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Losing DNA to become human: bigger brains, smoother penises

We now have a wealth of information in the areas of human genomics and genetics, and we know a bit about some regions of DNA or genes that were subjected to accelerated, recent evolution in the human lineage, however, we still don’t know much about the genotypic basis of many human-specific anatomical, physiological, and behavioral traits. In other words, we do not know precisely what bits of DNA make us human.  A fascinating article was just published by a multidisciplinary team of geneticists and computational biologists, led by David Kingsley of Stanford University in the highly prestigious journal Nature, describing a comparison of chimpanzee and human genomes, that reveled >500 regions of DNA that were lost in humans, but are present in chimpanzees and highly conserved on other primates and other mammals, such as mice.  As usual, simplistically we tend to focus on gains, so we think that we must have some additional DNA, or some radically different DNA sequences that differentiate us from other animals. But sometimes, less is more. It appears that missing DNA sequences can help explain what makes us humans.

There were over 500 regions of DNA missing in our genome that are highly conserved in chimpanzees, ranging in size from tens of kilobases to just a few bases, the average being ~2000 base pairs.  The missing DNA bits seem to be mostly located outside of the coding regions of genes (those regions that direct the production of RNA or proteins), but are preferentially located in regulatory regions, in other words, regions of DNA that turn genes on or off, or that direct their expression in specific tissues, or at specific times during development. This is not surprising, given that small changes in regulatory regions are likely to result in more massive phenotypic changes than simple mutations in genes that may change just one amino acid out of an entire protein.  The relatively new branch of evolutionary developmental biology, or Evo-Devo, for short, is hot in pursuit of the keys to what makes us humans, mice, mice, and flies, flies.


One of the regions that called the scientists’ attention was in the regulatory region of the androgen receptor, the protein that interacts with the male hormone testosterone, and mediates its effects. They studied the effects of the chimpanzee and mouse DNA region that is missing in our genome, by introducing these “missing” sequences into transgenic mice and following their expression in these engineered mouse embryos. This DNA region regulating androgen receptor expression determined that the androgen receptor was expressed in vibrissae, the sensory whiskers that all of us recognize in our dogs and cats, and in rodents), and in the genitals of males, resulting in the typical epidermic spikes present in the penises of most mammals, including chimpanzees, but totally absent from the human penis. So now we know that losing this DNAS region around the androgen receptor made us lose our sensory whiskers and smoothen our penises. The authors speculate that the smoother penis makes for very different sex than chimpanzees have, with increased penetration time before ejaculation, which could possibly lead to increased pair bonding, and possible monogamy between human mate partners. The monogamy conclusion seems to be a bit of a stretch to me, but the pair bonding part makes sense: longer, more enjoyable sex acts make for stronger pair bonds.


The second missing DNA bit that the scientists studies is in the regulatory region of a gene called GADD45G, which suppresses cell growth. When introduced in transgenic mice, that DNA region directed expression of a marker gene that produces blue color, into the engineered mouse’s forebrain.  If this region is present, the growth-controlling gene is expressed in and the forebrain growth is curtailed.  This strongly suggests that loss of DNA regions in the human lineage could have led to increased brain growth.


The authors do not claim to have resolved the quandary of what bits of DNA make us humans, but their two examples of regulatory regions that we lost are a step in the right direction. We now need to take into account not only what gains or changes of DNA have occurred as a result of evolution of the human lineage, but what bits of genetic information we have shed along the path to becoming human.


You can read more at Science Daily here. The original Nature article can be found here (may not work without a subscription).


[Note: this is my original piece describing the research, I welcome comments: was it interesting? was it clear? did it bore you to tears?, etc. Thanks].

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Here is the abstract of the original paper:

Human-specific loss of regulatory DNA and the evolution of human-specific traits

Nature Volume: 471, Pages: 216–219

Date published: (10 March 2011)


Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown1. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes2, 3, 4, 5. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species6, 7, 8. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage9, 10. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G)11, 12, a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations6, 7, 8 and inactivation events13 long proposed to have an important role in human evolutionary divergence.

And as usual a great blog post by Ed Yong from Not Exactly Rocket Science, who, unlike me, is a world class science journalist and writer.


Control Altered by Deletion – is lost DNA behind our bigger brains ...

Where genes are concerned, less is sometimes more. Cory McLean, Phillip Reno and Alex Pollen from Stanford University have found many stretches of DNA that are missing in our genomes but are otherwise shared by chimps and other mammals. They think that the loss of these sequences coincided with the evolution of our larger brains, and the loss of features like whiskers and penis spines. Our genome’s loss has been our gain.

The trio found 583 stretches of DNA in the chimp genome that are shared with a variety of different mammals, except for humans. They called these sequences hCONDELs (short for “highly conserved deletions”). Except for one, they are all “enhancers”, stretches of DNA that control other genes, but aren’t genes themselves. They are overlords that have managed the activity of genes throughout the mammal family tree, but that abruptly abandoned their posts in the human branch.

 The team found that hCONDELs cluster next to two main groups of genes – one that affects our neurons, and another that controls how we respond to hormones like testosterone or oestrogen. “We chose to follow up on one gene in each of these two categories,” says Daivd Kingsley, who led the study.

One of the hCONDELs affects a gene called the androgen receptor (AR), which produces a protein of the same name. Think of the AR protein as a machine – it’s switched on by hormones like testosterone, and it drives the development of male physical features, everything from penises to facial hair. The AR gene contains the instructions for making this machine, and the enhancers tell the body where and when to build it.

In chimps and mice, one of these enhancers instructs an embryo to build the AR protein in specific parts of the face and genitals. As the embryo grows up, it develops facial whiskers and spines on its penis. Because we don’t have this enhancer, we don’t build AR in the same places, and we never develop these features that are normally found in other mammals.

We might have facial hair, but we lack the sensitive whiskers that many other mammals use. That’s understandable for vision is our main sense. But why did we lose penis spines, and why do other animals have them in the first place? The spines aren’t there to inflict injuries (as those of many insects are). They’re hair-like and sensitive. Without them, sex is probably a less stimulating activity for human men than for other male mammals, and it takes relatively longer.


Read the rest here.

Well, I wonder how we'd be able to sit comfortably all day long with a tail.

Good thing we got rid of that too.

Well, chimps don't have tails either, so the DNA we lost (or gained) to be tailless cannot be found by this method of comparative genomics with the chimpanzee, but we could look for that "tail" bit of DNA by comparing our genomes and chimp genomes with, for example, rhesus monkeys' genome :-)


Often when commuting in the NYC subway, I wished I had a prehensile tail, so I can hold the handles, open my e-reader, and in the meantime put my backback back on my back, without having to balance like a surfer in Waikiki :-)

What the genome confirms about what observation of evolution can only speculate is just amazing. People who claim Atheists must be spiritually barren have not contemplated long how part of every other living thing is in us.

From Wired blogs:


Genetic Errors Nixed Penis Spines, Enlarged Our Brains

Geneticists have linked the physical appearance of humans to patches of DNA lost in the 5 million years since we shared a common ancestor with chimpanzees. One loss prevented men from growing penile barbs, which chimps possess. Another enlarged some regions of our brain.

“We can know what makes us human, what makes us physically different from other animals and why,” said developmental geneticist Gill Bejerano of Stanford University, an author of the March 10 study in Nature.

Only 2 percent of the DNA in our genome forms protein-coding genes. The rest, once called “junk DNA,” helps control and coordinate gene activity. Out of this regulatory coordination, physiological complexity emerges.

Bejerano’s team started by comparing the genomes of chimpanzees and macaque monkeys, which share a 20-million-year-old common ancestor. They identified regions that hadn’t changed in chimps, then compared these to corresponding stretches of the human genome. They found more than 500 mutations known as deletions, or stretches of DNA present in chimps but lost in humans.

Two deletions, one near a male hormone-signaling gene and another near a neural development gene, were especially intriguing. Tweaking those genes in mice suggested possible roles for the loss: eliminating penile spines and boosting cerebral cortex growth.

From the Daily Dish 

Monogamy And Penis Spines

Megan Scudellari summarizes new research:

Hundreds of deletions in non-coding DNA have helped sculpt human evolution, including an increase in brain size and the loss of sensory whiskers and penis spines, proposes a study published this week in Nature.

Jen Phillips goes deeper into the science with the study's lead author, Cory McLean:

Humans (like mice and chimps) have an androgen receptor gene that's necessary to develop penis bumps (penile spines, in scientific terms). Humans, at some point along the evolutionary road, lost the DNA needed to activate that receptor, and thus, do not have "spines" on our penises anymore. ... Human penile spines, if they existed, would probably be similar to chimps', which have a polka dot-esque distribution and are made of keratin, the same tough-yet-yielding substance that makes up our hair and nails.

The first time I heard "penile spines" I thought "ouch". But then, when McLean told me they were made out of keratin, I thought, hmmm, maybe the bumps increased female pleasure rather than diminished it. Think of ribbed condoms or bump-laden vibrators

Stephanie Pappas connects the dots:

Penile spines are exactly what they sound like: small spines on the head of the penis of many animals. Plenty of animals sport the spikes, including a type of beetle called the bean weevilwhose hard, sharp spikes scar the female beetle's reproductive tract during sperm delivery. Many rodents, primates, such as marmosets, and even pythons whose Y-shaped hemipenis is often spined in order to grip the walls of the female's opening, known as a cloaca.

In species with penile spines, Kingsley said, females tend to mate with multiple males. Penile spines may have evolved to clear out a competitor's sperm – or to abrade the female's vagina, making her less likely to mate with others. Either way, Bejerano said, "the loss of the spines is most often seen in species that have gone more the monogamous way."

Scicurious explains that the "spines" in the case of the chimp are more like "goosebumps", all that "removing the competitor's sperm" seems to me to be speculation, it's be interesting to see some data, however, the chimps may object to the research :-)

Friday Weird Science: Penis Spines, what are they REALLY?

Mar 11 2011 Published by scicurious under Friday Weird Science

I’m sure by now everyone here has heard about the Penis Spine Story. The actual paper involved bigger brains as well as penis spines…but who cares about brains when PENIS SPINES are around?? Yeah I didn’t think so.

When I read the coverage of the penis spines, and heard it was the technical term, I was really confused. I thought, isn’t the technical term the baculum? The bone in the penis of animals like mice and chimps and dogs, which facilitates erections. Humans don’t have them. Penis Spine, baculum, makes sense, right? I was completely mystified as to why people weren’t just calling it the baculum and seemed to be talking like there was more than one!!! Surely they didn’t mean something like THIS:

(Courtesy of Ed. Hurts just thinking about it…)

And lo and behold, they DID mean ACTUAL PENIS SPINES!!! BE STILL MY HEART. I still didn’t believe it, until Eric Michael Johnson (who will be doing another post on the penis spine paper over at Zinjanthropus! Check it out!) mentioned a need for a paper. And the paper…was on penis spines. The actual spines!

Osman Hill. “Note on the male external genitalia of the chimpanzee” Proceedings of the Zoological Society of London, 1944.

Science. You couldn’t MAKE this stuff up.


So basically, the author, Dr. Hill, got an opportunity to study a freshly dead chimpanzee. Unlike previous specimens which got preserved in bad solutions, this one was SO freshly dead that they were able to preserve the body in the kind of fluid usually used for human embalming (he doesn’t specify, but seeing as it’s 1944, I’d bet on some formaldehyde in there). Why Dr. Hill was particularly interested in examining the penis, I don’t know. But he drew it VERY carefully.

Count yourself lucky, the original view is a LOT larger. What you’re looking at here is the view looking up between the legs, like you’re staring at the taint, which is toward the bottom of the picture. The penis sticks up at the top, and you can note the extremely large testicles of the chimp. Testicle size in primates has an inverse correlation with monogamy, so you can see that chimps are VERY NON-monogamous.

What Dr. Hill noted upon examination of the penis was a series of tiny BUMPS on the surface of the glans (the head) of the penis. He wanted to study this in more detail, and took a sample. Yeah, he skinned the penis. He was also able to compare his adult specimen with the specimens of a fetal chimp and two teenage chimps.

In describing the basic form of the penis, it seems just like…a penis. Unlike humans, chimp penises taper toward the end, but they do have a foreskin. Also, it’s lightly hairy. But it’s when he starts talking about the spines that the true poetry comes out.

The surface of the glans is beset, especially on its lateral surface, with
numerous low, horny elevations, of yellowish-brown colour, sharply distin-
guished from the pale rosy tint of the remainder of the epithelial covering.
These papillae are hard t o the touch and impart a roughness to the finger

You can see there the little dots meant to represent the penis spines. In comparison, the fetal and adolescent chimps had them too, though the fetal chimp penis spines were described as “gelatinous” and relatively clear.

In detail, the spines are on average about 0.35mm wide. He goes into the cellular structure, but it’s nothing out of the ordinary, except that the spines are…hard. In comparison to the rest of the skin. He describes them as “cornified”, and they appear to be composed kind of like callouses…only tiny spines. Tiny corny spines.

While the author is mostly concerned with the potential evolution of the spines, I’m more concerned with their function. What are they FOR?! Why are they THERE?! One hypothesis is that they are actually more stimulating for the male (ribbed for his pleasure, anyone?), and therefore promote quicker sex. This could be especially important in promiscuous species, where it’s important to get it over and done as quickly as possible, and on to the next! This means that humans, who don’t have penis spines (thank goodness), find sex LESS stimulating, and it takes them longer. This might be ideal for promoting social bonding in humans, while in chimps social bonding via sex is far less important. But there are other possibilities. It’s possible that bumps and ridges on the penises of promiscuous species are good for scooping out the sperm of competitors.

I just wonder what the girl chimps think.

Hill (1944). Note on the male external genitalia of the chimpanzee Proceedings of the Zoological Society of London

I may now die happy, I am fully educated on the nature of penis spines in Chimpanzees.


But seriously I was very curious as to what "spines" really meant in this context. Thank you for the research.

So much to learn; so little time to learn it. Damn!


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