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 UCSD’s 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 didn’t 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.”
“We’ve only looked for microinversions in 0.1 percent of the genomic sequence from several mammals, and we can already confirm many of today’s ideas about the history of evolution. When similar analyses extend to one percent of the genomes under investigation, we’ll have a 10 fold increase in data. This should shed light on splits between species that have been debated in molecular evolution,” explained Pavel Pevzner, the senior authors on the paper, a computer science and engineering professor at UCSD’s Jacobs School of Engineering, and director of the newly-established Center for Algorithmic and Systems Biology (CASB) at the UCSD Division of Calit2.
“This microinversion detection method could be used for detecting human structural variants once we have the necessary data,” explained Ben Raphael, a professor of computer science at Brown University. Raphael is the second author on this paper and a former postdoctoral researcher at UCSD.
To create InvChecker, the researchers modified an existing software system created at UCSD by Glenn Tesler, in order to make it better at detecting microinversions and differentiating microinversions from other genomic rearrangements. Such false positives are generally not useful in understanding the history of evolution and can introduce error to the reconstruction of phylogenetic trees.
With InvChecker, the researchers analyzed the CFTR region in a collection of mammal species. CFTR is a heavily studied and highly conserved, gene rich area of human chromosome 7 that is home to the cystic fibrosis gene.
“It’s quite a subtle problem to find microinversions. Our goal is to use these tiny inversions to develop a history of species,” said Pevzner.
The researchers also used InvChecker to study the specific differences between humans and chimpanzees. They found that 80 percent of the microinversions between humans and chimps that were proposed last year are, in fact, repeat-induced artifacts and not microinversions. The researchers also uncovered 167 human-chimp microinversions recently missed by scientists using software other than InvChecker.
“This finding doesn’t change the conclusions between humans and chimps, but is does say that the detection of microinversion needs to be done carefully,” said Chaisson. “InvChecker does a more careful job of comparing sequences than previous attempts to find microinversions.”
With InvChecker, you can take the same genomic region from two species sequences, partition them into regions that are unique to one species or common to both (orthologous), and find how the order of these regions relates between the two species.
“We are looking for orthologous sequences in reverse order that are surrounded by elements in forward order. That’s a microinversion,” Chaisson explained.
Microinversions have certain advantages over other evolutionary signals used for studying evolution such as amino acid changes, Chaisson explained. “With microinversions, it’s easy to develop evolutionary relationships between species and difficult to debate whether one species is inverted relative to another species.”
With InvChecker and microinversions, researchers are not limited to comparing species that are evolutionarily close, as is the case when using other genomic features like repetitive sequences and deletions for phylogenetic analysis. The new process can also detect microinversions that are the result of convergent evolution and thus do not play a role in tracking evolution and defining phylogenies.
Once the researchers have the microinversion data, they use it to reconstruct phylogenies using an algorithm that attempts to move “back in time” by iteratively undoing microinversions and bringing the existing species closer to the ancestral mammalian genome.
Daniel Kane | EurekAlert!
Molecular microscopy illuminates molecular motor motion
26.07.2017 | Penn State
New virus discovered in migratory bird in Rio Grande do Sul, Brazil
26.07.2017 | Fundação de Amparo à Pesquisa do Estado de São Paulo
Strong light-matter coupling in these semiconducting tubes may hold the key to electrically pumped lasers
Light-matter quasi-particles can be generated electrically in semiconducting carbon nanotubes. Material scientists and physicists from Heidelberg University...
Fraunhofer IPA has developed a proximity sensor made from silicone and carbon nanotubes (CNT) which detects objects and determines their position. The materials and printing process used mean that the sensor is extremely flexible, economical and can be used for large surfaces. Industry and research partners can use and further develop this innovation straight away.
At first glance, the proximity sensor appears to be nothing special: a thin, elastic layer of silicone onto which black square surfaces are printed, but these...
3-D shape acquisition using water displacement as the shape sensor for the reconstruction of complex objects
A global team of computer scientists and engineers have developed an innovative technique that more completely reconstructs challenging 3D objects. An ancient...
Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.
For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...
What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.
To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...
26.07.2017 | Event News
21.07.2017 | Event News
19.07.2017 | Event News
26.07.2017 | Physics and Astronomy
26.07.2017 | Life Sciences
26.07.2017 | Earth Sciences