The Nuances In Evolution

Published in Lab Times 07-2013.

Apes Faces

Have you ever wondered why chimpanzees, which share about 98% of our genetic material, are strikingly primitive in development and behavior? Researchers led by Tomas Marques-Bonet look beyond their genes for the answers. Here’s the gist of their discoveries…

Last year, a video of 18-month Tansy Aspinall playing with her dad’s pet gorilla went viral on YouTube. Dad Damian, a gorilla conservationist, had willingly left his daughter with the gorilla. Through his daring gesture, Damian wished to flaunt the tenderness and parenting skills of his favorite primate.

If you watched Ape Genius on the National Geographic, you sure would be fascinated by the remarkable problem-solving abilities of chimps. Not only are they very quick learners and need little training to perform complex tasks, but they can also team up with humans, as if they were peer, in group activities. They live in small societies, they can use tools, communicate with signs and they can empathize and deceive, all very much like us. Or wait, almost.

Chimps, gorillas, bonobos and orangutans are grouped into hominids or in other words, great apes that fall into the same family as humans. The earliest hominids are thought to have evolved from the more primitive gibbons some 15 million years ago. The gorilla and the chimp diverged 10 million years later while the modern human (Homo sapiens sapiens) appeared only 400,000 to 250,000 years ago. Despite the long and eventful evolutionary periods that interspersed great apes and human speciation, it is surprising that a massive 98% of genetic material has remained unchanged. But how does a mere 2% difference account for all the developmental and behavioral traits that are unique to humans?

Evolutionary biologists have been trying to understand what makes humans distinct from our closest ancestors. Aided by high-throughput assays that permit genome-wide studies, Tomas Marques-Bonet, a professor at the Pompeu Fabra University (UPF), Barcelona, Spain, has uncovered epigenetic differences in the genomes of great apes that are a major cause for divergence of man. The Comparative Genomics lab led by Tomas has recently published their findings in PLoS Genetics (PLoS Genetics vol.9(9):e1003763).

Here’s where to look

The Bonet lab has been probing into the genomic diversity of the apes and comparing it with our own. The basis of their research is that the enormous phenotypic differences in humans and chimps cannot be explained merely by DNA sequence. It is more likely that elements regulating gene expression, the so-called epigenetic factors, underlie such differences.

“How and when did we become human?”, taunted Tomas during his postdoctoral years at UPF and later, in the lab of Evan Eichler in Seattle, USA. “Back then, we ascribed copy number variations (CNVs) and chromosomal rearrangements to the origin of separation between humans and chimpanzees”, he recalls. CNVs such as gene duplications are more dramatic than single base mutations and are thus, a major contributor to species diversity. The duplicated gene allows for higher divergence as it is free from selection pressures, unlike the original copy, and can mutate to acquire novel functions and in some instances, alter disease susceptibilities. “We used a whole-genome shotgun sequencing approach and found that unlike single base pair mutations, the gorilla and chimpanzee genome have several instances of gene duplications”, he elaborates his work (Nature 457:877-881). They found that the duplication events roughly correlated with the positive pressures in the environment. For example, the chimps and humans are enriched in events comprising neuronal activity, muscle contraction and signal transduction genes. These events are thought to have coincided with the use of stone tools at the beginning of the Stone Age and concurred with the development of the neocortex. Similarly, certain adaptability genes viz. the gene coding for amylase, an enzyme that digests starch, underwent copy number expansions in humans but not in chimps allowing local populations to adapt to high starch diets.

“Though there seemed to be a genomic burst of duplication activity during primate evolution, I was convinced that the behavioral and phenotypic traits that stand out in man are not simply the result of changes in DNA. I thought we should look beyond the surface. I felt it was important to look at factors that regulate gene expression – those that turn on or off genes and those that keep a check on the amount of product – and determine whether and how they exert differential effects in apes versus man”, Tomas reasons as he points at epigenetic modifiers on promoters as potential causes for evolutionary divergence.

Epigenetics chip in

Though the Bonet lab is still very new, the members have been making remarkable progress in resolving the diversity between great apes and man. In their latest paper (PLoS Genetics vol.9(9):e1003763), the team employed array-based methylation assays to identify genome-wide methylation profiles in human and primate samples. “My most favorite moment of this paper was when we actually got the raw data to analyze. Though methylation chips have been used extensively to probe human samples, we used it here for the first time to explore great apes and we were initially uncertain if the technology would even work for this purpose”, Tomas discusses the exciting moment.

It took over two years of collecting primate blood samples from zoos and sanctuaries before the group could even begin their analyses. Using chip technology, they compared methylation profiles of CpG islands, which are stretches of cytosine and guanine nucleotides upstream of gene promoters.  Hypermethylation of the cytosine in CpG islands normally silences gene transcription while hypomethylation has the opposite effect. Such alterations in CpG methylation thus constitute epigenetic means of gene regulation. “While promoters themselves are conserved in their epigenetic signatures in man and other primates, the intergenic regions where the CpGs are found are not”, explains Irene, a graduate student in the lab and the first author of the paper. Detailed profiling of methylation patterns at these sites revealed that methylation at about 10% of the CpGs tested is significantly different between man and chimpanzee, estimating about 2500 genes that may show at least some differences. This number far exceeds that affected by CNVs. As Tomas explains, “the significance of the study is actually in the fact that scores of genes whose upstream methylation profiles vary among the species tested are perfectly conserved in their amino acid sequences”. In other words, if we went by just the gene or protein sequences, we would miss out on the strikingly different gene regulatory patterns which are potentially a major cause for divergence.

The language of evolution

“It was hard but not impossible to tease out normal variations in the genome from real differences that underlie species diversity”. With rigorous controls for differences in blood cell type among others, the Bonet lab identified 171 genes in humans with unique methylation patterns. The best part of their results was trying to figure out what these changes mean. “We do not have access to expression data, so it is very hard to be able to interpret these changes at the phenotypic level”, Tomas remarks with frustration. Nevertheless, using gene ontology assays they uncovered that the 171 genes were rather enriched for human-specific traits. “Genes involved in the regulation of blood pressure and the development of the semicircular canal of the inner ear have distinct CpG methylation patterns in humans. Indeed, a better circulatory physiology and the need for maintaining balance evolved to support upright locomotion unique to man”, the Spanish scientist exclaims.

One can only guess what these epigenetic changes mean – species divergence – but it may take a long while before we can translate these differences to specific phenotypes. Their research opens ample prospects for further studies as Tomas points out, “it may be worthwhile to try to better understand why selected genes are differentially methylated during evolution and what may be the underlying mechanisms”.

Wild imaginations

Towards the end of the conversation, Tomas expresses his concerns as a naturalist. “The chimps and great apes are nature’s best tools for this kind of research. It is unfortunate that today, they are among the endangered. We are bound to conserve them not just because they are beautiful creatures but also because they are the only means to understand our own genome and they alone offer the best explanations to our disease susceptibilities.” He hopes to someday be able to make a lab trip to Africa to watch these rare species in their natural habitat.

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