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Fishing for the Origins of Genome Complexity
December 16, 2005Biologists at Georgia Tech have provided scientific support for a controversial hypothesis that has divided the fields of evolutionary genomics and evolutionary developmental biology, popularly known as evo devo, for two years. Appearing in the December 2005 issue of Trends in Genetics, researchers find that the size and complexity of a species' genome is not an evolutionary adaptation per se, but can result as simply a consequence of a reduction in a species' effective population size.
"As a general rule, more complex organisms, like humans, have larger genomes than less complex ones," said J. Todd Streelman, assistant professor in the School of Biology at the Georgia Institute of Technology and co-author of the study. "You might think this means that animals with the largest genomes are the most complex - and for the most part that would be right. But it's not always true. There are some species of frogs and some amoeba that have much larger genomes than humans."
To help explain this paradox, a pair of scientists from Indiana University and the University of Oregon published a hotly-contested hypothesis in 2003. It said that most of the mutations that arise in organisms are not advantageous and that the smaller a species effective population size (the number of individuals who contribute genes to the next generation), the larger the genome will be.
"We agreed with some of the criticisms of the hypothesis - that one had to remove the effects of confounding factors like body size and developmental rate," said Streelman. "We were able to remove the effects of these confounding factors and test whether genome size is adaptive."
Their test consisted of analyzing data from 1,043 species of fresh and saltwater ray-finned fish. Previous data on genetic variability had established that freshwater species have a smaller effective population size than their marine counterparts. If the hypothesis was correct, the genome size of these freshwater fish would be larger than that of the saltwater dwellers. It was.
Then they matched the data with estimates of heterozygosity, a measure of the genetic variation of a population. Again they found that species with a smaller effective population had larger genomes.
"We see a very strong negative linear relationship between genome size and the effective population size," said Soojin Yi, assistant professor in the School of Biology and lead author of the study. "This observation tells us that the mutations that increase the genome tend to be slightly deleterious, because population genetic theories predict such a relationship."
"The interesting thing here is that biological complexity may passively evolve," said Yi. "We show that at the origins, it's not adaptive mutations, but slightly bad ones that make the genome larger. But if you have a large genome, there is more genetic material to play with to make something useful. At first, maybe these mutations aren't so good for your genome, but as they accumulate and conditions change through evolution, they could become more complex and more beneficial."
Georgia Institute of Technology
"We agreed with some of the criticisms of the hypothesis - that one had to remove the effects of confounding factors like body size and developmental rate," said Streelman. "We were able to remove the effects of these confounding factors and test whether genome size is adaptive."
Their test consisted of analyzing data from 1,043 species of fresh and saltwater ray-finned fish. Previous data on genetic variability had established that freshwater species have a smaller effective population size than their marine counterparts. If the hypothesis was correct, the genome size of these freshwater fish would be larger than that of the saltwater dwellers. It was.
Then they matched the data with estimates of heterozygosity, a measure of the genetic variation of a population. Again they found that species with a smaller effective population had larger genomes.
"We see a very strong negative linear relationship between genome size and the effective population size," said Soojin Yi, assistant professor in the School of Biology and lead author of the study. "This observation tells us that the mutations that increase the genome tend to be slightly deleterious, because population genetic theories predict such a relationship."
"The interesting thing here is that biological complexity may passively evolve," said Yi. "We show that at the origins, it's not adaptive mutations, but slightly bad ones that make the genome larger. But if you have a large genome, there is more genetic material to play with to make something useful. At first, maybe these mutations aren't so good for your genome, but as they accumulate and conditions change through evolution, they could become more complex and more beneficial."
Georgia Institute of Technology
Genome Current Events and Genome News RSSTime of day matters to thirsty trees, U of T researcher discovers
The time of day matters to forest trees dealing with drought, according to a new paper produced by a research team led by Professor Malcolm Campbell, University of Toronto Scarborough's vice-principal for research and colleagues in the department of cell and systems biology at the St. George campus.
Genetic analysis helps dissect molecular basis of cardiovascular disease
Using highly precise measurements of plasma lipoprotein concentrations determined by nuclear magnetic resonance spectroscopy (NMR), researchers led by Daniel Chasman at Brigham and Women's Hospital and Harvard Medical School in Boston, MA, the Framingham Heart Study in Framingham, and the PROCARDIS consortium in Stockholm, Sweden and Oxford, England performed genetic association analysis across the whole genome among 17,296 women of European ancestry from the Women's Genome Health Study.
Gene mismatch influences success of bone marrow transplants
A commonly inherited gene deletion can increase the likelihood of immune complications following bone marrow transplantation, an international team of researchers reports in the November 22 advance online issue of Nature Genetics.
Scientists at UA, collaborating institutions decode maize genome
Scientists from the University of Arizona led by Arizona Genomics Institute director Rod A. Wing and from collaborating institutions have deciphered the complete genetic code of the maize plant for the first time.
Ancestry attracts, but love is blind
People preferentially marry those with similar ancestry, but their decisions are not necessarily based on hair, eye or skin colour.
WPI Researchers Take Aim at Hard-to-Treat Fungal Infections
A team of researchers at the Worcester Polytechnic Institute (WPI) Life Sciences and Bioengineering Center at Gateway Park has developed a new model system to study fungal infections.
Technique finds gene regulatory sites without knowledge of regulators
A new statistical technique developed by researchers at the University of Illinois allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors.
Causative gene of a rare disorder discovered by sequencing only protein-coding regions of genome
For the first time, scientists have successfully used a method called exome sequencing to quickly discover a previously unknown gene responsible for a mendelian disorder.
New research into the mechanisms of gene regulation
A team led by Penn State's Ross Hardison, T. Ming Chu Professor of Biochemistry and Molecular Biology, has taken a large step toward unraveling how regulatory proteins control the production of gene products during development and growth.
Maize cell wall genes identified, giving boost to biofuel research
Purdue University scientists have helped identify and group the genes thought to be responsible for cell wall development in maize, an effort that expands their ability to discover ways to produce the biomass best suited for biofuels production.
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