Phylogenomics of the carrot genus (Daucus, Apiaceae).

@article{Arbizu2014PhylogenomicsOT,
  title={Phylogenomics of the carrot genus (Daucus, Apiaceae).},
  author={C. Arbizu and Holly Ruess and D. Senalik and P. Simon and D. Spooner},
  journal={American journal of botany},
  year={2014},
  volume={101 10},
  pages={
          1666-85
        }
}
UNLABELLED • PREMISE OF THE STUDY We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species.• METHODS We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs… Expand
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References

SHOWING 1-10 OF 85 REFERENCES
Molecular Phylogeny of Daucus (Apiaceae)
TLDR
Bayesian analyses of individual regions analyzed separately and averaged over multiple trees with *BEAST software provided a phylogeny at variance with the concatenated approach, most notably in firmly imbedding Turgenia latifolia within Daucus. Expand
Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae).
TLDR
Comparing the genetic diversity of wild and cultivated accessions suggested the absence of a genetic bottleneck during carrot domestication, and results suggest an origin of domesticated carrot in Central Asia. Expand
Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?
TLDR
This study confirms and quantifies the utility of using DNA sequences from different parts of the genome in phylogenetic studies to avoid possible bias in the sampling and reveals and summarized the extensive discordance among COSII markers. Expand
Reassessment of Practical Subspecies Identifications of the USDA Daucus carota L. Germplasm Collection: Morphological Data
TLDR
The purpose of this study is to explore morphological support for subspecies within , including the phenetically similar , which is part of the same clade as , with the long-term goal of resolving taxonomic disagreements and developing a practical system to classify variation within this economically important species. Expand
A multi gene sequence-based phylogeny of the Musaceae (banana) family
TLDR
The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae and shows that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Expand
Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives
TLDR
The results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage and other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. Expand
An isozyme-based assessment of the genetic variability within the Daucus carota complex (Apiaceae: Caucalideae)
TLDR
Daucus carota sensu lato is a phenotypically variable Eurasian species complex that has been naturalized and cultivated worldwide and indicates that the recognized subspecies have diverged only slightly from one another with respect to the enzymes surveyed. Expand
Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci.
TLDR
The first multi-locus DNA sequence-based phylogenetic study of the Ambystomatidae is presented, which robustly resolved many deep and relatively shallow clades within Am bystoma and has greater similarity with previous allozyme and mitochondrial sequence- based phylogenetic estimates. Expand
Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species
TLDR
Low copy nuclear Conserved Ortholog Set genes were found to be highly informative in phylogenetic reconstruction of congeneric species, where introns provide a higher proportion of parsimony informative sites in comparison with traditional phylogenetic markers such as ITS and matK. Expand
Amphitropic amphiantarctic disjunctions in Apiaceae subfamily Apioideae
TLDR
It is suggested that the dispersal events of these umbellifer taxa were facilitated by favourable ecological conditions in the Southern Hemisphere (climatic cooling of the late Palaeogene/early Neogene) rather than by increased dispersal opportunities. Expand
...
1
2
3
4
5
...