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SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information
We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi‐gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with…
Cryptic species as a window on diversity and conservation.
DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.
An outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy is concluded.
Episodic radiations in the fly tree of life
- B. Wiegmann, Michelle Trautwein, +24 authors D. Yeates
- Biology, MedicineProceedings of the National Academy of Sciences
- 14 March 2011
It is demonstrated that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy and parasitism in the history of fly evolution over 260 million y.
The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification.
Evidence is provided based on 43,137 COI sequences from 12,459 Metazoan species that barcoding gaps based on mean interspecific distances are artificially inflated and that only smallest inter Specific distances correctly reflect that species identification gets more difficult as more species are sampled.
Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly
A higher‐level phylogenetic hypothesis is proposed for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade.
Evolutionary History of the Hymenoptera
Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding
- Danwei Huang, R. Meier, P. Todd, L. Chou
- Biology, MedicineJournal of Molecular Evolution
- 8 February 2008
The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and…
Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
- Emily Hare, Brant Peterson, Venky N. Iyer, R. Meier, M. Eisen
- Biology, MedicinePLoS genetics
- 1 June 2008
It is demonstrated here that regulatory sequences whose binding sites have been almost completely rearranged can still produce identical outputs, and it is concluded that the molecular machinery that connects regulatory sequences to the transcription apparatus is more flexible than previously appreciated.