ArticlePloS one2013
Networks in a large-scale phylogenetic analysis: reconstructing evolutionary history of Asparagales (Lilianae) based on four plastid genes.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 83 citations in OpenAlex.
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- The origin and diversification of Amaryllidaceae: A phylogenetic and biogeographic analysis.American journal of botany · 2025Article
- Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data.BMC plant biology · 2025Article
- The Agavoideae: an emergent model clade for CAM evolutionary biology.Annals of botany · 2023Review
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- Time-calibrated phylogenies reveal mediterranean and pre-mediterranean origin of the thermophilous vegetation of the Canary Islands.Annals of botany · 2023Article
- Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics.Annals of botany · 2023Article
- A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences.Frontiers in plant science · 2023Article
- Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships ofFrontiers in plant science · 2022Article
- Telomeric DNA sequences in beetle taxa vary with species richness.Scientific reports · 2021Article
- Phylogeny and biogeography ofPlant diversity · 2021Article
- Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae).Scientific reports · 2021Article
- The complete plastome of the South African species,Mitochondrial DNA. Part B, Resources · 2021Article
- Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of thePeerJ · 2021Article
- Divide to Conquer: Evolutionary History of Allioideae Tribes (Amaryllidaceae) Is Linked to Distinct Trends of Karyotype Evolution.Frontiers in plant science · 2020Article
- The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data.Frontiers in plant science · 2020Article
- Article
- Evidence of mitochondrial DNA in the chloroplast genome of Convallaria keiskei and its subsequent evolution in the Asparagales.Scientific reports · 2019Article
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.
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