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Software, evolution and micro-inversions -- improving the building of phylogenetic trees

Biologists will be able to reconstruct the process of evolution, determine relationships between species and build phylogenetic trees with greater accuracy thanks to a new method for identifying microinversions, which are extremely short strings of inverted nucleotides.

This new work from researchers at UC San Diego and Brown University will appear in the online version of PNAS on December 18, 2006.

Microinversions usually tens to thousands of base pairs in length can only be detected if you have the exact nucleotide sequence of the same genomic region for all the species you are considering. Many recent studies have pointed to microinversions as large sources of genetic diversity that have not previously been characterized, and the new research from UCSD provides a more careful and accurate approach to identifying microinversions.

As more fine-grained genomic data becomes available, microinversions will be increasingly important in understanding genetic diversity both between and within species, said Mark Chaisson, the first author on the paper and a Bioinformatics Ph.D. student from UCSDs Jacobs School of Engineering.

This method might be able to provide evidence for the entire mammalian phylogeny, such as the presence of an afrotheria clade, he said.

Using data from their microinversion detection technique an open-source software system called InvChecker the researchers reconstructed the phylogenetic tree for 15 mammals. This work largely confirmed the existing phylogenetic tree that connects these mammals.

Three years ago, we didnt know microinversions existed, explained Pevzner. When they were discovered, there was a lot of skepticism. In the last year, scientists have discovered just how common they are in evolution even in variation between humans, which is why they are such a hot topic today.

Weve only looked for microinversions in 0.1 percent of the genomic sequence from several mammals, and we ca
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Contact: Daniel Kane
dbkane@ucsd.edu
858-534-3262
University of California - San Diego
18-Dec-2006


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