Featured Research

from universities, journals, and other organizations

Software, Evolution And Micro-inversions: Improving The Building Of Phylogenetic Trees

Date:
December 20, 2006
Source:
University of California - San Diego
Summary:
Researchers will reconstruct the process of evolution, determine relationships between species and build phylogenetic trees with greater accuracy thanks to new method for identifying extremely short strings of inverted nucleotides called "micro-inversions." This new work from researchers at UC-San Diego and Brown University will appear in the online version of PNAS on Dec. 18, 2006.

The character matrix for 67 microinversions in 15 species (Upper) and the matrix after performing the first 49 good inversions (Lower). Each column represents an orthologous inversion locus. Red and green cells represent inversion loci in opposite orientation, and gray cells correspond to ? signs (unknown orientation). Columns with a single green cell are inversions unique to a species. The number of inversions performed on each species is shown to the left of Lower.
Credit: Image courtesy of University of California - San Diego

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.

Related Articles


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.


Story Source:

The above story is based on materials provided by University of California - San Diego. Note: Materials may be edited for content and length.


Cite This Page:

University of California - San Diego. "Software, Evolution And Micro-inversions: Improving The Building Of Phylogenetic Trees." ScienceDaily. ScienceDaily, 20 December 2006. <www.sciencedaily.com/releases/2006/12/061219095514.htm>.
University of California - San Diego. (2006, December 20). Software, Evolution And Micro-inversions: Improving The Building Of Phylogenetic Trees. ScienceDaily. Retrieved December 17, 2014 from www.sciencedaily.com/releases/2006/12/061219095514.htm
University of California - San Diego. "Software, Evolution And Micro-inversions: Improving The Building Of Phylogenetic Trees." ScienceDaily. www.sciencedaily.com/releases/2006/12/061219095514.htm (accessed December 17, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Wednesday, December 17, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

When You Lose Weight, This Is Where The Fat Goes

When You Lose Weight, This Is Where The Fat Goes

Newsy (Dec. 17, 2014) Can fat disappear into thin air? New research finds that during weight loss, over 80 percent of a person's fat molecules escape through the lungs. Video provided by Newsy
Powered by NewsLook.com
The Hottest Food Trends for 2015

The Hottest Food Trends for 2015

Buzz60 (Dec. 17, 2014) Urbanspoon predicts whicg food trends will dominate the culinary scene in 2015. Mara Montalbano (@maramontalbano) has the story. Video provided by Buzz60
Powered by NewsLook.com
Rover Finds More Clues About Possible Life On Mars

Rover Finds More Clues About Possible Life On Mars

Newsy (Dec. 17, 2014) NASA's Curiosity rover detected methane on Mars and organic compounds on the surface, but it doesn't quite prove there was life ... yet. Video provided by Newsy
Powered by NewsLook.com
Ivory Trade Boom Swamps Law Efforts

Ivory Trade Boom Swamps Law Efforts

Reuters - Business Video Online (Dec. 17, 2014) Demand for ivory has claimed the lives of tens of thousands of African elephants and now a conservation report says the illegal trade is overwhelming efforts to enforce the law. Amy Pollock reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins