Wednesday, December 20, 2006
History-hunting geneticists can still follow familiar trail
Mitochondrial DNA* remains useful for unlocking population secrets:
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 (see below) 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."
Source: University of Florida PR Tuesday, December 19, 2006.
Based on the following two papers from the journal Science:
 Comment on "Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals"
Connie J. Mulligan, Andrew Kitchen, Michael M. Miyamoto
Science 1 December 2006:
Vol. 314. no. 5804, p. 1390
Bazin et al. (Reports, 28 April, 2006, p. 570) found no relationship between mitochondrial DNA (mtDNA) diversity and population size when comparing across large groups of animals. We show empirically that species with smaller populations, as represented by eutherian mammals, exhibit a positive correlation between mtDNA and allozyme variation, suggesting that mtDNA diversity may correlate with population size in these animals.
 Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals
Eric Bazin, Sylvain Glemin, Nicolas Galtier
Science 28 April 2006
Vol. 312. no. 5773, pp. 570 - 572
Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering approximately 3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species, or in small than in large organisms. Nuclear loci, in contrast, fit these intuitive expectations. The unexpected mitochondrial diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies.
*Mitochondrial DNA (mtDNA) is DNA that is located in mitochondria. This is in contrast to most DNA of eukaryotic organisms, which is found in the nucleus. Nuclear and mtDNA are thought to be of separate evolutionary origin, with the mtDNA being derived from bacteria that were engulfed by early precursors of eukaryotic cells. Thus in cells in current organisms, the vast majority of proteins found in the mitochondria (approx 1500 in mammals) are encoded by nuclear DNA: some, if not most, are thought to have been originally of bacterial origin and have since been transferred to the nucleus during evolution. In mammals, 100% of the mtDNA contribution to a zygote is inherited from the mother and this is true for most, but not all, organisms. Currently, human mtDNA is present at 100-10,000 copies per cell, with each circular molecule consisting of 16,569 base pairs with 37 genes, 13 proteins (polypeptides), 22 transfer RNA (tRNAs) and two ribosomal RNAs (rRNAs). (More)
** Connie Mulligan - Research Interests:
Our lab analyzes molecular genetic variation in order to reconstruct the evolutionary history and relationships of human populations and human pathogens. Specifically, we are interested in 1) biocultural evolution of populations in the Horn of Africa and the Arabian peninsula, 2) processes of colonization and migration as revealed in East Asia and the New World, 3) identification of genetic variants involved in complex diseases using alcohol dependence as a model system, and 4) use of ancient DNA to reconstruct past genetic diversity and evolutionary history. We assay genetic variants in the mitochondrial genome, the sex chromosomes, and the autosomes in order to provide the most complete and accurate representation of human evolution. For disease studies, we focus on candidate genes and for ancient DNA studies, we assay high copy number genes or genomes, such as mitochondrial DNA. We study populations from around the world with an emphasis on Horn of Africa/Arabian, New World, and East Asian groups. Some of the current projects in the lab include: Colonization and Migration, Disease, Ancient DNA. (More)
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