ReviewApplications in plant sciences2018
Practical considerations for plant phylogenomics.
Review in Applications in plant sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
83 citing papers in PubMed.
- Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ecology and evolution · 2026Article
- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
- Cloning and Expression Studies of Osmotin-Like Protein Gene from Solanum nigrum in Escherichia coli.Molecular biotechnology · 2026Article
- The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization.Systematic biology · 2026Article
- Comparative and phylogenetic analyses based on the complete chloroplast genomes of Limonium (Plumbaginaceae) species.BMC plant biology · 2025Article
- Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae.Scientific reports · 2025Article
- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
- Homoploid hybrid speciation and recurrent hybridization along the northwestern Iberian mountain chains.Annals of botany · 2025Article
- Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics.BMC biology · 2025Article
- Comparative and phylogenetic analysis of complete chloroplast genomes ofFrontiers in plant science · 2025Article
- Plant pangenomes for crop improvement, biodiversity and evolution.Nature reviews. Genetics · 2024Review
- Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.Systematic biology · 2024Article
- Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae).Annals of botany · 2024Article
- Historical biogeography and evolutionary diversification ofPlant diversity · 2024Article
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- Complete Chloroplast Genomes ofCurrent genomics · 2023Article
- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
- Retrieval of long DNA reads from herbarium specimens.AoB PLANTS · 2023Review
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project-dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-and-coming technologies that may help propel the field even further.
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