021 - academic.oup.com
MSCquartets is an R package for species tree hypothesis testing, inference of species trees
and inference of species networks under the Multispecies Coalescent model of incomplete …

Evaluation of methods to detect shifts in directional selection at the genome scale

L Duchemin, V Lanore, P Veber… - Molecular Biology and …, 2023 - academic.oup.com
Identifying the footprints of selection in coding sequences can inform about the importance
and function of individual sites. Analyses of the ratio of nonsynonymous to synonymous …

[HTML][HTML] A note on likelihood ratio tests for models with latent variables

Y Chen, I Moustaki, H Zhang - psychometrika, 2020 - Springer
The likelihood ratio test (LRT) is widely used for comparing the relative fit of nested latent
variable models. Following Wilks' theorem, the LRT is conducted by comparing the LRT …

Identifiability of species network topologies from genomic sequences using the logdet distance

ES Allman, H Baños, JA Rhodes - Journal of mathematical biology, 2022 - Springer
Inference of network-like evolutionary relationships between species from genomic data
must address the interwoven signals from both gene flow and incomplete lineage sorting …

Gene tree discord, simplex plots, and statistical tests under the coalescent

ES Allman, JD Mitchell, JA Rhodes - Systematic Biology, 2022 - academic.oup.com
A simple graphical device, the simplex plot of quartet concordance factors, is introduced to
aid in the exploration of a collection of gene trees on a common set of taxa. A single plot …

The tree of blobs of a species network: identifiability under the coalescent

ES Allman, H Baños, JD Mitchell, JA Rhodes - Journal of mathematical …, 2023 - Springer
Inference of species networks from genomic data under the Network Multispecies
Coalescent Model is currently severely limited by heavy computational demands. It also …