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Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences.
Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae).
- T. Couvreur, A. Franzke, I. Al‐Shehbaz, F. Bakker, M. Koch, K. Mummenhoff
- BiologyMolecular biology and evolution
The resulting tree, the largest in number of genera and markers sampled to date and covering the whole family in a representative way, provides important insights into the evolution of the family on a broad scale.
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
Results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
Chloroplast Phylogeny of Asplenioid Ferns based on rbcL and trnL-F Spacer Sequences (Polypodiidae, Aspleniaceae) and its Implications for Biogeography
A phylogenetic framework from which the historical biogeography of asplenioid ferns can be inferred for Europe and North America is presented, showing a separation of the deeper branches into tropical and temperate clades.
How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens
Results from this study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions (<200–300 bp) in order to maximise outcomes.
Origin and diversification of the Greater Cape flora: ancient species repository, hot-bed of recent radiation, or both?
Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens
It is shown that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling.
Positive selection in phytotoxic protein-encoding genes of Botrytis species.
DNA Damage in Plant Herbarium Tissue
This study quantitatively assess post-mortem DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA and suggests that reliable sequence data can be obtained from her barium specimens.
DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods
- R. van Velzen, Emanuel Weitschek, G. Felici, F. Bakker
- Biology, Computer SciencePLoS ONE
- 17 January 2012
Six methods in their ability to correctly identify recently diverged species with DNA barcodes are compared: neighbor joining and parsimony, nearest neighbor and BLAST, and the diagnostic methods DNA-BAR, and BLOG, indicating that the diagnostic method BLOG is a consistently better method overall.