What is truth: Consensus and discordance in next‐generation phylogenetic analyses of Daucus

  title={What is truth: Consensus and discordance in next‐generation phylogenetic analyses of Daucus},
  author={D. Spooner and H. Ruess and S. Ellison and D. Senalik and P. Simon},
  journal={Journal of Systematics and Evolution},
High‐throughput (next‐generation) DNA sequencing has removed barriers to data quantity and quality, and it has produced phylogenies with high statistical support. Such data are useful to address phylogenetic congruence among individual genes. Concatenated analyses of unlinked genes often produce well‐resolved phylogenetic trees with bootstrap support on major nodes at or approaching 100%, but they have been criticized for providing incorrect phylogenies for various reasons to include a history… Expand
HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets
HybPhaser provides a novel approach to detect and phase hybrids in target capture datasets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal leading to more robust phylogenetic analyses. Expand
Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)
The chromosomal distribution of carrot centromeric repeats (CentDc) was explored by means of fluorescence in situ hybridization (FISH) and detailed karyomorphological analysis in 16 accessions and the presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. Expand
Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk
  • J. Wen, Warren L. Wagner
  • Art
  • 2020
This special issue honors Dr. Vicki Ann Funk (26 November 1947–22 October 2019), who passed away after a battle with an aggressive cancer (Fig. 1). Dr. Funk was a Botanist at the SmithsonianExpand
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
This study showcases that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach. Expand
Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
With the decreasing cost and availability of many newly developed bioinformatics pipelines, next‐generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming hasExpand
Issue Information


Mitochondrial DNA Sequence Phylogeny of Daucus
It is concluded that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies. Expand
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
It is argued that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS), and that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, are essential for progress. Expand
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches
These approaches include whole genome sequencing to target microsatellites, transcriptome sequencing, Exon‐Primed Intron‐Crossing sequencing (EPIC), targeted enrichment (or sequence capture), RAD sequencing (RAD‐Seq), and genome skimming. Expand
Genome-scale approaches to resolving incongruence in molecular phylogenies
The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life. Expand
Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid.
A well-resolved plastid phylogeny of Daucus is produced and the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastID genome is identified. Expand
The gene tree delusion.
It is argued that it is illogical to apply coalescence methods to complete protein-coding sequences and distorted true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescent methods to difficult phylogenetic problems. Expand
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.
Many of S&G's criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is aSpecial case of emerging network models in phylogenomics. Expand
Phylogenomics of the carrot genus (Daucus, Apiaceae).
The utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species is explored and a useful subset of markers and approaches are highlighted for future studies of dominant topologies in Daucus. Expand
Concordance trees, concordance factors, and the exploration of reticulate genealogy
It is argued that a primary concordance tree, a tree built from clades that are true of a plurality of the genome, provides a useful summary of the dominant phylogenetic history for a group of organisms. Expand
Phylogenetic Incongruence: Window into Genome History and Molecular Evolution
The field of systematic biology has been revitalized and transformed during the last few decades by the confluence of phylogenetic thinking with ready access to the tools of molecular biology and a growing awareness that reliance on a single data set may often result in insufficient phylogenetic resolution or misleading inferences. Expand