Gene-tree reconciliation with MUL-trees to resolve polyploidy events

GWC Thomas, SH Ather, MW Hahn - Systematic biology, 2017 - academic.oup.com
… Incongruence caused by error in gene tree inference or incomplete lineage sorting (ILS) can
be … The inferred MUL-tree and species network for the baker's yeast data. BY: baker's yeast …

Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae)

J Mccann, TS Jang, J Macas… - Systematic …, 2018 - academic.oup.com
… to the same event), we can infer the age of allopolyploids within the … tree prior with constant
population size was used for the gene trees, while the Yule prior was used for the species tree

Phylogenetics of allopolyploids

B Oxelman, AK Brysting, GR Jones… - Annual Review of …, 2017 - annualreviews.org
… from several species to infer gene and/or species trees or networks. … gene trees, which are
then used as data for species tree inference, or make simultaneous coestimation of gene and …

Genomic histories of polyploidy, diversification, and admixture in a Hawaiian plant radiation

C Lindqvist, C Tomlin, S Rajaraman, J Sebesta… - 2023 - researchsquare.com
… ) and these other apparent high-polyploid taxa are interspersed … same progenitor inferred
301 for the WNA Stachys/Hawaiian mint … the Hawaiian genera and closest 408 North American

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

ND Wagner, L He, E Hörandl - bioRxiv, 2019 - biorxiv.org
… can be used for gene tree and species tree reconstruction. The … We inferred phylogenetic
relationships on concatenated … of the origin on the high polyploid willows remain elusive. Hence…

Inferring Patterns of Hybridization and Polyploidy in the Plant Genus Penstemon (Plantaginaceae)

PD Blischak, CE Thompson, EM Waight, LS Kubatko… - BioRxiv, 2020 - biorxiv.org
… angiosperms that has rapidly radiated across North America. … amplicons, we inferred species
trees and networks for 38 … resampling, the gene tree contributions to the species-level splits …

Allopolyploid origin and diversification of the Hawaiian endemic mints

CM Tomlin, S Rajaraman, JT Sebesta… - Nature …, 2024 - nature.com
… among the Hawaiian mints and their closest North American … these other apparent high-polyploid
taxa are interspersed … the same progenitor inferred for the WNA Stachys/Hawaiian mint …

Autopolyploidy, allopolyploidy, and phylogenetic networks with horizontal arcs

KT Huber, LJ Maher - Bulletin of Mathematical Biology, 2023 - Springer
… In the case of AlloPPnet, a phylogenetic network is inferred using, … tree for PADRE is to try
and construct it as a consensus multiple-labelled tree from a set of multiple-labelled gene trees

[HTML][HTML] Phylogenomic relationships and evolution of polyploid Salix species revealed by RAD sequencing data

ND Wagner, L He, E Hörandl - Frontiers in Plant Science, 2020 - frontiersin.org
… We inferred phylogenetic relationships on concatenated … the necessity of sampling the
gene trees at each locus. This is … on the origin on the high polyploid willows are necessary. …

Revisiting the bicontinental allopolyploid origin of Australasian Lepidium species with amplicon sequencing of 15 nuclear genes

RD Smissen, S Walker, PB Heenan - Plant Systematics and Evolution, 2024 - Springer
… and clade C species are sister to North American species. In … in a group of high polyploid
Lepidium species. It is possible … split information from multi-label gene trees we present has a …