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. History-Hunting Geneticists Can Still Follow Familiar Trail

Over the eons, random mutations enter the genetic code of all species. By tracking similarities and differences of mtDNA, scientists gain insight about the size of groups and how they moved around the world.
by Staff Writers
Gainesville FL (SPX) Dec 31, 2006
As the world's first explorers branched away from humanity's birthplace in east Africa some 65,000 years ago, distinct mutations accumulated in the DNA of each population, essentially providing a genetic trail for modern researchers to follow. Recently some scientists have raised doubts about this classic genetic system to study ancient migrations of people and to estimate the populations of people or animals as they existed tens of thousands of years ago.

But University of Florida researchers writing this month in an online edition of Science validate the approach, which involves tracking sequences of mitochondrial DNA, also known as mtDNA.

"The study of mtDNA has helped to demonstrate the African origin of our species and the relationship between living humans and the Neanderthals," said Connie Mulligan, an associate professor of anthropology in the College of Liberal Arts and Sciences and an assistant director of the UF Genetics Institute. "MtDNA data have also been used to establish the time and route of major events in human history, such as the expansion of Neolithic farmers into Europe, and the settlement of the New World."

MtDNA has made headlines recently because of initiatives such as the National Genographic Project, a multimillion-dollar endeavor to reconstruct humanity's ancient migrations, and because of well-publicized efforts to track the ancestral roots of Oprah Winfrey and other personalities.

Located within the hundreds of energy-producing mitochondria that lie outside the nucleus of our cells, mtDNA is unlike the DNA inside the nucleus of a cell that contains genes from both of our parents -- in people and animals mtDNA is exclusively passed from mothers to their children.

For humans, this means that all of the mtDNA in our cells are copies of our mothers' mtDNA, which in turn were copies of their mothers' mtDNA. In this way, mtDNA progresses through the ages, springing from what many scientists believe was a common ancestral mother.

But over the eons, random mutations enter the genetic code of all species. By tracking similarities and differences of mtDNA, scientists gain insight about the size of groups and how they moved around the world.

"When you look at ancient migration, you're always asking the question, 'How big was the population, how many were there?'" said Michael Miyamoto, a professor and associate chairman of zoology in UF's College of Liberal Arts and Sciences. "The field has worked from the premise that the more mtDNA variation you saw, the larger the population was that carried that variation, just like there would be a greater diversity of T-shirts or shoes within a larger population than a smaller population."

However, the connection between mtDNA and population size was questioned this year when French scientists analyzed vast groups of gene sequences from more than 3,000 animal species. They speculated that an evolutionary tendency for species to keep helpful genes and sift out detrimental ones, called "natural selection," preferentially affects mitochondrial diversity, making mtDNA less useful for population size estimates.

"From a conservation perspective, when scientists look at census counts of animals and how the population size may be increasing or decreasing, the study of mtDNA tells us about the level of genetic diversity in a population, which is important in making conservation decisions on endangered species," Mulligan said. "If this approach were not credible, it could potentially have a bearing on future policy decisions, as well as affect literally hundreds of previous studies on humans and other mammals."

UF Genetics Institute scientists analyzed publicly available mtDNA datasets of 47 species of mammals -- a subset of the animals that were in the French study -- as well as associated data on protein diversity in the same species. A greater variety of proteins indicates more diverse DNA, because DNA contains a species' blueprints for manufacturing protein -- and the French scientists agreed that protein diversity did correlate with population size.

All that remained for UF researchers to do to reinstate mtDNA diversity as indicative of population size was to determine that protein diversity and mtDNA diversity were correlated.

"The researchers showed a correlation between mitochondrial DNA and genetic variation in a way that has never been done before," said Marc Allard, an associate professor of biology at George Washington University who was not involved in the study. "Population geneticists have used mitochondria for all kinds of work for 20 years, and to think that mtDNA didn't correlate with population size was clearly going against the dogma. This study shows the dogma is safe in mammals and probably in vertebrates, as well."

earlier related report
San Diego CA (SPX) Dec 31 - 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 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.

Related Links
University of Florida
University of California - San Diego
All About Human Beings and How We Got To Be Here

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