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Duke Team Explores Role of Coding, Non-Coding Changes in Human Evolution

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Changes to non-coding parts of the genome have contributed to key adaptations during human evolution, including neural development, according to a new paper by researchers at Duke University.

By looking at how regions of positive selection correspond to gene functions in six published surveys of non-coding and coding sequences in the human genome, the team found that non-coding and coding changes affect distinct functional gene groups. Whereas adaptations to genes involved in neural functions have largely involved changes to non-coding sequences, those affecting other processes such as immunity, olfaction, and male reproduction have apparently been dominated by coding changes. The research appeared online last night in the Proceedings of the National Academy of Sciences.

"The finding that neural adaptation has occurred mainly via non-coding changes is particularly important in view of the remarkable cognitive innovations in the human lineage," senior author Gregory Wray, a Duke University biology professor and director of the Duke Institute for Genome Sciences and Policy's Center for Evolutionary Genomics, and his colleagues wrote.

As such, they explained, the findings are consistent with the notion that "major phenotypic differences between humans and chimpanzees reflect changes in gene regulation rather than in protein structure."

Wray and his team used PANTHER and Gene Ontology classifications to look at how positive selection patterns relate to gene function in three surveys each of non-coding and coding sequences.

Their results suggest neural development and function — including processes such as neurogenesis, neuron differentiation, and neuron migration — have adapted through changes to non-coding sequences.

On the other hand, the researchers found that adaptations affecting immunity and defense, chemosensory perception, sperm function, and so on typically involved changes to coding sequences.

When the team integrated these findings with information on gene expression patterns using data from the Novartis Gene Expression Atlas, they found that coding changes were also more common in genes with tissue-specific expression.

Nevertheless, genes specifically expressed in neural tissue tended to contain evidence of positive selection in non-coding regions, while genes expressed in male reproductive tissue more often contained signals of positive selection in coding regions.

Together, the researchers explained, the results hint that changes affecting coding and non-coding parts of the human genome may have fueled distinct processes during human adaptation.

Based on such findings, they emphasized that researchers will need to assess both coding and non-coding sequences in order to understand the evolutionary processes that have occurred in the human genome.

"[S]tudying adaptive coding changes alone, which has long been a major focus of research in evolutionary genetics, can yield an incomplete and unbalanced picture of adaptive evolution," the researchers wrote, "which can be significantly extended and enriched by studies of adaptive non-coding changes."

Even so, the team noted, additional research is needed to gain a more refined view of the coding and non-coding changes that have occurred during human adaptation — and to assess the role that similar changes have played during the evolution of other animals.

"A full understanding of which traits adapt mainly via coding changes versus non-coding changes and why must await the maturity of functional genomics," the researchers explained. "In particular, many more functional annotations of non-coding sequences are needed."

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