Mutations That Affect Phenotype

Pardon the awkward title of this post. What I would like to do in this post is revisit something I mentioned in the first part of my review of Science and Human Origins in that post I mentioned a paper by Jianzhi Zhang called “Parallel Functional Changes in the Digestive RNases of Ruminants and Colobines by Divergent Amino Acid Substitutions.” The paper looked at mutations in the pancreatic RnNase of ruminants and colobines and found nine mutations in colobine RNase and five -different- mutations in ruminant RNase. The fact that Zhang found fourteen different mutations that affected pancreatic in much the same way prompted Zhang to come up with an estimate of how many different mutations can affect the function of the Rnase. He concluded that this number was somewhere between 16-44. So, of those 16-44 theoretical mutations 14 had been identified.

I have found a more graphic example to illustrate the point. The picture below illustrates the Melanocortin 1 receptor (MC1R)

(Picture Source)

The picture is self explanatory. The black colored dots are mutations that cause melanism, the green dots are mutations linked to coat color changes in rock pocket mice, the red are mutations that cause red fur or hair, the blue are mutations that cause red hair in humans and possibly melanism in other species. Not shown are the mutations in the -COOH that affect coat color in retrievers and other dogs.

The point is that there are many ways to a new function and to say that unless a given specified pathway is followed evolution can’t happen is clearly nonsense.

Majerus and Mundy (2003) Mammalian melanism: natural selection in black and white. TRENDS in Genetics: 19(11)585-588
Zhang (2003) Parallel Functional Changes in the Digestive RNases of Ruminants and Colobines by Divergent Amino Acid Substitutions. Molecular Biology and Evolution 20(8):1310-1317

Interesting Science News

Still working on my review of Science and Human Origins (yes, I have been somewhat lazy when it comes to blogging) in the meantime enjoy the following items.

Gorilla Genome Sequenced!

The gorilla genome has been sequenced and yields some interesting insights on human evolution. The research is reported in Nature. The article is open access. Here is the abstract:

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In30%of the genome, gorilla is closer tohuman or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing.Wealso compare the western and eastern gorilla species, estimating an average
sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

The Genetics of Stay at Home Vs “Exploratory” Butterflies

Science Daily has a fascinating bit on butterflies called Butterflies That Explore and Colonize New Habitats Are Genetically Different from Cautious Cousins.This extended quote from the press release is fascinating:

In the new study, another gene variant also stood out as an important indicator of butterfly flight ability. New-population females were more often missing a small part of the succinate dehydrogenase gene (Sdhd) and this small deletion was associated with the ability to maintain flight for a greater duration. “The Pgi gene variant seems to be associated with sprinting, and the Sdhd gene variant appears to be associated with endurance,” Marden said. “It’s easy to see why these traits and their associated genes would be found at higher frequencies in new populations. Better flight ability allows certain butterflies to be able to reach and settle new habitat patches.”

Wheat, the paper’s lead author, said, “We already knew about Pgi from previous work in other butterflies and what has been done so far in the Glanville fritillary butterfly. Now with Sdhd we have two genes in the same carbohydrate-metabolism pathway containing alleles of major effect for ecologically important traits.” Marden also commented on the differences in gene expression involving protein dynamics. “Butterflies obtain protein only during larval feeding, whereas the adults rely on nectar, from which they obtain only carbohydrate,” he said. “The timing and level of expenditure of stored proteins is one way to manipulate life history in a species where no more protein will be available to the adult.”

The paper is being published in Molecular Ecology, if someone has access and can send me a copy I would appreciate it. The paper can be found here:

Christopher W. Wheat, Howard W. Fescemyer, J. Kvist, Eva Tas, J. Cristobal Vera, Mikko J. Frilander, Ilkka Hanski, James H. Marden. Functional genomics of life history variation in a butterfly metapopulation. Molecular Ecology, 2011; DOI: 10.1111/j.1365-294X.2011.05062.x

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Orangutan Genetics: Begging for an Article

There are a couple of interesting articles on Orangutan genteics out. The first, published in Nature (and is open acess), announces the sequencing of the Orangutan genome. Results are kind of interesting. From Science Daily (I haven’t had a chance to read the Nature article yet):

However, in a surprising discovery, the researchers found that at least in some ways, the orangutan genome evolved more slowly than the genomes of humans and chimpanzees, which are about 99 percent similar.

“In terms of evolution, the orangutan genome is quite special among great apes in that it has been extraordinarily stable over the past 15 million years,” says senior author Richard K. Wilson, PhD, director of Washington University’s Genome Center, which led the project. “This compares with chimpanzees and humans, both of which have experienced large-scale structural rearrangements of their genome that may have accelerated their evolution.”

King Tutankhamun’s Family and Genetics

Back in February of 2010 I blogged about a research paper on Tutankhamun. In that post I focused on the paleopathological findings of the Hawass et al article and didn’t really mention the genetic research and resulting identification of Tutankhamun’s family. Recently this second aspect of the Hawass et al study have bubbled to the surface.

Ancient DNA From Homo floresiensis: Redux

Extracting DNA from Homo floresiensis has been tried in the past with no luck. Nature News reports on a new attempt to obtain DNA from a Homo floresiensis molar. What struck me is interesting from the story is this bit:

Begging for an article, again…sigh

Can someone send me a copy of the paper below?

New Genes in Drosophila Quickly Become Essential
Sidi Chen, Yong E. Zhang and Manyuan Long

Science 17 December 2010:
Vol. 330 no. 6011 pp. 1682-1685
DOI: 10.1126/science.1196380
http://www.sciencemag.org/content/330/6011/1682.abstract

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Body Mass and Genetics

This is really interesting. It concerns a study in Science Translational Medicine that looked at DNA methylation and body mass. From Science Daily:

The Independent Origins of Blood/Oxygen Transport Mechanisms

This is pretty cool. Science Daily PhysOrg mentions research in PNAS

An extended excerpt from Science Daily PhysOrg: