A clear, molecular view of how human color vision evolved

December 18, 2014
eye

Many genetic mutations in visual pigments, spread over millions of years, were required for humans to evolve from a primitive mammal with a dim, shadowy view of the world into a greater ape able to see all the colors in a rainbow.

Now, after more than two decades of painstaking research, scientists have finished a detailed and complete picture of the evolution of human color vision. PLOS Genetics is publishing the final pieces of this picture: The process for how humans switched from ultraviolet (UV) vision to violet vision, or the ability to see blue light.

"We have now traced all of the evolutionary pathways, going back 90 million years, that led to human color vision," says lead author Shozo Yokoyama, a biologist at Emory University. "We've clarified these molecular pathways at the chemical level, the genetic level and the functional level."

Co-authors of the PLOS Genetics paper include Emory biologists Jinyi Xing, Yang Liu and Davide Faggionato; Syracuse University biologist William Starmer; and Ahmet Altun, a chemist and former post-doc at Emory who is now at Fatih University in Istanbul, Turkey.

Yokoyama and various collaborators over the years have teased out secrets of the adaptive evolution of vision in humans and other vertebrates by studying ancestral molecules. The lengthy process involves first estimating and synthesizing ancestral proteins and pigments of a species, then conducting experiments on them. The technique combines microbiology with theoretical computation, biophysics, quantum chemistry and genetic engineering.

Five classes of opsin genes encode visual pigments for dim-light and color vision.

Bits and pieces of the opsin genes change and vision adapts as the environment of a species changes.

Around 90 million years ago, our primitive mammalian ancestors were nocturnal and had UV-sensitive and red-sensitive color, giving them a bi-chromatic view of the world. By around 30 million years ago, our ancestors had evolved four classes of opsin genes, giving them the ability to see the full-color spectrum of visible light, except for UV.

"Gorillas and chimpanzees have human color vision," Yokoyama says. "Or perhaps we should say that humans have gorilla and chimpanzee vision."

For the PLOS Genetics paper, the researchers focused on the seven genetic mutations involved in losing UV vision and achieving the current function of a blue-sensitive pigment. They traced this progression from 90-to-30 million years ago.

The researchers identified 5,040 possible pathways for the amino acid changes required to bring about the genetic changes. "We did experiments for every one of these 5,040 possibilities," Yokoyama says. "We found that of the seven genetic changes required, each of them individually has no effect. It is only when several of the changes combine in a particular order that the evolutionary pathway can be completed."

In other words, just as an animal's external environment drives natural selection, so do changes in the animal's molecular environment.

In previous research, Yokoyama showed how the scabbardfish, which today spends much of its life at depths of 25 to 100 meters, needed just one genetic mutation to switch from UV to blue-light vision. Human ancestors, however, needed seven changes and these changes were spread over millions of years. "The evolution for our ancestors' vision was very slow, compared to this fish, probably because their environment changed much more slowly," Yokoyama says.

About 80 percent of the 5,040 pathways the researchers traced stopped in the middle, because a protein became non-functional. Chemist Ahmet Altun solved the mystery of why the protein got knocked out. It needs water to function, and if one mutation occurs before the other, it blocks the two water channels extending through the vision pigment's membrane.

"The remaining 20 percent of the pathways remained possible pathways, but our ancestors used only one," Yokoyama says. "We identified that path."

In 1990, Yokoyama identified the three specific amino acid changes that led to human ancestors developing a green-sensitive pigment. In 2008, he led an effort to construct the most extensive evolutionary tree for dim-light vision, including animals from eels to humans. At key branches of the tree, Yokoyama's lab engineered ancestral gene functions, in order to connect changes in the living environment to the molecular changes.

The PLOS Genetics paper completes the project for the evolution of human color vision. "We have no more ambiguities, down to the level of the expression of amino acids, for the mechanisms involved in this evolutionary pathway," Yokoyama says.

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15 comments

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Vietvet
4.5 / 5 (8) Dec 19, 2014
Let's see jvk try to fit this into his "model".
Modernmystic
4.5 / 5 (8) Dec 19, 2014
My guess is carrots....don't carrots effect the eyes?

JVK
1 / 5 (6) Dec 19, 2014
Article excerpt:
This observation is consistent with the results of epistatic adaptive evolutionary studies such as antibiotic resistance [2], drug resistance [41], coenzyme evolution [2], [42] and coevolution of two ecotypes [43] in microbial systems as well as the evolution of hormone receptors [7], visual pigments [44] and hemoglobins [45] in vertebrates.


Epistasis is nutrient-dependent and controlled by the metabolism of nutrients so species-specific pheromones that link RNA-directed DNA methylation and RNA-mediated events to the amino acid substitutions that differentiate all cell types in all individuals of all species. "All cell types" includes species-specific cell types in all tissues of all organs of all organ systems in humans as exemplified in my model of biologically-based cause and effect: http://www.ncbi.n...24693353

Vitamin A is probably important to DNA repair and genomic stability.
Uncle Ira
3.8 / 5 (10) Dec 19, 2014
http://www.ncbi.nlm.nih.gov/pubmed/24693353.


That same stinky love potion article again? JVK-Skippy you are shameless. Your stinky love potions is more powerful than Zephir-Skippy's AWT stuffs. They are the answer for every single article ever written about anything.
JVK
1.7 / 5 (6) Dec 19, 2014
When Metabolism and Epigenetics Converge http://www.scienc....summary Conclusion:
The presence of metabolite "niches" within specific chromatin subdomains has been proposed (2) and is conceptually intriguing when placed in parallel with the idea of nuclear subcompartments and transcription "hubs" (16). As connections between epigenetics and metabolism emerge, it may be possible to consider new pharmacological interventions for a variety of pathological conditions.


The link from nutrigenomics to cell type differentiation has since also been detailed in the context of pharmacogenomic profiles that may help others to distinguish between pathological effects of mutations, which perturb protein folding, and beneficial effects of amino acid substitutions on cell type differentiation due to the added stability of DNA in organized genomes. https://www.youtu...G_9EEeeA
JVK
1.7 / 5 (6) Dec 19, 2014
The origin of the language of life
http://phys.org/n...ife.html

Excerpt: "... the genetic code could have had a simple beginning whereby information about protein sequences was stored in the physiochemically complementary mRNA sequences."

My comment: This clearly links the dawn of creation to light-induced amino acid substitutions in plants and animals. From there, it links creation via nutrient-dependent RNA-directed DNA methylation and RNA-mediated events to amino acid substitutions that differentiate all cell types of all individuals in all genera via conserved molecular mechanisms.

This finding is one that could be expected by anyone with enough common sense to realize that all organisms must eat and that none mutate into another species. That's why this finding may not have been anticipated by evolutionary theorists.
Vietvet
5 / 5 (7) Dec 19, 2014
@jvk

"that none mutate into another species."

Thanks. Best laugh I've had all day.
Vietvet
5 / 5 (6) Dec 19, 2014
@jvk

"This clearly links the dawn of creation"

I take this to mean you are referring to Genesis.
Captain Stumpy
4.5 / 5 (8) Dec 20, 2014
may help others to distinguish between pathological effects of mutations, which perturb protein folding, and beneficial effects of amino acid substitutions on cell type differentiation due to the added stability of DNA in organized genomes
so, what you are SPECIFICALLY saying here is that- IN the following experiments
http://www.oeb.ha...oeb.html
http://myxo.css.m...dex.html
there were NO beneficial mutations?

that goes against your own model,jk! your own model http://www.ncbi.n...24693353 makes mutations remember.. I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so now you say all mutations are perturbed...s o YOUR MODEL is perturbed!
YOUR WORDS
NOT MINE
JVK
1 / 5 (5) Dec 20, 2014
I take this to mean you are referring to Genesis.

I'm referring to physical evidence of how protein folding occurs via what is known about chemistry and conserved molecular mechanisms that link amino acid substitutions to cell type differentiation in plants and animals.

Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins http://www.pnas.o...abstract

However, I understand why you might think I was referring to Genesis. You seem to know what it says in Genesis, and what it says can be explained by what is currently known about physics, chemistry, and the conserved molecular mechanisms of RNA-mediated amino acid substitutions and protein folding.

You also seem to believe in the pseudoscientific nonsense of evolutionary theory. Did someone teach you to believe in ridiculous theories, or did you decide to do that rather than learn about biological facts?
JVK
1 / 5 (5) Dec 20, 2014
"that none mutate into another species."

Thanks. Best laugh I've had all day.


What are you laughing about? If you are familiar with what it says about light-induced amino acid substitutions in Genesis, how could you believe that light energy and nutrient energy are not linked via the bio-physically constrained chemistry of protein folding to RNA-mediated cell type differentiation and all extant biodiversity? There are established links between ecological variation and ecological adaptation.

Are you laughing because you believe that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." ? -- http://www.amazon...99661731

If so, serious scientists who understand the basic principles of biology and levels of biological organization will be laughing at you. Most creationists will merely pity you and others who are biologically uninformed.
Uncle Ira
3.9 / 5 (7) Dec 20, 2014
What are you laughing about?


Well I won't speak for him non. But I am laughing about you Cher. You are a funny man.

If you are familiar with what it says about light-induced amino acid substitutions in Genesis,


That was good for another laugh, thanks. So you found the "light-induced amino acid substitutions" in the Genesis, eh? No wonder you are so confused about everything.

Are you laughing because you believe that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." ?


Yeah Skippy we are laughing at stuffs like that and stuffs like this,,,,,,,,,,,,,,,,,,,,,,

Most creationists will merely pity you and others who are biologically uninformed.


That's why you stay so mad all the time. People is laughing at you all the time. But Skippy, that's on you, you are the couyon who keeps giving out things to laugh at.
alfie_null
5 / 5 (4) Dec 21, 2014
You also seem to believe in the pseudoscientific nonsense of evolutionary theory. Did someone teach you to believe in ridiculous theories, or did you decide to do that rather than learn about biological facts?

We listen to what real scientists have to say. A whole lot of pretty smart folks. Vs. you all by your lonely self and your peculiar beliefs.
JVK
1 / 5 (3) Dec 21, 2014
We listen to what real scientists have to say.


You believe the biologically uninformed. Serious scientists do not. That's why your beliefs are based on pseudoscientific nonsense at a time when serious scientists have learned about bio-physical constraints on the chemistry of protein folding that prevent mutations from linking metabolic networks to genetic networks at any level of examination from atoms to ecosystems.

http://www.cell.c...)01497-4 reported as:

DNA Loop-the-Loops
A new full-genome map indicates how DNA is folded within the nuclei of human cells.
http://www.the-sc...e-Loops/

Nutrient-dependent pheromone-controlled feedback loops are linked to chromatin loops across species via conserved molecular mechanisms. The feedback loops link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all species.
JVK
1 / 5 (2) Dec 21, 2014
Vs. you all by your lonely self and your peculiar beliefs.


What kind of science idiot makes such ridiculous claims?

See this book chapter by Brosius: The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function http://cshperspec...abstract

Alternatively, see any other chapter from the same book. Stop claiming that you listen to what real scientists have to say when you don't know who they are.

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