ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2016
Multilocus inference of species trees and DNA barcoding.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed.
- The monophyly of Nycteria and Polychromophilus parasites: a missing piece in the evolution of malaria and other Haemosporida.Malaria journal · 2026Article
- UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).Systematic biology · 2025Article
- Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study inEcology and evolution · 2025Article
- Multiple contact zones and karyotypic evolution in a neotropical frog species complex.Scientific reports · 2024Article
- Article
- At a crossroads: Genetic lineages and dispersal routes ofBiodiversity data journal · 2024Article
- Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae.Ecology and evolution · 2023Article
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
- When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships.Molecular ecology resources · 2022Article
- Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization.Evolution; international journal of organic evolution · 2022Article
- Genetic and geographical delineation of zoonotic vector-borne helminths of canids.Scientific reports · 2022Article
- Article
- Recognizing species as a new focus of virus research.PLoS pathogens · 2021Article
- Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae).PloS one · 2021Article
- Article
- Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae).Systematic biology · 2020Article
- Genomic biosurveillance of forest invasive alien enemies: A story written in code.Evolutionary applications · 2020Review
- Article
- The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data.Frontiers in plant science · 2020Article
- PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees.BMC evolutionary biology · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.