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Interdisciplinary Research Extends Reach of Genomics, Scientists Say

NEW YORK (GenomeWeb News) – Two new papers in Science are highlighting the importance of interdisciplinary research for understanding everything from genotype and phenotype to community and ecosystem biology.
The first, from researchers at Northern Arizona University, West Virginia University, and the University of Tennessee, deals specifically with ecosystem genetics — the way genomes in a community interact. It argues that ecology and genomics should be integrated so that researchers can understand communities and ecosystems based on genetic and genomic information.
“A genomics perspective can further add to our understanding of community structure and ecosystem processes by elucidating the specific genes, alleles, and epigenetic mechanisms that underlie community heritability and ecosystem phenotypes,” lead author Thomas Whitham, a population and community ecologist and ecological geneticist at Northern Arizona University, and his colleagues wrote. “[Q]uantifying the genetic covariance among species is key to understanding the evolution of communities and ecosystems.”
In communities and ecosystems where hundreds or thousands of species interact, relationships between these species can produce a selection pressure on one or more of the species involved. That means genomic studies in the lab likely won’t completely explain real-world genomes. It also means that communities and ecosystems can have heritable properties.
Even so, some species are more influential than others, Whitham told GenomeWeb Daily News. These so-called “foundation species” have the most profound and widespread downstream effects on other species. “You don’t need to do the genetics of everything because there are a few key drivers in every ecosystem in the world,” Whitham said.
For example, he noted, poplar trees are a foundation species that influence the genetics of everything from associated birds to soil microbes that help cycle nutrients. In the case of poplar, a model organism, genetic information is already available.
Not all foundation species happen to be model organisms, though, Whitham said. Consequently, the authors call for more genetic and genomic investigations of non-model foundation species to facilitate genetic community and ecosystem research. “I think this argues for a whole new suite of model organisms that are drivers in their ecosystems,” he said.
Because individual species can dramatically influence other species in their environments, Whitham said, it is important to consider the potential ecosystem and community consequences of introducing new species to an environment.
Although it had a different focus, a second Science paper underscored the importance of interdisciplinary research. Duke University biologists Philip Benfey and Thomas Mitchell-Olds described the challenges associated with translating genotype to phenotype. Doing this successfully, Benfey told GWDN, will likely require collaboration between two fields that have tended to remain separated: systems biology and population genetics/evolutionary biology.
That’s because, unlike the old view of linear pathways, most genes seem to function in networks. And, Benfey and Mitchell-Olds argue, researchers need to take these networks into account when trying to relate genotype to phenotype.
Systems biology tools and approaches are one way to overlay several types of information in order to understand phenotypic effects within these networks. For instance, Benfey said, geneticists can get a completely different level of information by looking at complete genome sequences than they can from looking at specific SNPs.
In addition, Benfey noted, different types of information — at different levels — will be particularly salient and informative depending on the question being asked. For example, Benfey and Mitchell-Olds noted, “[c]urrent methods rarely provide genome-wide analyses at the level of individual cell types or tissues, thus diluting or even losing critical information.”
And as researchers move from cells and tissues to individuals, populations, and ecosystems, the complexity increases even further, necessitating an integrative approach towards genomics and other fields of biology. “This is the challenge of biology,” Benfey said. “The challenge, the beauty, and the horror of biology.”

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