How did human vision evolve? A new study offers an answer

Molecular biologists at the University of California created the IQ-TREE computer model to trace the evolutionary history of genes related to human vision.
Mrigakshi Dixit
Representational image
Representational image


Human evolution is a complex, slow, and long process that has shaped our bodies in relation to our surroundings. Understanding how organs evolved into what they are today has long been a goal of evolutionary theorists. Among them, there has been some conundrum about how vision evolved.  

This complex evolutionary question had even stumped the legendary Charles Darwin. The stepwise evolution of the eye, according to Darwin, was the most difficult to explain. 

We may have some necessary clues to fill the knowledge gap of eye evolution, thanks to modern technology. 

Identifying vision gene

A team of molecular biologists at the University of California created the IQ-TREE computer model program to trace the evolutionary history of genes related to human vision.

Using this model, they discovered potential evidence of "interdomain horizontal gene transfer," which led to the formation of the eye in vertebrates. The movement of genetic material between different types of organisms is referred to as horizontal gene transfer.

In a Twitter post, study author Matt Daugherty mentioned: "At least one innovation that led to the current structure of vertebrate eyes did not occur from stepwise "tinkering" with genes that exist in other animals, but came from introduction of novel DNA from bacteria by horizontal gene transfer."

This study began from the idea that vertebrates got their eyesight through the transfer of light-sensitive genes from microbes.

The team analyzed over 900 genetic sequences to find a potential human eye gene candidate in other creatures, particularly microbes. The findings identified a promising candidate known as interphotoreceptor retinoid-binding protein or IRBP. This gene, which was originally from bacteria, first appeared in ancient vertebrate-like eyes around 500 million years ago. 

“We demonstrate that IRBP, a highly conserved and essential retinoid shuttling protein, arose from a bacterial gene that was acquired, duplicated, and neo-functionalized coincident with the development of the vertebrate-type eye >500 Mya,” added the research paper.

According to the research paper, this gene is essential for all vertebrate vision. It evolved over time, leading to light sensitivity and, eventually, the development of organs such as eyeballs. Surprisingly, this gene is absent in many invertebrates.

The findings have been reported in the Proceedings of the National Academy of Sciences. 

Study abstract:

The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate-specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that the acquisition of bacterial genes has had on vertebrate evolution.

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