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 …

[BOOK][B] ReCombinatorics: the algorithmics of ancestral recombination graphs and explicit phylogenetic networks

D Gusfield - 2014 - books.google.com
Combinatorial structure and algorithms for deducing genetic recombination history,
represented by ancestral recombination graphs and other networks, and their role in the …

Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae …

EA Myers, RM Rautsaw, M Borja, J Jones… - Systematic …, 2024 - academic.oup.com
Abstract.—Phylogenomics allows us to uncover the historical signal of evolutionary
processes through time and estimate phylogenetic networks accounting for these signals …

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

E Gross, L van Iersel, R Janssen, M Jones… - Journal of Mathematical …, 2021 - Springer
Phylogenetic networks can represent evolutionary events that cannot be described by
phylogenetic trees. These networks are able to incorporate reticulate evolutionary events …

Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae: Desmognathus) Uncovered by Estimating Higher-Level Phylogenetic Networks

RA Pyron, KA O'Connell, EA Myers… - Systematic …, 2025 - academic.oup.com
Reticulation between radiating lineages is a common feature of diversification. We examine
these phenomena in the Pisgah clade of Desmognathus salamanders from the southern …

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 …

Identifying species network features from gene tree quartets under the coalescent model

H Baños - Bulletin of mathematical biology, 2019 - Springer
We show that many topological features of level-1 species networks are identifiable from the
distribution of the gene tree quartets under the network multi-species coalescent model. In …

On encodings of phylogenetic networks of bounded level

P Gambette, KT Huber - Journal of mathematical biology, 2012 - Springer
Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics
research. Like phylogenetic trees, such networks canonically induce collections of …

A practical algorithm for reconstructing level-1 phylogenetic networks

KT Huber, L Van Iersel, S Kelk… - IEEE/ACM Transactions …, 2010 - ieeexplore.ieee.org
Recently, much attention has been devoted to the construction of phylogenetic networks
which generalize phylogenetic trees in order to accommodate complex evolutionary …

Feature selection using multi-objective evolutionary algorithms: application to cardiac SPECT diagnosis

A Gaspar-Cunha - Advances in Bioinformatics: 4th International Workshop …, 2010 - Springer
An optimization methodology based on the use of Multi-Objective Evolutionary Algorithms
(MOEA) in order to deal with problems of feature selection in data mining was proposed. For …