Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

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

20.12.2006
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 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!
Further information:
http://www.ucsd.edu

Further reports about: Chaisson Evolution InvChecker UCSD microinversion phylogenetic

More articles from Life Sciences:

nachricht Rainbow colors reveal cell history: Uncovering β-cell heterogeneity
22.09.2017 | DFG-Forschungszentrum für Regenerative Therapien TU Dresden

nachricht The pyrenoid is a carbon-fixing liquid droplet
22.09.2017 | Max-Planck-Institut für Biochemie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: The pyrenoid is a carbon-fixing liquid droplet

Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.

A warming planet

Im Focus: Highly precise wiring in the Cerebral Cortex

Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.

The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Rainbow colors reveal cell history: Uncovering β-cell heterogeneity

22.09.2017 | Life Sciences

Penn first in world to treat patient with new radiation technology

22.09.2017 | Medical Engineering

Calculating quietness

22.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>