Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives [PDF]
PeerJ, 2015 Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently.
Susan R. Strickler +6 more
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Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae) [PDF]
Frontiers in Plant Science, 2022 The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when ...
Rebeca Hernández-Gutiérrez +8 more
doaj +2 more sources
How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example [PDF]
Frontiers in Plant Science, 2022 A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading ...
Martha Kandziora +5 more
doaj +2 more sources
Fine-scale phylogenetic discordance across the house mouse genome. [PDF]
PLoS Genetics, 2009 Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified.
Michael A White +4 more
doaj +4 more sources
Phylogenomic Analyses Reveal Species Relationships and Phylogenetic Incongruence with New Member Detected in Allium Subgenus Cyathophora [PDF]
PlantsSpecies characterized by undetermined clade affiliations, limited research coverage, and deficient systematic investigation serve as enigmatic entities in plant and animal taxonomy, yet hold critical significance for exploring phylogenetic relationships ...
Kun Chen +6 more
doaj +2 more sources
Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts [PDF]
BMC Plant BiologyPhylogenomic data enriched with informative loci have significantly improved phylogenetic resolution and facilitated the elucidation of evolutionary mechanisms underlying phylogenetic discordance. Species of the East Asian lineage (EAL) within the Allium
Rui-Yu Cheng +7 more
doaj +2 more sources
Insights into the plastome evolution and phylogenetic relationships of Lepidium (Brassicaceae) [PDF]
BMC Plant BiologyBackground Lepidium represents one of the most species-rich genera in the Brassicaceae, encompassing numerous taxa with excellent medicinal value. Although the plastome architecture of Brassicaceae has been extensively characterized, its evolutionary ...
Ting Ren +4 more
doaj +2 more sources
The Phylogenomic Framework and Infrageneric Classification of Temperate Asian Caraganeae (Leguminosae, Papilionoideae) [PDF]
Ecology and EvolutionThe legume tribe Caraganeae, consisting of the genera Caragana, Calophaca, and Halimodendron, is a mid‐sized, shrubby clade mainly found in temperate Central and Eastern Asia. Within this tribe, Caragana is the largest genus comprising 63–74 species, and
Na Wang +6 more
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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae) [PDF]
PeerJ, 2020 Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single
Tian-Wen Xiao +5 more
doaj +2 more sources
Frontiers in Plant Science, 2022 Disentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and polyploidy.
Phen Garrett +9 more
doaj +1 more source