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Phylogenomic Study Points to Convergent Evolution in Humans and Elephants

NEW YORK (GenomeWeb News) – An American research team has garnered phylogenomic evidence supporting the notion that genes involved in brain function arose through convergent evolution in the ancestors of humans and elephants.

In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, researchers from Michigan, Washington, DC, and New York compared thousands of gene sequences from more than a dozen vertebrate genomes.

Based on the pattern of silent (synonymous) and amino acid changing (non-synonymous) nucleotide substitutions in these genes, the team concluded that adaptive evolution has acted on similar brain-related genes in the human and elephant lineages — particularly those involved in aerobic energy metabolism.

In some respects such results confirm previous findings in humans, senior author Derek Wildman, a genetics researcher at Wayne State University, told GenomeWeb Daily News. But the findings also reveal how convergent evolution led to similar adaptations in elephants.

Past studies suggest that many genes that contribute to brain function in humans contain footprints of past adaptive evolution. Based on such studies, the researchers suspected that genes involved in brain function might show similar patterns in the elephant, another long-lived, large-brained animal with complex social patterns.

"Because large brains arose convergently in different mammalian lineages, it is feasible to explore whether putative brain-important genes that evolved at accelerated rates during humankind's ancestry also evolved at accelerated rates in non-primate lineages where brain mass increased compared with related lineages with relatively smaller brain mass," Wildman and his co-authors wrote.

To test this, the researchers used data from the National Center for Biotechnology Information RefSeq transcript database to compare roughly 6,000 non-redundant genes from the genomes of 15 sequenced vertebrate species, including representatives from four mammalian lineages — a marsupial, monotreme, bird, and amphibian.

In particular, the researchers were interested in nucleotide substitution patterns consistent with adaptive evolution, which they picked out by assessing the synonymous and non-synonymous nucleotide substitution rates for each gene as well as the ratio of non-synonymous to synonymous changes.

"Theory predicts that the silent changes are less likely to be detrimental than the non-synonymous — amino acid changing — mutations," Wildman said. But, he explained, non-synonymous changes may also produce beneficial changes that are then selected during adaptive evolution.

In general, the team found that the nucleotide substitution rate in the genes tested was relatively low in humans and elephants compared with the other animals. But some human and elephant genes had elevated ratios of non-synonymous to synonymous nucleotide changes, particularly mitochondrial genes and genes involved in processes such aerobic energy metabolism.

The researchers did not see the same pattern in mice, which belong to the same branch of the mammalian tree as humans, or in the hedgehog tenrec — another animal in the same Afrotherian branch of the tree as the elephant, but one with a much smaller brain and shorter life span.

"Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes," the team wrote. "In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage."

On the other hand, genes involved in processes such as immune system function, molecular transduction, and sensory perception seem to have undergone adaptive evolution in several different vertebrate lineages.

Researchers will need to sequence and analyze additional genomes to get a better handle on when the adaptations resembling those in the human lineage occurred in the elephant lineage, Wildman explained.

He and his team are in the process of trying to tease apart how the adaptively evolved genes identified in the current study function in the elephant brain, including when and where they are expressed during development.

Wildman noted that down the road it also will be interesting to learn more about adaptive evolution patterns that have given rise to other large-brained animals, such as whales and dolphins. "It will be interesting to see if the same processes occurred in other animals," he said.