Evolution’s Usual Suspects: 2. Hijackers in Rehab

Have you ever had a cold that you just couldn’t shake? One that seemed to take months to release its vicious grip on your abused body? Definitely NOT fun. Now imagine an infection that hangs on for millions of years. Yep, we’ve all got it, and what’s worse, when we became infected, it wasn’t just with the common cold either. We came down with things like ebola and many, many other horrors, and we still have them. Why aren’t we dead yet? Read on.

I’ve been writing a series about the twisting tale of evolutionary genetic engineering that has effectively glued us together from parts that are as disparate as Neanderthals (my first post of the series, “Cavemen in Your Genes”) and bacteria (“Evolution’s Usual Suspects: 1. Plagiarizing Wizards”). This is the next installation of that series, continuing the theme of primordial “crimes” that birthed the chimaera that we call human. Last time, I rambled about how bacteria plagiarize each other’s DNA by the process of horizontal gene transfer. Like a child building a Lego structure, they can snap foreign DNA into their own chromosome. This process speeds up evolution by allowing beneficial mutations to spread across a much larger community with lightning speed. Today’s crime sets our body’s defenses bristling: hijacking.

Although we humans possess a few genes that bacteria have spliced into our chromosomes (yes, you are part bacterium! How does that make you feel?), only a very small part of our genetic heritage appears to be bacterial. Big deal, right? Sure, it’s an interesting process, but so what if it makes only a small splash in our history?

Genetic Hijacking

Well, it turns out that another group of even stranger “life” forms is responsible for about 8% of our genome — over 98,000 sections of DNA. That’s a big splash in our gene pool. I have placed the word “life” into quotation marks because these entities push the definition of life to its limits. These creatures are very, very tiny, much smaller than bacteria. They are viruses, specifically a group of viruses called endogenous retroviruses (ERVs).

What does this mean? Let’s back up a bit and build it up from its parts.

Recall that a virus is really just a protective shell of protein housing a relatively short string of genes that consists of the instructions for making more protein coat and genes. That’s basically it. How does it “live”, being so simple? It hijacks the cellular machinery of other DNA-based life forms, and it absolutely requires such a host for any sort of activity at all. Viruses are the very distilled essence of a parasite. Parasitism is ALL they do. This is why their identity as living things is questionable: are viruses really alive when floating completely inertly between the animals, plants and bacteria that they infect?

When viruses encounter a cell, they enter it in various ways, depending on the type of virus. I think that bacteriophage viruses are the most marvelous by far: they look like Apollo moon landers and they inject their DNA into bacteria using what amounts to a molecular syringe.

A bacteriophage virus, named thus because it attacks bacteria. Notice the simplicity of its parts: a string of DNA surrounded by a coat of protein to protect it from the environment. Looking like an Apollo lunar lander, bacteriophages attach themselves to the cell walls of bacteria by their tail, which then contracts, pumping the DNA into the bacterial host in a spring-like action that resembles the discharge of a syringe. (Image: Adenosine, redrawn from Pbroks13)

Once inside the cell, the viral DNA subverts the cell’s own protein factories (ribosomes), and gets to work. Such work, in the case case of viruses, is to make more viruses. Lots more. So much, in fact, that they eventually accumulate to the point that they burst the cell open — much like the chest-burster alien in Ridley Scott’s classic film. And just as the Hollywood alien made a rather nasty mess of its victims, viruses can similarly reduce their unfortunate host’s cells (and sometimes the entire host) to a bloody mess. The most infamous example is ebola, a particularly virulent hemorrhagic virus from Africa that causes blood vessels to disintegrate, leading to an agonizing bleeding death.

But hang on…isn’t the common cold also a virus? Yes, and it doesn’t generally dissolve its victims. Most viruses are not as aggressive and globally destructive as ebola or the Marburg virus. Most of them might cause local damage by destroying some cells, but they reign in their ferocity before they kill their victims. Why?

Evolution of Avirulence: It Pays Off to be Nice

Comparatively benign viruses are one stable result of natural selection, and they demonstrate evolution especially well. The process by which they arise from vicious viruses is called the evolution of avirulence. This means that viruses are selected by their host’s survival patterns to become less virulent or lethal. It’s simple logic:

Suppose Virus A is a ferocious killing machine, slaughtering its hosts with ebola-like efficiency within a few days (= highly virulent), whereas Virus B is like the common cold, causing a few annoying symptoms as it destroys some cells, but not very aggressive, and leaving its host alive (= relatively avirulent). Which type will survive and spread better?

Although Virus A will produce a lot more copies of itself in any one host (hijacking nearly all of the host’s cells to produce more Virus A), it handicaps its own spread through the population of hosts. Why? It’s because hosts die so quickly that they have little chance of shaking hands with other hosts and spreading the virus. Also, other hosts may learn to keep their distance from an infected individual that is rapidly dissolving into a nasty mess. So Virus A has a serious chance of going extinct.

Virus B, on the other hand, produces relatively few copies of itself in a single host, but the resulting symptoms are so benign that the host might not even realize that it’s infected before it shakes hands with, kisses, or wrestles with others. The virus therefore has a great chance of spreading to other hosts, securing its survival. Over the whole population of hosts then, Virus B actually produces more copies of itself than Virus A. So Virus B is a better competitor than Virus A, and over time B will likely replace A in the population.

But random mutations sometimes cause individuals of Virus A to lose some of their efficiency (by damaging their genetic code), thus reducing their aggression…and making them more like Virus B. Because this mutated population will survive better than the original fierce one (we showed this above), it will ultimately replace the original population. Over time, the descendants of the originally nasty Virus A evolve into relatively more benign forms very much like Virus B. This is the evolution of avirulence by natural selection. It pays off to refrain from ruining your landlord.

Bunny Boom’s Bust Blunted

Neat idea, but do we ever actually see this happen? Yes. One well-know example involves the myxoma virus in rabbits [1]. Rabbits are a severe pest in Australia because they were introduced by humans to an ecosystem where they lacked natural enemies. As a result, they multiplied like…well, bunnies. Their skyrocketing populations devastated the local plant life and crops. Among the methods of population control applied to them was the the disease myxomatosis, transmitted by the nasty tumor-causing myxoma virus.

Rabbits at a watering hold in Australia. Yep, they bred like bunnies. (Image: National Archives of Australia)

The myxoma virus was found in Uruguay, where it only affected rabbits in a relatively mild way. However, when it was accidentally released in Europe, it quickly obliterated 90% to over 99% of rabbits in some populations (which lacked the immune defenses of rabbits from Uruguay), killing within 14 days. So the virus was deliberately released in Australia in the 1950s to curtail the rabbit population there. It was initially very successful, killing nearly 90% of rabbits within two years. Over time, however, the virulent form of the virus was replaced by avirulent forms, which now have a mortality rate of only about 50% — still high, but only about half of the original potency.

Actually, the evolution of avirulence is a combination of natural selection on both the host and the virus, because a virulent virus represents an extraordinarily strong force of selection on the host, whittling down a lot of the host population that does not possess especially strong immune defenses. In the end, the parties meet somewhere in between: the virus loses some of its aggression and destructiveness, and the host evolves strengthened immune defenses. The rabbit-myxoma case is thus a textbook example of what is referred to by evolutionary biologists as coevolution, meaning that two life forms influence each other’s direction and rate of evolution. Indeed, if you are interested in reading about the documentation of evolution in action, the case of rabbits versus myxoma virus is not a bad place to start.

Retroviruses: Not from the ’80s

OK, so viruses can evolve to lose some of their punch, and can coexist with host populations without ravaging them. But how on earth did they manage to sneak into our genome? If they hijack cells and then merely dispense of the remains, then how can their genetic material be passed on to our children? To answer this, we turn to a very special group of viruses called retroviruses.

Retroviruses have a neat trick. They can “upload” their genetic material to the chromosomes of their hosts, which allows them to piggyback on their host’s DNA, simplifying their job of replication and avoiding detection by the host. Stealthy.

No, retroviruses are not from the ’80s. Rather, their name refers to the “backward” way in which they transfer the information that resides on their genetic blueprints. (By the way, Retro fans, I’m not calling you backward; “retro” merely means “in reverse”.) Retroviruses are the only known life forms to store genetic material in the form of RNA (ribonucleic acid) instead of DNA (deoxyribonucleic acid). RNA normally functions like a work order, the chemically “active” form of the instructions encoded in DNA, making these instructions ready for translation into proteins. But retroviruses use RNA for information storage as well. Retroviruses make use of the host’s own means of copying genetic material into RNA to make more of themselves. To do this, they must make a DNA copy of themselves (using a special copying enzyme, called “reverse transcriptase”) and insert this DNA into the host’s genome. The “retro” in their name comes from this backward order of the usual direction of copying: RNA copied to DNA.

So retroviruses have a kind of dual identity: when they are floating between hosts, their genetic material consists of RNA, but when they have infected a host, they are really just a section of DNA in the host’s genome, in a form known as a “provirus”. It is in the provirus state that they became part of our genetic heritage, for once among our genes, they can be passed on to our children if they infect sperm or egg cells (or the progenitors of sperm and eggs). Infecting egg cells is a great way for a retrovirus to get free population growth without expending any energy if the egg cell becomes fertilized: because the provirus gets copied each time the host cell divides, its numbers can swell from one provirus copy to several trillion as the fertilized egg cell divides repeatedly and the host grows into a mature individual.

You can imagine how difficult it is to detect retrovirus infection and to treat it, once the provirus hides among our own genes. Retroviruses are some of the sneakiest pathogens and therefore cause some nasty and persistent diseases. AIDS, caused by the human immunodefficiency virus (HIV) is probably the best known, but a viral nature is also suspected for several autoimmune diseases such as multiple sclerosis [2]. Retroviruses can linger in our genes in a dormant provirus state for long periods until a suitable trigger comes along; perhaps stress of some kind. The factors that induce activity of the virus are not always well understood.

Sometimes, these proviral retroviruses never even wake from their DNA slumber. A suitable mutation may make them unable to become activated, and in such cases they become endogenous retroviruses, or ERVs, which become incorporated permanently in our DNA. Many of them then fall into the huge pool of “junk” DNA that separates our useful genes on our chromosomes. We can still recognize them as being related to exogenous (not permanently implanted) retroviruses when we analyze their DNA sequences. In fact, a recent study of the human genome has yielded the amazing result that not only is about 8% of our genome composed of ERVs, but that many of their gene sequences are disturbingly closely related to ebola, marburg virus and bornavirus [3].

Luckily, virulent though their ancestors were, most ERVs in our genome are effectively like a fly splattered on a wall at this point — most of them, that is. There are a few exciting exceptions, which paint a really neat picture of evolution leading to a sort of “rehabilitation of a felon”.

Hijackers in Rehab: Beneficial ERVs

Having become stuck in the genomes of organisms as diverse as bacteria and primates, some ERVs do not idle along as inert junk DNA but have evolved with their host to actively benefit the composite creature that forms from their union. It’s reminiscent of the premise of the 1958 movie The Defiant Ones, in which two escaped convicts, linked by a chain, learn to cooperate to evade capture, even though they do not get along well at first.

The Liverpool Endemic Strain of a common infectious bacterium found in hospitals worldwide is the most virulent form of the species Pseudomonas aeruginosa. Recently, a team of scientists led by Dr. Craig Winstanley of the University of Liverpool found that this virulent strain differed from less aggressive strains of the bacterium by about 10% of its genome [4]. Most interestingly, much of the DNA constituting this 10% difference was made up of prophages — the bacterial equivalent of provirus ERVs. Somehow, the viral genes made this bacterium more competitive than its conspecifics (others of the same species). This is a wonderful example of how evolution can proceed via not just mutation but by the fusing of two organisms. Thus, this is one mechanism by which we see an increase in complexity. It’s a little like the genetic fusion that Jeff Goldblum’s character experiences in the 1986 remake of “The Fly“.

A second example of beneficial ERVs hits closer to home. Amazingly, an ancient ERV similar to HIV may be responsible for promoting the prevention of cancer in primates [5]. Comparison of gene sequences of several primate species suggests that they were infected by a HIV-like retrovirus around 40 million years ago. This retrovirus became incorporated as an ERV, but it also then appears to have transformed into what is called a transposable element, popularly called a “jumping gene”. Transposable elements do just that — they make copies of themselves and reinsert their copies in multiple places in the genome, much like an ERV is expected to behave, and they appear to have descended from ERVs. The importance in the present case is that a DNA-repairing protein produced by primate cells, called p53, bound particularly well to the ERV (many proteins bind or stick to DNA for various reasons, including stabilizing them), and therefore was able to act on a much larger number of genes after the ERV spread itself around the genome. As a result, its protective capacity increased enormously, and is today sometimes referred to as “the guardian of the genome”. DNA repair, as you may know, is important in cancer prevention, because many cancers result from errors in copying DNA or from damaged DNA. Therefore, an initially viral infection 40 million years ago may have turned beneficial and ultimately facilitated an increased competitiveness of primates.

Finally, if you’re an expectant mother, have you ever stopped to wonder why your body does not reject your child the way it would respond to an infection? After all, the genetic contribution from dad makes the child genetically different from you, and the fetus should be perceived by the body as foreign tissue, much as a transplanted organ. But there is obviously no immune response (fortunately!), so what’s going on? It turns out that some very ancient ERVs have evolved to fill the role of a kind of immune system regulator that prevents the body from attacking the baby and placenta, in a process called gestational immune tolerance [6, 7]. This makes sense if you think about it, for viruses are experts at circumventing the body’s immune system. Therefore, an immunosuppressant role of a fully integrated ERV is a natural extension of its ancient viral activity. In fact, the presence and activation of ERVs during pregnancy in nearly all mammals, such as sheep [8], has led to the hypothesis that the ERVs were partly responsible for the evolution of viviparity (gestation of an embryo within a mother’s body) from oviparity (egg-laying).

A human fetus at 5 weeks of age. (Image: Ed Uthman, MD)

The role of endogenous retroviruses in host functions is very strong evidence for coevolution of host and parasite. Arguments of creationists against the idea hinge on (1) the assumption that mutations can only lead to degeneration of health (which is demonstrably untrue; see short discussion in my last blog entry) and (2) the inexplicability of an infectious origin for ERVs that have a fixed chromosomal position (i.e. ERVs that do not move around in the chromosome like jumping genes). It simply seems unlikely to creationists that this could have occurred based on the cosmopolitan distribution of such ERVs across so many species. By contrast, the most parsimonious (simplest) explanation, which does not require the intervention of an intelligent agent (and which is supported elegantly by observation), is that such ERV infection occurred in organisms extremely long ago, and that the resulting ERVs were passed down to all of the descendants of these species, in all of the lineages of life that branched out from such common ancestors. Of course it’s possible that all of life, the universe and everything were created only 6000 years ago and were made to look exactly as though they were 13.7 billion years old, but this explanation requires many more assumptions to support it. The entire purpose of science is to seek out the most parsimonious explanation for a set of observations, because experience repeatedly shows that the most parsimonious explanation tends to be the right one.

References

1. Dwyer G, Levin S.A., Buttel L. (1990) A simulation model of the population dynamics and evolution of myxomatosis. Ecological Monographs. 60: 423-447.

2. Mameli G, Astone V, Arru G, Marconi S, Lovato L, Serra C, Sotgiu S, Bonetti B, Dolei A (2007). Brains and peripheral blood mononuclear cells of multiple sclerosis (MS) patients hyperexpress MS-associated retrovirus/HERV-W endogenous retrovirus, but not human herpesvirus 6J Gen Virol. 88 (Pt 1): 264–74. doi:10.1099/vir.0.81890-0

3. Belyi VA, Levine AJ, Skalka AM. Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate GenomesPLoS Pathogens, 2010; 6 (7): e1001030 DOI:10.1371/journal.ppat.1001030

4. Winstanley et al. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosaGenome Research, 2008; DOI: 10.1101/gr.086082.108

5. Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. PNAS. 104: 18613-18618 (FREE ACCESS)

6. Mi S, Lee X, Li X, et al. (Feb 2000). Syncytin is a captive retroviral envelope protein involved in human placental morphogenesisNature 403 (6771): 785–9.doi:10.1038/35001608

7. Luis P. Villarreal (Sep 2004). Can Viruses Make Us Human? Proceedings of the American Philosophical Society 148 (3): 314 (FREE ACCESS)

8. Dunlap KA, Palmarini M, Varela M, et al. (2006). Endogenous retroviruses regulate periimplantation placental growth and differentiationProceedings of the National Academy of Sciences 103 (39): 14390–5. doi:10.1073/pnas.0603836103

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Evolution’s Usual Suspects: 1. Plagiarizing Wizards

Our Chimaeric Evolutionary Roots: The Primordial Crimes That Birthed Us

In my last post (“Cavemen in Your Genes“), I described the idea that this bizarre creature we call human (and indeed much of life on earth) is a lot like Frankenstein’s monster, a quilt of many disparate parts patched together by chimaeric forces of evolution. We saw evidence in our genes for hanky-panky between modern humans and Neanderthals (which were once thought to have been our ancestors, but are now known to have been a different species altogether).

But our inter-species promiscuity is the least interesting or tortuous aspect of our pedigree. And I’m afraid I have bad news about our heritage: our ancestors were victimized by and involved knee-deep in a primordial crime syndicate billions of years old. The severity of misconduct spanned the gamut from relatively petty purse snatching or grave robbing to forced entry, kidnapping and all-out hijacking. It’s a crime drama billions of years in the making and written in the tome of our genes.

Plagiarizing Wizards and Grave Robbers of Old

It all began in some backwater lagoon or hydrothermal vent in the multibillion-year depths of Archaean time, when a bacterium found it in its capacity to grab what was not its own to take. Since then, bacteria have become the most accomplished plagiarists of all time. They are unscrupulous scoundrels that feel no remorse nor pangs of conscience (nor anything at all, given their lack of a complex nervous system or nerves of any kind at all) at taking other’s writings and incorporating them into their own manuscripts, all without assigning proper credit.

A cross-section image of a bacterium. Note the red knot of material in the center. That is the coiled mass of its DNA, in a region called the nucleoid. (Image: LadyofHats)

I’m talking about horizontal gene transfer of DNA. Back up a bit. The long thread of a creature’s DNA molecule is like a wizard’s scroll of spells (others have used the analogy of a blueprint that contains the instructions for the manufacture and maintenance of an entire organism, including instructions for the proper order of reading of the blueprint — but the magical metaphor is more fun and colorful, and nearly equally applicable, so long as we are careful not to take it too literally, for there’s no real magic here).

So, with disclaimer in place, DNA is a veritable compendium of incantations (genes and operons, which are like powerful words and sentences composed of combinations of a few molecular ‘letters’) that can be invoked to create useful machines (proteins, enzymes) when they are read (by the cell’s RNA polymerase molecules) to accomplish any task necessary for the creature’s survival. For example, there are passages in this book of magic that allow the creature’s cells to disintegrate poisons or to convert useful food molecules into energy or to build outboard motors to propel it away from danger or toward new feeding grounds.

A section of a DNA molecule, 12 links (nucleotides) long. Genes consist of similar (though usually considerably longer) sections of DNA.

The cell accomplishes its wizardry by invoking one of its minions — a little molecular device called RNA polymerase — to read entries from the scroll of DNA, and then the ‘spoken’ words of the spell (in the form of RNA molecules) are translated into useful machines by other minions called ribosomes. Thus are the micromachines called enzymes created from the DNA spell book for use by the cell.

The magic of the translation of RNA (the long diagonal string scrolling to the left) into a protein (the chain that grows slowly upward at the center of the image as amino acids are added to it) at the ribosome (the big irregularly shaped structure composed of green and yellow subunits). The blue objects that zip to the center of the ribosome and then zip away are T-RNA molecules, whose job it is to ferry amino acids to the site of the ribosome and donate their amino acid to add to the growing protein chain. When the protein is completely assembled, it is released from the ribosome and goes off to accomplish whatever task it was constructed to perform. (Image: Bensaccount)

Over millions and billions of years of time, bacterial wizards have written (by the gradual accumulation of mutations that rewrite DNA) huge troves of such magical spells in response to pressures or opportunities presented by their environment (e.g. the need to dismantle toxins in their vicinity, or the opportunity to use a new food supply if only the bacterium had the enzymes needed to liberate useful energy from this food molecule by breaking it down, just like energetic fire is generated by the uncontrolled breakdown of energy-rich molecules in wood).

Often another bacterial species possesses the genes needed to take advantage of such opportunities or to save it from dangers. If bacteria were capable of human emotions, envy would flow thickly among its neighbors. But sometimes the well-endowed bacterium fortuitously dies, spilling its contents (including its DNA) into the environment when its cell wall disintegrates. The fragments of its DNA disperse, adding to the pool of slowly decomposing DNA already around from other deaths. Genes, genes everywhere! At the scale of microbes, the world is like a field blowing with pages (fragments of DNA) torn from thousands of books (genomes), in various stages of decay. And some of these pages still contain intelligible spells (genes or groups of genes).

The long winding string of a DNA molecule floating freely after being released by a bacterial cell, photographed with an electron microscope. (Image: SeanMack)

Here is where things get really amazing. Our own cells are generally only capable of inheriting genetic material from our parents (be they modern humans or, in the deep past, occasionally Neanderthal), and our cells would consider this freely floating discarded DNA as useless. But many bacteria can take these DNA fragments into their cells and incorporate them into their own DNA, like gluing pages into a book!

Remarkably, bacteria can therefore ‘inherit’ genes not only from their ancestors but from their environment, and this DNA need not have belonged to anything remotely related to them. This is called horizontal gene transfer, also known as lateral gene transfer (“horizontal” or “lateral” referring to the passage of DNA between individuals of potentially the same generation, rather than being passed ‘down’ — ‘vertically’ — to the next generation) [1].

Further, because a bacterium is just a single cell, transformation of its DNA by the incorporation of this alien DNA transforms the genetic identity of the entire organism, and it is then inherited by all of the cell’s progeny as well. For this to work in us, the new genes would have to be added to our sperm or egg cells, the only types of our cells that pass their DNA on to the next generation.

A single cell of the bacterium Escherichia coli dividing multiple times to form a bacterial colony. (Image: Stewart et al., 2005)

Evolution Accelerated by Horizontal Gene Transfer

So can you begin to see how much faster evolution may progress using lateral gene transfer than using simple mutation alone? Suddenly the whole world is a laboratory on which a cell can draw to gain access to new genes generated in mutations in tens of thousands of other species. Indeed, a mathematical model by Michael Deem and Jeong-Man Park [2] demonstrates that horizontal gene transfer would increase the speed of evolution by quickly spreading useful mutations across large populations and communities of life forms. Contrary to what creationist proponents claim, beneficial mutations DO occasionally occur (e.g. the evolution of nylon degradation in bacteria [3]); horizontal gene transfer then helps to preserve them against loss by propagating them like gossip on the internet. Beneficial mutations do not need to be common as long as they can catch on and spread as quickly as wildfire.

Even more amazingly, there is evidence that under stressful conditions (e.g. heavy metal-polluted waterways), the rate of horizontal gene transfer between bacteria increases, as if stress induces a more urgent swapping of genetic ideas for a solution. Conditions such as these result in bacteria that acquire genes to detoxify heavy metals. Such a situation would even further accelerate the process of evolution, because useful mutations are spread around more intensely precisely in the environments in which they could make the most difference.

In a more frightening example of horizontal gene transfer, we have increasingly seen the rapid evolution of bacteria that resist being killed by antibiotics [4]. In many cases, one species of pathogenic (disease causing) bacterium acquires the genes that break down antibiotics from another species, allowing the ability to hop from one species into another, and multiplying our problems.

To bacteria then, the world is littered with great ideas ripe for the scavenging. The little grave robbers absorb some of the genetic remains of their dead neighbors and add them to their own genetic blueprint. They have no laws to discourage plagiarism, and there is no copyright on the genes they acquire this way.

Evidence Written in DNA

But how do we know that horizontal gene transfer has really been a part of evolution? Aside from the myriad instances in which microbiologists have actually observed it to happen in bacteria (e.g. the process of bacterial transformation), we can see evidence when a gene sequence that is characteristic of one species suddenly shows up in another species. This is kind of like the finding of Neanderthal genes in our genome, but (1) bacteria do not need to practice sex, for they can have ‘children’ by simply dividing asexually, and (2) bacteria can acquire genes from other species that are vastly more distantly related to them than are Neanderthals from us. And we see evidence for this.

Graphical representation of horizontal gene transfer. The branched tree-like structure represents the evolutionary lineage (geneological tree) of representatives of earth's major types of life forms. Sometimes genes can be transferred (horizontal gene transfer) between otherwise distantly related species. This is illustrated by bridges forming between branches of the tree, where genes 'jump' from one lineage to another. (Image: Barth F. Smets, Ph.D.)

An example exists in the scientific field around which some of my own research in microbiology revolved: the wild world of photosynthetic bacteria. An ancient group of bacteria (called anoxygenic phototrophs, which means “light-eaters that do not generate oxygen”) are capable of using light from the sun to generate energy to power their cells, in a way similar to but not identical to that of plants and algae [5].

An aerial photograph of grand Prismatic Spring, a hydrothermal vent (spewing super-heated water from volcanic fissures) in Yellowstone National Park. Some of the orange color of the rim of the spring pool is due to solar-powered anoxygenic phototrophic bacteria. (Image: Jim Peaco, National Park Service)

In fact, these bacteria were probably the first solar-powered life on earth, and amazingly, they might have originally evolved to use light not from the sun but from the glowingly-hot water spewing from geysers (hydrothermal vents) in the otherwise pitch-black deep sea…but that’s a story for another day. For now, suffice it to say that their DNA contains a long string of code for the construction of all the proteins and colorful light-trapping pigments (making the cells brilliant hues of orange, purple, red, yellow, green and blue, depending on the species) needed for the cell to capture and store light energy. There are several different distantly related groups of these photosynthetic bacteria, and each has evolved a different type of this pigment-protein machinery to capture light, and the DNA code of each can be read and used to identify which lineage of bacteria it comes from, each lineage possessing a vastly different characteristic code. Sometimes, however, you find a bacterium from one major group possessing the genes for the light-capturing machinery of a completely different group, completely as if the genes from the other group had been pasted into the normal DNA of this species [6]. This phenomenon is seen in many species of bacteria. Sometimes, a single cell will even possess the genes of more than one type of photosynthetic machinery, and one might be incomplete [7], as if the bacterium absorbed a set of genes from a DNA fragment that had already begun to decompose in the environment and was missing some parts.

Our Bacterial Identity

So we see extensive evidence for the evolution-accelerating phenomenon of lateral gene transfer in bacteria. But has it influenced our own evolution? Apparently, yes. Molecular biologists (who study DNA and other molecules of life) have found evidence that bacterial genes have been pasted into our own genome as well [8, 11]. This apparently has not happened too often, and it may be because it is much more common in single-celled life forms that are used to consuming material (including DNA) in their environment [9] instead of relying on the nicely predictable supply of food that a cell experiences in return for its participation in a multicellular (many-celled) life form. Nevertheless, a few of our genes appear to have had bacterial roots.

How might this happen? We’re not completely sure yet, but there is a precedent in nature. The bacterium called Agrobacterium tumefaciens has cellular machinery that gives it the amazing ability to take some of its own DNA and transplant it into the DNA of a plant. This action has a parasitic purpose in nature, leading to the production of a specialized tumor in the plant that helps the bacterium survive as a kind of parasite in its host. The result though, is that the plant’s genome becomes been infected (‘transfected’ is the actual word used) by the genetic material of a bacterium, and its DNA now also harbours bacterial DNA. It is easy to imagine how a similar process may have occurred in which parasitic bacteria produced changes in animal hosts to their advantage, but which resulted in a genetically modified host animal. This bacterial “transfection” is the basis on which much of the genetically modified food industry has been built.

So there we have it: plagiarism and grave robbing by bacteria has helped to build up our own genome. Not a large part, true, but bits of bacteria are nevertheless a part of our genetic identity (and later on, we’ll see how, in a completely different way, bacteria are a hugely greater part of us than most of us realize). In the next post, I’ll focus on a much more invasive crime — genetic hijacking by viruses — that our ancestors suffered (and continue to suffer), but which has contributed much more extensively to our genes.

References

1. Syvanen M (January 1985). Cross-species gene transfer; implications for a new theory of evolutionJ. Theor. Biol. 112 (2): 333–343. doi:10.1016/S0022-5193(85)80291-5

2. Park, J.M., Deem, M.W. 2007. Phase diagrams of quasispecies theory with recombination and horizontal gene transfer. Physical Review Letters. 98. doi: 10.1103/PhysRevLett.98.058101

3. Ohno, S. 1984. Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequenceProceedings of the National Academy of Sciences of the United States of America. 81:2421-2425.

4. Akiba T, Koyama K, Ishiki Y, Kimura S, Fukushima T 1960. On the mechanism of the development of multiple-drug-resistant clones of ShigellaJpn. J. Microbiol. 4: 219–27.

5. Yurkov, V.; Csotonyi, J.T. 2009. New light on aerobic anoxygenic phototrophs. In Hunter, N.; Daldal, F.; Thurnauer, M.C.; Beatty, J.T. (eds.) The Purple Phototrophic Bacteria, pp. 31-55. New York, NY: Springer Science + Business Media B. V.

6. Igarashi, N., harada, J., Nagashima S., Matsuura, K., Shimada, K., Nagashima, V.P. 2001. Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. Journal of Molecular Evolution. 52: 333-341. doi: 10.1007/s002390010163

7. Qiang Zheng, Rui Zhang, and Nianzhi Jiao. 2011. Genome sequence of Citromicrobium strain JLT1363, isolated from the South China Sea. The Journal of Bacteriology. 193: 2074-2075

8. Ponting, C.P. 2001. Plagiarized bacterial genes in the human book of life. Trends in Genetics. 17:235-237.

9. Andersson, J.O. 2005. Lateral gene transfer in eukaryotes. Cellular and Molecular Life Sciences. 62: 1182-1197. doi: 10.1007/s00018-005-4539-z

10. Stewart EJ, Madden R, Paul G, Taddei F (2005). Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol. 3 (2): e45.

11. Francisca C. Almeida, Magdalena Leszczyniecka, Paul B. Fisher and Rob DeSalle. 2008. Examining Ancient Inter-domain Horizontal Gene Transfer. Evolutionary Bioinformatics. 4: 109-119.

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Cavemen in Your Genes

The familiar nursery rhyme (…What are little boys made of? Frogs and snails and puppy-dogs’ tails…) has more merit than many of us realize. Indeed, mother nature is the eldest and most accomplished genetic engineer among us. In the next posts I’m going to highlight the unexpected ways in which we have been patched together over the last couple of billion years to arrive at the chimaera that we call human.

Blending Via Sex

We’re all a blend of our ancestors. Some of it is quite a straightforward process: being diploid, your paired chromosomes are the sum of half of your father’s set and half of your mother’s. Each of their genetic complement is, in turn, a union of their own mothers and fathers, each of whom acquired their genes from two parents before them, and so on and so forth. Therefore, your own genetic material is really a hodge-podge of an ever widening ancestral pool the further back you look. This is the result of genetic blending via sex. Sexual blending is fun, but relatively intuitive.

Kinky Twists

Now things get twisted. Until recently, sex was the only major source of genetic blending known to be going on, but the world has recently begun to look a lot more interesting with the advent of genetic sequencing. Scientists can now peer into the genome (full DNA blueprint) of an individual and read the sequences of nucleotide bases (the units of the DNA molecule, like links in a chain) that compose the genes. And guess what? We are not who we thought we are.

Although there is some variation in the gene sequences of different individuals of a species, each species has characteristic sequence codes in certain genes that set it apart from other species. These sequences slowly change over many generations as mutations accumulate at a slow clocklike rhythm (providing an “evolutionary clock”) that records the evolutionary route that species took as they diverged from each other. Biologists have amassed extensive databases of these characteristic gene sequences against which to compare newly discovered creatures and to determine where they fit into the evolutionary tree of life. The genetic “evolutionary clock” even allows us to estimate the time that has elapsed since two species shared a common ancestor. Such measurements support the fossil record by indicating that chimpanzees and humans diverged around 6 million years ago [1]. Sometimes not only a single gene but the entire DNA sequence of an organism is read and catalogued, yielding invaluable information about the physiology as well as the evolutionary history of an organism.

From these studies came a huge surprise: characteristic gene sequences of one species are often found spliced into the genome of completely unrelated species, including us. Ponder this fact for a moment: our DNA is not completely our own. Some of it (about 1 to 4 percent) is Neanderthal [2], more (8%) is viral [3], and we even have colonies of highly evolved decendents of bacteria living in each of our cells [4].

How can this shuffling have happened? Hold on to that image of promiscuity that may be forming in your mind, for we’ll need to build on it substantially. Fascinating new discoveries are shedding light on the ancient ghosts that haunt the dark corners of our chimaeric genetic identity. What I find most exciting about these discoveries is that they give us a peek into the engine of evolution, bringing us several steps closer to understanding the complex mechanisms by which it works. Together, they weave a remarkable tapestry of the interplay between scientific discovery and the techniques used to make those discoveries.

The Loopy Tree of Life

The evolutionary or phylogenetic ‘tree of life’, which represents how life forms are related to each other, is commonly roughly thought of as a repeatedly branching bush, with a common ancestor at the base and all living or extinct species at the tips of the twigs. It’s a geneology of genetic material. However, research increasingly suggests that this evolutionary tree should be thought of more as a net, with not only branching but also fusing.

Phylogenetic tree of life. You are at about position 11:30, between the rat (Rattus) and the chimpanzee (Pan). (Image: Ivica Letunic)

Over time, the single twig of a species may branch as two populations diverge from each other genetically, forming two new twigs — two new species that are reproductively isolated from each other. Usually, simple geographic separation (via a river, a highway, etc.) is enough to set two populations of a species on different roads. Once they are separated (and remain so for a long time), the evolutionary clock kicks in and mutations accumulate in slightly different ways in each population. Since there is no blending by interbreeding, a big difference in mutations eventually builds up in each population. The precise mechanism of achieving reproductive isolation is not completely understood, but eventually the genes of each population differ by enough mutations that their members cannot produce viable young if they were crossed (either sperm and egg are not compatible, or the two sets of chromosomes do not align properly, or something else), or if their young survive, they are sterile. At this point, the two populations have become different species. This is the commonly understood process of speciation, the generation of new species.

The world is not black and white though, and there is rarely a point at which the two populations suddenly don different species’ jerseys (though exceptions exist, such as genome duplication in plants, but I’ll cover these later). Geographic separation often needs to continue for a long time before enough mutations have accumulated to render the two populations biochemically unable to interbreed. By the time this is achieved, the two species may look substantially different (for example, due to different environments exerting different forces of natural selection on each population). We may easily assign them to different species based on their looks alone, but their populations may still be able to interbreed.

A good example of this flexibility in appearance (called ‘phenotypic plasticity’) is dogs. Chihuahuas and Irish wolfhounds are genetically still the same species. Dog breeding has only been practiced for a short time compared to the evolution of, say, wolves and coyotes. Dogs have been under extremely intense selection pressure during that time, and even though strong selection pressure can generate huge visual differences, there has been insufficient time for the slow march of mutations in the right places to actually prevent eggs and sperm from becoming biochemically incompatible.

A dog with the results of genetic blending: puppies. (image: Stephan Gillmeier)

Sometimes even truly separate species, with genetic incompatibility, will occasionally produce viable young when crossed. Domestic dogs can sometimes successfully breed with wolves and produce puppies. In fact, this phenomenon is one of the dangers currently facing polar bears. Polar bears (Ursus maritimus) are an ice age adapted animal, and they originally descended from brown bears (Ursus arctos) under selection pressure for white coats to hide them from their prey (they have other interesting adaptations, but that’s the most visually obvious one). It was recently found that the most recent matriline (geneology of mothers) of polar bears arose around 20,000 to 50,000 years ago in Ireland, during the last ice age [5]. The polar climate helped to keep them physically separated from brown bears even after the glaciers of the Wisconsian ice age retreated, but global warming now threatens to force them further south, where they may encounter brown bears again. It turns out that polar bears and brown bears can produce viable offspring frequently enough that the intermixing of their populations would lead to genetic blending that could wipe out the distinct white polar bear by homogenization.

So polar bears and brown bears are an example of two twigs of the evolutionary tree of life likely coming together again and fusing into a single branch, forming a kind of loop of genetic material over time, first separating and then rejoining. The tree of life is loopy. (In fact, due to horizontal gene transfer and endosymbiosis, it’s a lot more loopy than you’d think, but I’ll cover those topics further in a subsequent post.)

Phylogenetic tree of life showing both divergence (branching) and horizontal gene transfer (fusion of branches). (Image: Barth F. Smets, Ph.D.)

How Cavemen Got into Your Genes

Enter the human lineage. Our particular branch of the tree of life, the genus Homo, has a fascinating prehistory, especially as it pertains to globetrotting. The fossil evidence of our evolutionary history has really grown a lot in the last few decades, and there are now hundreds of specimens. (It’s unfortunate that creationist proponents who reject the idea of our evolution from other apes continue to focus on the relative dearth of the human fossils that existed during much of the last century. As a result, they have not kept up with recent research and continually report terrible underestimates of the volume of fossils; I’ll cover this issue in a later post.)

Australopithecus africanus reconstruction. (Sculpture by Toni Wirts)

Genus Homo descended from the African Australopithecus around 2.5 million year ago. As early as 1.9 million years ago, Homo erectus left Africa, traveling as far as Java and China (and probably evolving into Homo floresiensis — popularly known as ‘the hobbit’ — in Indonesia, which survived until maybe only 13,000 years ago). This was the first human exodus from Africa.

Human evolution and migration patterns. (Image: Reed DL, Smith VS, Hammond SL, Rogers AR, Clayton DH; 2004)

Then, around half a million years ago, one population of Homo heidelbergensis, a descendent of H. erectus, left Africa again and spread over Europe, eventually giving rise to Homo neanderthalensis, better known as the Neanderthals. This was the second major wave of migration. Meanwhile, our direct ancestors, likely another population of H. heidelbergensis, remained in Africa, with Homo sapiens arriving on the scene around 200,000 years ago.

History from here somewhat mirrors the brown bear/polar bear story. Like the polar bear, Neanderthals may have been an ice age adapted species, living through four glacial maxima (ice ages) as the global climate swung from warm interglacial times to the bitterly cold deep freeze of glatiation in the sequence of stages known as the Pre-Illinoian, Illinoan, Sangamonian and Wisconsin. Even between glaciation events, they remained an exclusively northern species of human, and none of their remains have been found in Africa.

Finally, between 50,000 and 100,000 years ago, a harsh climatic shift in Africa appears to have stimulated the egress of our species from the continent after nearly wiping us out (H. sapiens may have dwindled to under 1000 individuals). This was the third and last major migration of Homo out of Africa. There may have been additional exoduses from Africa involving other human species, but we know that there was a minimum of three excursions.

It must have been a weird time to be alive, 30 to 50 millenia ago. It was one of the few times in history when the planet was home to more than one directly interacting species of human at a time. Archaeological evidence indicates that H. sapiens and H. neanderthalensis met in Europe. The tone of those meetings is not terribly clear, but the rapid demise of Neanderthals upon the invasion of our species (they were gone by 24-40 millenia ago) implies that competition was quite severe [7]. However, until recently, it was unknown what was the answer to the obvious question: with so much interaction, was any flirting taking place?

The advent of genetic sequencing has begun to provide a fascinating positive answer to that question. For the first time, scientists are not limited to infering the depth of interactions by archaeology alone. Molecular biologists sequenced the entire genome (about 3 billion base pairs of DNA) of three Neanderthal individuals found in Vindija Cave in Croatia [9, 10, 11]. Such an analysis is so far only possible for relatively young fossils (this one was about 40,000 years old), because DNA is a relatively fragile molecule and probably would not survive fossilization over millions of years. An initial comparison with the DNA of living humans suggested that up to 2% of the genome of non-Africans was contributed by Neanderthals, probably via interbreeding about 60,000 years ago.

A more recent study by Yotova and others [2] has expanded on these results by mapping the distribution among modern humans of genes with versions that are strongly suspected to be Neanderthal in origin. What Yotova’s team has done is demonstrate the exchange of genetic material between the migrants among our ancestors and Neanderthals. Their research revealed that a small section of the human X-chromosome (the female sex determining chromosome, of which women have two copies and men have one) appears to have come from Neanderthals. Certain genes, such as the dystrophin gene (which codes for an essential protein needed for proper connectivity of muscle cells and deficiencies of which are partly responsible for muscular dystrophy) have different versions (differing slightly in their DNA coding sequences) that can be attributed to different populations. For example, the B006 version of the dystrophin gene is known to come from Neanderthals, based on the previous whole-genome sequenging work. Yotova’s team found that 9% of non-African people in a survey of 6092 living humans possessed Neanderthal genes. Interestingly, the finding that Neanderthal genes were essentially absent in African populations supports the idea that migrant humans acquired the genes by interbreeding with Neanderthals after leaving Africa. Not surprisingly, the new genetic evidence supports what archaeological finds have been telling us all along regarding the spread of our species over the earth.

So there it is: the genetic smoking gun of sexual blending between our species and Neanderthals after we left Africa. Most importantly, the presence of Neanderthal genes in our own DNA shows not only that some human-Neanderthal couples could bear children, but that at least some of those children were fertile themselves. Clearly, there was enough similarity between our two species that we were not completely reproductively isolated from each other. Because of the strong competition between the two species, one was almost certainly not absorbed into the other and only a little genetic material from Neanderthals was retained in our genome. Nevertheless, this is a good example of gene flow not only from ancestors down to descendents within a species (called vertical transmission) but also between species, allowing genes to effectively jump from one species into another. The benefit of this union to our species may have been significant: following the population bottleneck in Africa around 50,000 years ago, genetic diversity of our species was severely reduced. A shallow gene pool is dangerous because it offers little variation in traits on which a species can lean when faced with a crisis such as infection. This is part of the problem associated with inbreeding. The injection of additional genetic material from Neanderthals may have replenished a bit of the lost variation.

This cross-species transfer of DNA by interbreeding is a remarkable phenomenon in itself, but in an upcoming post, I will highlight an even more fascinating phenomenon: horizontal gene transfer, by which species exchange genetic material with each other or splice their genes into another’s genome without even resorting to sexual reproduction. This phenomenon also causes ‘loops’ to appear in the tree of life, but these loops exist on a much grander scale.

For now, you may have a genetic excuse if somebody accuses you of dragging your knuckles.

References

1. Arnason U, Gullberg A, Janke A (1998) Molecular timing of primate divergences as estimated by two nonprimate calibration pointsJ. Mol. Evol. 47 (6): 718–27.doi:10.1007/PL00006431.

2. V. Yotova, J.-F. Lefebvre, C. Moreau, E. Gbeha, K. Hovhannesyan, S. Bourgeois, S. Bedarida, L. Azevedo, A. Amorim, T. Sarkisian, P. H. Avogbe, N. Chabi, M. H. Dicko, E. S. Kou’ Santa Amouzou, A. Sanni, J. Roberts-Thomson, B. Boettcher, R. J. Scott, D. Labuda. (2011) An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations. Molecular Biology and Evolution 28: 1957 doi: 10.1093/molbev/msr024

3.  Belshaw, R; Pereira V; Katzourakis A; Talbot G; Paces J; Burt A; Tristem M. (2004) Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA 101: 4894–99. doi:10.1073/pnas.0307800101

4. J. Cameron Thrash, Alex Boyd, Megan J. Huggett, Jana Grote, Paul Carini, Ryan J. Yoder, Barbara Robbertse, Joseph W. Spatafora, Michael S. Rappé, Stephen J. Giovannoni. (2011) Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific Reports 1 DOI: 10.1038/srep00013

5. Ceiridwen J. Edwards, Marc A. Suchard, Philippe Lemey, John J. Welch, Ian Barnes, Tara L. Fulton, Ross Barnett, Tamsin C. O’Connell, Peter Coxon, Nigel Monaghan et al. (2011) Ancient Hybridization and an Irish Origin for the Modern Polar Bear MatrilineCurrent Biology DOI: 10.1016/j.cub.2011.05.058

6. Reed DL, Smith VS, Hammond SL, Rogers AR, Clayton DH (2004) Genetic Analysis of Lice Supports Direct Contact between Modern and Archaic Humans. PLoS Biology 2: e340 doi:10.1371/journal.pbio.0020340

7. P. Mellars, J. C. French. (2011) Tenfold Population Increase in Western Europe at the Neandertal-to-Modern Human Transition. Science 333: 623 DOI: 10.1126/science.1206930

8. Letunic, I (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23(1): 127-8.

9. Green, Richard E.; et al. (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330–336. doi:10.1038/nature05336

10. Noonan, James P.; et al. (2006) Sequencing and Analysis of Neanderthal Genomic DNA. Science 314: 1113–1118. doi:10.1126/science.1131412

11. Green, R.E.; et al. (2010) Draft full sequence of Neanderthal Genome. Science. 328: 710-722. DOI: 10.1126/science.1188021

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Archaeopteryx: Should Feathers Fly Over Its Fall?

The discovery of Archaeopteryx 150 years ago provided elegant (and well-timed) support for Darwin’s theory of evolution, laid out in detail only two years earlier in his 1859 publication of On the Origin of Species [1]. The exquisitely preserved plumage of Archaeopteryx, combined with its toothy beak, long bony tail and fingered hands marked the animal as a clear example of an evolutionary intermediate between reptiles and birds [2]. This was especially vindicating in Darwin’s day because the fossil record then was still relatively devoid of specimens predicted by evolution to bridge the morphological gap between major groups (e.g. birds) and their alleged ancestors (e.g. reptiles). In fact, for 150 years, Archaeopteryx has been considered by many people to be the first bird. What a title to be expected to uphold! Well, today, the discovery of the small feathered dinosaur (Xiaotingia) is causing a great flap in the media because a reanalysis of the relationships among dinosaurs and birds prompted by this discovery suggests that Archaeopteryx is not a bird after all, but rather a small feathered dinosaur [3]. But should feathers fly over Archaeopteryx‘s hop to a nearby branch of the tree of life?

No.

First, a bit of background and applause for the very unfortunately overshadowed discovery that sparked the collective media gasp. Xiaotingia zhengi was a small crow-sized dinosaur with long, graceful arms that were equipped with both feathers and clawed fingers [3]. The fossil’s marvelous state of preservation is characteristic of many Chinese specimens that are helping paleontologists trace out the early evolution of birds. Xiaotingia strongly resembled its (currently) nearest known relative, Anchiornis huxleyi, also from late Jurassic China. Both species are closely related to Archaeopteryx lithographica. The news that is making waves comes from the redrawn family tree of Archaeopteryx among birds and dinosaurs once the relateness of Xiaotingia is also considered. Under these conditions, Archaeopteryx no longer perches on the branch in common with the lineage of modern birds but rather on the branch of the deinonychosaurs, which include dinosaurs such as Velociraptor. It appears that Archaeopteryx was not the ‘first bird’, an unknown animal to which other feathered fiends (e.g. Epidexipteryx, Jeholornis or Sapeornis) now appear closer related. But the popularity of this news suggests that the fall of Archaeopteryx from its perch is a lot more important than it really is.

Anchiornis, the closest known relative of the newly described Xiaotingia, to which it bears a striking resemblance. (Image: Julius T. Csotonyi)

Why am I raising a stink about the outcry over Archaeopteryx‘s fall from grace? As a microbiologist, I’ve seen this kind of rearrangement of classification happen time and again with the bacteria that I study. I merely take it with a shrug, or occasionally a sigh when it causes me more work to account for it in the discussion section of the scientific paper describing a species. But Archaeopteryx commands a kind of public awe that the microbial subjects of my research could only envy, had they the means. In particular, Archaeopteryx holds a near-iconic position as an example of an evolutionary intermediate, the ‘first bird’, not yet even free of its reptilian bonds. Should any discovery threaten to shoo the first bird from its perch, proponents of creationism are anticipated to rush in headlong to claim that evolutionary biologists had misinterpreted the fossil, that it was not an intermediate between animal ‘kinds’ at all. True, this discovery changes things a bit, but not in the way that creationists would have us think, and certainly not in a way that threatens to topple the very foundations of evolution. Allow me to explain.

Creationists unreasonably demand evolutionary biologists and paleontologists to supply evidence for evolution in the form of “transitional forms”. These organisms are supposed to provide a bridge between living animal “kinds” (as defined by the Bible, which, by the way, does not elaborate on the precise meaning of the word). Their assertion is that god created different “kinds” of animals (we might assume that birds and reptiles belong to different “kinds”), and that one “kind” does not evolve into another. But it is flawed reasoning to require that we find an animal that is half way between one major taxonomic (i.e. related by classification) group (e.g. birds, class Aves, or slightly more inclusively, Avialae), and another (e.g. reptiles, class Reptilia).

It’s useful to think of today’s well-separated classes of vertebrates like the islands of a volcanic archipelago: they arose from one source of upwelling magma, but as it rose, the source branched, forming several seamounts; the ocean now separating them hides the connectivity that they possessed in the deep sea, in deep time before they recently reached the surface. Similarly, it’s unreasonable to expect to find something half way between major animal groups after they have changed so much from their common ancestor. Extinction has hidden a lot of detail of the path of evolution leading to modern groups. Rather, we should expect to find fossils of ancestors of both lineages that increasingly resemble each other the further back in time that we look, but not necessarily resembling either major living group. We are really searching for a common ancestor, not a mythical crocoduck.

This brings up another problem. Given how difficult it is for a dead thing to become fossilized (a lot of conditions need to be met to preserve its remains for millions of years), we cannot expect to find every link in the chain of descendents between a modern species and a distant ancestor. The best we can hope for is a string of highly disjointed dots. So how do we really know whether we have ever recovered a true common ancestor of two groups at all? We don’t. In fact, it is astronomically more likely that what any presumed evolutionary sequence of fossils represents is not a direct line of ancestry or a geneology, but rather a series of species each of which has branched off and evolved independently a short distance from the line of ancestry that we seek. Finding these fossils is analogous to walking through an autumn forest and picking up leaves that fell from tips of tree branches rather than from the main trunk (let’s pretend that trees can bear leaves directly on their trunks and on their branches, for the purpose of argument). Trees have a lot more branches than main stems or trunks, and therefore it is muchmore likely that if we pick up a leaf at random, it will have come from a side branch somewhere. We will probably never hold the fossil of the real ‘first bird’.

But cry no tears, for this doesn’t matter. We can still reasonably reconstruct an evolutionary sequence, and guess very well at the appearance of a hypothetical common ancestor, using only the remains of species that have evolved a small amount since branching from the common ancestor or the line of ancestry. All we need to do is look at the characteristics that they share (those characteristics that have not evolved significantly since the branch point). The last common ancestor between two species is likely to have possessed those characteristics that they still share. For example, we can hypothesize that the common ancestor of birds and closely related dinosaurs was also feathered, because there exist fossils of both early birds and undisputed dinosaurs that possess feathers. Moreover, if we have a whole series of fossils that may roughly delineate an evolutionary sequence (subject to the constraints of interpretation that I have just highlighted), then we can measure a whole bunch of their characteristics (wing length, beak length, presence or absence of claws on their hands, etc., etc.) and arrange them according to a hierarchy of most to least shared characteristics. This is the purvue of taxonomy and cladistics, the science of determining the relatedness of organisms on the basis of their physical characteristics. Arranging the fossils according to the hierarchy of their shared characteristics allows taxonomists to generate a ‘family tree’ of sorts (which they call a cladogram), outlining the order in which the species are likely to have descended along one or more lineages. Even though Archaeopteryx is not likely to be the common ancestor between birds and related dinosaurs, we are lucky to have uncovered it, for it nevertheless lies very near the common ancestor. And it is the proximity of Archaeopteryx to the hypothetical ‘first bird’ that has caused its classification to change.

But the effective change in the classification of Archaeopteryx as a result of the discovery of Xiaotingia is not large anyway. The nearer in time that we approach the evolutionary ancestor of birds and reptiles, the less meaning there is in the organizational category of “class” (using the taxonomic definition of the word, of which birds and reptiles each constitute a unit). If a wall is painted red on one end and gradually fades to blue on the other, then it is more difficult to categorize a section near the purple center as more red or more blue. The distinction loses practical meaning. Archaeopteryx is so near the common ancestor of birds and related reptiles that it takes only relatively small changes in the proportions or positions of its bones to toggle the animal between the bird and reptile classes. In fact, it is more useful and precise to compare Archaeopteryx not to members of Reptilia in general but rather to the specific reptile group to which it was most closely related, the small theropod dinosaurs known as the Deinonychosauria (known to most by the popularized term ‘raptors’).

Furthermore, it is a phenomenon very familiar to taxonomists (scientists who classify and name life forms) that the inclusion of additional species into a pool of species that are to be arranged into a hierarchy of relatedness (e.g. Kingdom > Phylum > Class > Order > Family > Genus > Species) can change the topology (the arrangement of connections) of the resulting cladogram (‘family tree’). This phenomenon is an unavoidable result of the statistical techniques that are used to calculate the most parsimonious (reasonable or simple) manner of branching of the tree of relatedness. It’s especially likely to happen when a new species is added that has features in common with two different groups. This new species exerts a kind of ‘mathematical gravity’ on other species that originally fell near the borderline between major groups. Such a fate has befallen poor Archaeopteryx. The inclusion of Xiaotingia into the mathematical analysis has plucked Archaeopteryx from Avialae and dragged it the very short distance into the neighboring Deinonychosauria on the basis of their shared characteristics. That’s all.

Archaeopteryx is no less a bird morphologically than it was before. The analysis that dethroned it was not a description of previously hidden anatomical features of the animal (e.g. milk ducts). As Witmer (2011) noted, Archaeopteryx still has the birdlike features of feathers, furcula (wishbone), three-fingered hands, long arms and retroverted pubis (backward-pointed hip bone) [4]. And, via the same type of cladistic analysis that removed Archaeopteryx from the bird class, future discoveries may bring Archaeopteryx back into the flock of Avialae once again.

So this is certainly not the end of the story. The point is that the inclusion of Archaeopteryx in either birds or reptiles is not as significant a point as it first seems because birds and the most closely related reptiles were a lot more similar in the days of Archaeopteryx than they are today. Furthermore, demonstrating the evolution of birds from dinosaurs, as we have seen, does not require possession of the actual ‘first bird’, whatever that may be.

References

1. Darwin, C. (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (1st ed.) London: John Murray.

2. Ostrom, J. H. (1976) Archaeopteryx and the origin of birds. Biological Journal of the Linnean Society 8:91–182.

3. Xu, X., You H., Du K., and Han F. (2011) An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475:465–470.

4. Witmer, L. M. (2011) An icon knocked from its perch. Nature 475:458–459.

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Wasp-Infested Dinosaur Eggs and the Science of Paleontology

Can you concieve of a nastier discovery in your fridge than a rotting egg? How about a rotting egg full of maggots? So then why are paleontologists Jorge Genise and Laura Sarzetti so enthused by their recent discovery of the fossilized remains of a rotting insect-ridden dinosaur egg?

Have you ever cracked open a sedimentary rock and found a fossil staring back at you that had been hiding inside? Remember how exciting that was. The fossil was probably a hard shell, or, if you were lucky, a bone. But imagine how excited you’d be if you’d found the fossilized remains of a soft-bodied creature, preserved against the odds under really special conditions. You’d then have some idea of the elation that paleontologists and paleoecologists feel when they turn up remains that take so much of the guesswork out of how a creature looked or how it lived millions of years before us.

Reconstruction of a Massospondylus dinosaur nesting site from South Africa, in which eggs and hatchlings were found. (Image: Julius T. Csotonyi)

It’s like Christmas morning for paleontologists when they discover eggs containing the intact embryos of dinosaurs [1], or when they unearth an animal with the identifiable remains of its last meal in its stomach [2]. Fossils like these are really special, because they not only preserve the form of long-extinct creatures, but also help fill in their behaviour or their sequence of development from hatchling to adult. It’s like being able to take a snapshot of the prehistoric world innumerable years ago.

But a rotting egg? What can it possibly tell us about the world of the Late Cretaceous, 70 million years ago? A lot, it turns out.

A team of researchers at the Museo Argentino de Ciencias Naturales recently reported in the research journal Palaeontology their discovery of the fossilized remains of a rotting dinosaur egg that had become colonized by wasps in Patagonia 70 million years ago [3]. The soft pupae (similar to butterfly cocoons) of metamorphosing young wasps were found inside the broken dinosaur egg.

Hang on — larval wasps often feed on other insects [4] or spiders [5]. What were they doing in dinosaur eggs? Their presence weaves an interesting story of scientific inference.

The egg was that of a titanosaur, a huge long-necked sauropod dinosaur, somewhat similar in appearance to the “Brontosaurus” with which many people are familiar (Brontosaurus, by the way, has since been renamed Apatosaurus).

The titanosaur egg had been forcefully broken long before it could hatch. Life was tough for dinosaur eggs and hatchlings. Although many adult dinosaurs were huge, their eggs were comparatively very small. The eggs of over 15-m (50-foot) long titanosaurs were only as large as those of ostriches. Eggs and hatchlings provided an easily captured and nutritious meal to any small carnivore sneaky enough to make it past the parental dinosaurs guarding a nest. These egg thieves included other dinosaurs, mammals and even snakes. In fact, a remarkable fossil announced last year shows a large — 3.5-m (11-foot) long — snake preserved in the act of raiding a titanosaur nest when the entire nest, snake, eggs, hatchling and all, was rapidly buried by sand [6].

Reconstruction of the remarkable fossil of the prehistoric snake, Sanajeh, raiding the nest of a titanosaur. (Image: Julius T. Csotonyi)

Whatever cracked the egg in the present case, once the egg was broken, the dinosaur embryo died, but there was a rich source of nutrients available for the taking by insects that could squeeze through the crack and lay their eggs inside. The pungent smell of the dead, rotting egg would have attracted scavenging insects. Several groups of insects, including ants, bees, moths and beetles, colonize decaying organic matter, and mole crickets are even known to scavenge the eggs of modern-day leatherback turtles [3].

However, based on comparing the fossilized remains with living animals on the basis of the shape, size and structure of the cocoons, and their presence in eggs, paleontologists concluded that the most likely identity of the fossilized cocoons is a wasp. Because wasp larvae (the equivalent of maggots) are almost exclusively parasites (living on resources provided by another creature, at that creature’s expense without providing a benefit in return) or parasitoids (parasites that ultimately kill and consume their hosts), the presence of the fossilized wasp cocoons in the dinosaur eggs most likely implies that other insects on which the wasps were feeding were also present in the egg. The wasps were the at the top of the food chain or a food web of insects, feeding on other insects, or on spiders that fed on other scavenging insects, that had invaded the egg before the wasps arrived.

This line of reasoning is a nice example of scientific inference leading to the generation of testable hypotheses. We make initial observations (wasp cocoons in a broken dinosaur eggs) and then use what we know about living animal communities (wasps are usually the tops predators in a food chain or food web of insects and spiders) to generate a prediction or hypothesis (broken dinosaur eggs were attacked by scavenging insects) that can be tested by future observations (other broken dinosaur eggs will be investigated for the presence of scavenging insect communities).

It also demonstrates that proper scientific investigations built on testable hypotheses can be performed without the need to conduct laboratory experiments. This is an important point to make, because some people wish to argue that evolution is not scientifically supported partly because they believe that paleontological studies are not truly scientific. This is untrue, for as we have seen, paleontologists can and do make testable predictions. Although we cannot ‘rewind the tape’ of life on earth and play it back repeatedly to see how life would evolve, we can perfom what we call ‘natural experiments’, in which we make predictions about the nature of future fossil discoveries based on what ecological and evolutionary theories tell us we should expect to see. Natural experiments are more difficult to control than laboratory experiments (i.e., it is more difficult to pin down sources of variation that can affect our predictions), but they abide by scientific principles nonetheless.

A wonderful example of the predictive power of evolution applied to the fossil record is the discovery of the fish-amphibian transitional form (some may call it a ‘missing link’) called Tiktaalik (which I will cover in more detail in a later post). As writer Jerry Coyne relates [7], a University of Chicago research team led by Dr. Neil Shubin was interested in finding evidence for the evolutionary transition from fish to amphibians. Several fish-like amphibians and amphibian-like fish had already been found, but Shubin was after something that was more intermediate than any species that were then known.

Based on the ages of undisputed examples of fish and amphibians, it was hypothesized that the ‘missing link’ should be found in rocks between 390 and 360 million years old. The hypothetical beast should also probably be found in a shoreline environment, where it had access to shallow water and land. The team applied these constraints of time and place to predict the rock formation in which the animal should be found. This was possible because, contrary to what creationist proponents would have us believe, the vast majority of fossils on earth are well-organized into a layered series that reflects their geological age, with younger strata above older ones. Since rocks matching the targetted age and prehistoric habitat were known from Ellesmere Island in the Canadian Arctic, Shubin’s team set up camp there and commenced their search.

After years of excavation, they were finally rewarded with an animal that they named Tiktaalik, which had features more intermediate between fish and amphibians than any previously known species [8].

Tiktaalik roseae, transitional between fish and amphibians. (Photograph: Eduard Solà)

Shubin’s nearly fruitless search demonstrates how difficult and statistically unlikely it is to find especially valuable fossils. We are therefore exceptionally lucky to have in our hands examples such as the wasp-infested titanosaur egg. However, these examples also demonstrate how vastly deep and rich is the geological well of evolutionary history hidden in the earth that we may plumb if we are diligent enough.

And I still prefer my insect-ridden rotten eggs aged 70 million years.

References

1. Reisz, R.R., D.C. Evans, H.-D. Sues, D. Scott. Embryonic skeletal anatomy of the sauropodomorph dinosaur Massospondylus from the Lower Jurassic of South Africa. Journal of Vertebrate Paleontology, 2010; 30 (6)

2. Hu, Y., Meng, J., Wang, Y. & Li, C. Large Mesozoic mammals fed on young dinosaurs. Nature, 2005; 433, 149−152 DOI: 10.1038/nature03102

3. Jorge F. Genise, Laura C. Sarzetti. Fossil cocoons associated with a dinosaur egg from Patagonia, Argentina. Palaeontology, 2011; 54 (4): 815 DOI: 10.1111/j.1475-4983.2011.01064.x

4. F. Maure, J. Brodeur, N. Ponlet, J. Doyon, A. Firlej, E. Elguero, F. Thomas. The cost of a bodyguard. Biology Letters, 2011; DOI: 10.1098/rsbl.2011.0415

5. Punzo, F. The Biology of the Spider Wasp Pepsis Thisbe (Hymenoptera: Pompilidae) From Trans Pecos, Texas. I. Adult Morphometrics, Larval Development and the Ontogeny of Larval Feeding Patterns. Psyche, A Journal of Entomology, 1994; 101 (3-4), 229-241. DOI: 10.1155/1994/70378

6. Wilson JA, Mohabey DM, Peters SE, Head JJ. Predation upon Hatchling Dinosaurs by a New Snake from the Late Cretaceous of India. PLoS Biology, 2010; 8(3): e1000322 DOI: 10.1371/journal.pbio.1000322

7. Coyne, J. Why Evolution is True. 2009; Viking. ISBN 9780670020539.

8. Daeschler, E.B., Shubin, N.H., Jenkins, F.A. Jr. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. 2006; Nature, 440 (7085): 757–763. DOI: 10.1038/nature04639

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The New Face of Museums

New Dinosaur Hall at the Natural History Museum of Los Angeles County

Today, we get to see the shiny new face of Dinosaur Mysteries, the dinosaur hall at the Natural History Museum of Los Angeles County. After an initial media event last week open to museum members, the exhibit opens to the public July 16, 2011 after three years of production effort by the Dinosaur Institute and contractors such as KBDA and myself.

Not only is the new exhibit now the west coast’s largest dinosaur exhibit, but it is also housed in two stately early-twentieth-century edifices, spanning two floors, with an open mezzanine to allow viewing of the central skeletons and the 20-foot-tall murals of dinosaurs and marine life (illustrated by yours truly).

Many of the dynamically and realistically mounted skeletons are composed of real fossilized bones rather than casts, featuring, among other things, a Tyrannosaurus growth series from chick to adult. What I find appealing as a scientist and educator is that the exhibit is organized in a way that encourages viewers to interpret the material in a scientifically question-driven way.

The exhibit also takes advantage of new digital technologies that are making museum visits around the world a much more enjoyable and interactive experience. The L.A. County Natural History Museum makes use of 30-inch digital displays with changing imagery that pans and zooms on restorations that I was commissioned to create for the museum showing what ecosystems probably looked like that are now preserved in the sedimentary rock of the Chinle (Triassic Period), Morrison (Jurassic Period) and Hell Creek (Cretaceous Period) Formations.

Swim the Ancient Seas of Ordovician Manitoba

Some museums have taken digital display technology to entirely new heights though. Among the leaders in the field is the Manitoba Museum in Winnipeg, Canada (which is also, by the way, home of the world’s largest trilobite). Last year, a phenomenal new exhibit opened, called Ancient Seas, and it must be seen to be believed.

Patrons take in the 3-panel panorama of the Ancient Seas exhibit at the Manitoba Museum. (Image courtesy of: Hans Thater, The Manitoba Museum)

It is best described by Dr. Graham Young, Museum Curator of Geology and Paleontology, and personal friend who maintains his own scientific blog, Ancient Shore, where among other colorful topics, the reader can find first hand accounts of scientific trips to hunt for fossils in the challenging Canadian subarctic. I recently had the pleasure to discuss the Ancient Seas exhibit with Graham. In his words:

The exhibit is a three-screen digital projection that depicts the tropical marine life that lived around what is now Churchill, Manitoba, about 450 million years ago. The creatures depicted in the video are all life forms that we find represented as fossils in central and northern Manitoba, and we have exhibited specimens of the fossils in front of and beside the video screens. I think that the exhibit is special because, first of all, the animators (Jilli and Lars at Phlesch Bubble) did a wonderful job of depicting the extinct life forms and placing them in their environmental context. It seems real enough that it permits visitors to suspend their disbelief. It is also special because it is depicting an actual preserved ancient place. Most reconstructions of past life use made up places; at Churchill we have an Ordovician boulder shoreline preserved in three dimensions, and the animators have placed the organisms into that place.

When we enter a museum and view a breathtaking exhibit such as Ancient Seas, jaw-dropping wonder often takes front seat in our minds, distracting us from the realization of how phenomenal an effort brought it into existence. I asked Graham to share with me the behind-the-scenes story of the production of the exhibit and his role as paleontologist:

I was involved in it from the get-go, really. We had seen an animation of the Burgess Shale that Phlesch Bubble had done at the Field Museum in Chicago, and it was suggested that we needed something of that sort for our Earth History Gallery.  I said that we would be able to do one only if we depicted that Churchill site, because it was the only place we knew enough about to do it justice.  So we came up with a specification for what would be depicted in the video, and we had to negotiate with the animators to determine what was actually do-able within time and budget.

I gathered together huge batches of scientific material, photographs, and diagrams, and sent them off to Jilli and Lars in Australia. They worked to develop digital models of the creatures, which they sent to me for review. In many cases, I didn’t think that I knew enough about the organisms, so I was able to draw on scientific experts in various countries to review the models and animations.  This is where it can be very helpful to have a scientist intimately involved in the process!  In some instances we had multiple episodes of going back and forth before we had a model which really depicted the creature the way it needed to be.  Jilli and Lars were very professional, very accommodating, and they put a huge amount of effort into ensuring that everything was as close to our conception of the creatures as humanly possible.

Then I also had to work with the designer to plan the space, and with the various collections and exhibit experts who prepared the specimens, made the mounts, installed lighting … I got to be involved in some way in just about every aspect of the exhibit.  It was a lot of work, but also a heck of a lot of fun, and it took about 18 months from the time the animators got started until we had the main part of the exhibit installed and open to the public!

A section of the Ancient Seas exhibit at the Manitoba Museum, featuring an Ordovician marine community. (Image courtesy of: Hans Thater, The Manitoba Museum)

The Future

The Manitoba Museum’s Ancient Seas exhibit is a prime example of the results of a progressive attitude that museum teams take toward exploiting developing technologies to creatively relate scientific findings to the public. Many museums are now utilizing not only touchable scale models, but also interactive motion-sensitive projections. But deciding how extensively to incorporate digital technology into museum displays is not a decision to take lightly; museum teams endeavor to share experiences with the public that the public might not be able to experience themselves. In the end, success will result from a careful balance struck between digital and real-life exhibits. These sorts of developments echo the view that Graham expresses about some of the directions in which he as a scientist foresees museum exhibits going:

…I really like the idea of having exhibits that allow the visitor to be more immersed in the experience.  I think we need to use sound and touch, as well as sight, to get experiences across.  I would really love to see some 21st century digital version of the early 20th century cycloramas…sort of dioramas in the round, but they can be wonderful exhibits (there is a superb old one in Iowa City).

I think that the best exhibits are the ones that choose the best medium for the material and the subject matter.  Which may mean some sort of video, or an interactive discovery experience, or simply a traditional artifact case.  We need to know what tools we can use, and be prepared to go as high or low tech as seems necessary.

Modern museums are like living things; they evolve to best suit their environment. This has the exciting implication that in our scientifically advancing era, museums are increasingly becoming an indispensable venue by which the public may access scientific research through a factually reliable, easy-to-understand and enjoyable multi-sensory experience.

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Dating Dinosaurs

When did the dinosaurs die out and how can we be sure? That’s kind of a trick question, actually, for evidence suggests that birds are the direct descendants of a group of small theropods (bipedal meat-eating dinosaurs). Therefore, not all dinosaurs have gone extinct.

Tylosaurus and the K-T impact event at the end of the Cretaceous. (Image: Julius T. Csotonyi)

Nevertheless, the vast majority of dinosaurs (the non-avian dinosaurs) died around 65 million years ago. Dinosaurs were the dominant terrestrial life forms on earth for over 160 million years, so it must have taken quite a disaster to wipe out such a successful group. A leading hypothesis involves the impact of a 10-km (6-mi) asteroid with what is now the Yucatan Peninsula in Mexico, creating the 180-km (112 mi) wide Chicxulub crater. Even that might not have been enough to do them in, and many scientists now lean towards the idea of a one-two punch delivered by the unfortunate coincidence of a massive wave of vulcanism (volcanic activity, from the Deccan Traps in India, a huge lava field) taking place at nearly the same time as the asteroid impact. Both events would have caused massive changes in global climate and therefore vegetation growth. In fact, the dinosaurs may already have been highly stressed by the time the fateful asteroid entered earth’s atmosphere.

Pachycephalosaurus and the approaching K-T asteroid, visible as a bright star. (Image: Julius T. Csotonyi)

However, it now seems as though dinosaurs may have been more tenacious than originally thought. Earlier this year, a research group at the University of Alberta led by Larry Heaman measured the age of a fossilized hadrosaur (duck-billed dinosaur) femur bone and found it to be only 64.8 million years old [1]. This may not look like a big difference, but it would mean that some dinosaurs may have survived the asteroid impact by about 700,000 years. That’s more than twice as long as humans of our species have been on earth. How could such a thing happen?

Actually, this should not surprise us too much if we really thing about it. If we know anything about life on earth, it is best summed up by Ian Malcolm’s line on Jurassic Park: “Life finds a way”. It’s very rare for an ecological disaster to wipe out all of something immediately. Usually, something survives, partly because the environment is heterogeneous enough to provide protected places where some life just happens to be located during the disaster. It’s akin to taking cover in the basement when a tornado passes overhead; the winds cannot reach some places. Similarly, there may have been places on earth where the dust and ash clouds raised by the asteroid impact cleared earlier, allowing earlier return of vegetation (and in turn, herbivores and the carnivores that fed on them).

The asteroid impact at the end of the Cretaceous was by no means the worst environmental disaster that life on earth has survived. There were times in earth’s distant past (710 and 635 million years ago) when nearly the entire planet was sheathed in ice. These events are known as “snowball earth”, and they made the recent ice ages with which we are familiar look like mild spring days by comparison. But even then, life found refuge near the equator, where the conditions were not quite as bad. Holing up in the relatively few life-sustaining niches, organisms quickly recovered (and diversified extraordinarily rapidly during the Cambrian period) once conditions improved. Later, at the end of the Permian period, about 251 million years ago, a global disaster involving massive climate change wiped out about 90% of life on earth. Again, however, even though this disaster took with it most of the bizarre mammal-like reptiles, a few survived, including the lineage that gave rise to mammals, and ultimately, us.

Darwinius masillae, an early primate. (Image: Julius T. Csotonyi)

Given how unlikely the fossilization process is, it’s not surprising that we haven’t begun to see evidence of some of the dinosaurian survivors of the Cretaceous extinction event (known as the K-T boundary) at the end of the Cretaceous until just now. Fossilization is a tricky thing, requiring a narrow range of conditions for it to work (e.g. quick burial of a body by sediments to prevent scavenging, and sufficiently low oxygen concentration to prevent decomposition by aerobic, or ‘air-breathing’, bacteria). Thus, only a very tiny sliver of all living things that die are expected to be preserved for millions of years by this process. As a result, we cannot reasonably expect to find a completely continuous fossil record, and proponents of creationism that hold up the discontinuity of the fossil record as an argument against evolution are ignoring this basic principle.

A recently deceased Brachylophosaurus, about to become entombed (and ultimately fossilized) by river sediments. (Image: Julius T. Csotonyi)

Given the difficulty of fossilization, it is not surprising that paleontologists have found a gap in the dinosaur fossil record prior to the Cretaceous extinction event (which can be detected by anomalies in the distribution of fossilized pollen, as well as often the presence of the element iridium, which is found at higher concentration in meteorites). They called it the ‘three-meter gap’, for the approximate thickness of this layer that is relatively devoid of dinosaur fossils. Indeed, perhaps dinosaurs had already been on their way out by then, and the Chicxulub impact was merely their coup de grace that finally did (most of) them in.

However, if some dinosaurs did survive the impact by several hundred thousand years, then we should see their remains everywhere in between, allowing of course, for the natural discontinuity of the fossil record. The best way to see through a discontinuity is to look for evidence of bones in enough places, because this increases our chance of finding those few skeletons that did manage to experience the right conditions for fossilization, even though there were not many around to begin with. The continual search for dinosaur fossils by paleontologists serves exactly this purpose.

And not surprisingly, bones are now starting to show up in the ‘three-meter gap’ too. A Yale University group, with Tyler Lyson as lead author of the study’s report, has found the horn of a Triceratops only 5 inches below the K-T boundary, implying an age only tens of thousands to a few thousand years before the impact. This is only around 0.01% of the time since the dinosaur extinction event.

So we’re throwing around huge numbers like 65,000,000 years. How can we be so sure about the accuracy of these ages? The answer lies in radiometric dating, which deduces the age of a rock sample by the proportion of a radioactive element and its decay product that the rock contains, given an extremely precisely known rate of decay of one radioactively unstable element into the other. Physics gives us this standard, and physics is the hardest science, giving us the most precisely known quantities. Radiometric dating is quite reliable. The problem that people have with believing its results stems, amazingly, from the same few anomalous results using these techniques that proponents of creationism keep raising into the spotlight, while ignoring the mountain of results that underscore the technique’s veracity.

What I find most interesting about Heaman’s study is that they use a newly developed direct radiometric dating method (by the rate of radioactive uranium decaying into lead) of measuring the age of the bone itself, not only the surrounding rock matrix. This new method confirms the age of the dinosaur bones to about the same as the surrounding rock strata (65 million years), providing an independent line of evidence supporting the age of the fossils ages. Independent lines of evidence (i.e. measuring something using a technique that is not dependent upon another technique) is very important, because the agreement between the results of different, unrelated methods gives the results much greater credibility.

This direct dating of fossilized prehistoric bone is especially important because creationists have long bemoaned the required dependence of our calculation of the age of fossils on measurement of the rock matrix in which they are found. This method is known as relative chronology. The age of the rock, it was claimed, may not accurately reflect the age of the fossil, because the fossil may have been transported into fissures in the rock (or buried atop the rock after older rock layers had been previously exposed by erosion) long after the rock was originally formed. Demonstration by Heaman’s team that the fossils themselves can now directly be dated by a physically reliable and precise technique, independent of the age of the surrounding sedimentary rocks, blows this complaint out of the water.

References

1. J. E. Fassett, L. M. Heaman, A. Simonetti. Direct U-Pb dating of Cretaceous and Paleocene dinosaur bones, San Juan Basin, New Mexico. Geology, 2011; 39 (2): 159 DOI: 10.1130/G31466.1

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Mole Rats on Morality

I’ll wager that mole rats are (apart from humans) some of the weirdest mammals on which you’ll ever lay eyes. Nevertheless, these odd little rodents have a lot to teach us about the evolution of our own tendency for cooperation or sense of morality. How? Let me back up a bit…

The other day, my wife and I were enjoying a pleasant stroll through a Tennessee riverside park. Searching for a sufficiently large stick to serve in our dog’s favourite game of save-the-log-from-drowning, I overturned a promising branch, and found its underside crawling with small black ants and fat white termites. Immediately, the science geek in me  exclaimed, “Cooool!” and my wife was immediately subjected to a short but enthusiastic rant about eusocial insects. Eusociality is a term used to describe the highest level of social organization in animals, in which societies are arranged into well-developed hierarchies, often with a single reproductive pair and a large number of workers. These societies are wonderfully complex and integrated. Have you ever squinted at a swarming ant nest and imagined it to be a single large creature, spreading amoeba-like tentacles to draw in food particles? Have you noticed how coordinated is the protective response to intruders such as the stick with which you poked at the nest? But what does this have to do with desert rodents? Or human morality, our apparent ability to distinguish between “right” and “wrong”?

Formosan termites. (Photo: USDA)

We all know that ants, bees, wasps and termites show an unusually high degree of social organization. But how many of us know that there’s a group of mammals that have similarly complex societies? No, I’m not thinking of our own humble species this time. Enter the mole rats, a group of about a dozen species of small, burrowing sub-Saharan African rodents with big incisor teeth that are located practically outside of their mouth so that they can dig with them without having to eat dirt. Their eyes are tiny, nearly vestigial organs, for vision is not a great asset in dark burrows. Cool adaptations to subterranean life.

But the really neat thing is that two of the species, the Damaraland mole rat (Cryptomys damarensis) and the naked mole rat (Heterocephalus glaber), have eusocial societies remarkably similar to those of ants. Now this is REALLY cool. Naked mole rats are the weirdest of the two, and have the most ant-like colonies. They’re also the downright ugliest. As their name suggests, they are practically hairless, and they look for all the world like a cross between a newborn mouse and a sharpei dog. Although they are mammals, they are incapable of regulating their body temperature physiologically the way we do, so in order to warm up, they huddle together in warm parts of their burrows.

Naked mole-rat. (Photo: Roman Klementschitz)

Naked mole rats live in groups of around six or seven dozen finger-sized individuals, most of which are sterile workers in two size classes: smaller ones mainly gather food (tubers) and dig burrows (spanning more than a mile in cumulative length); the larger ones fill the protective role of soldiers, again just like in ant nests. There’s even a queen, a single enlarged female whose role it is to breed with two or three males and produce copious workers for the colony. And, just like ants, these workers have a very low genetic diversity — they are extremely closely related, like what you get in a community with extensive inbreeding. In fact, in light of this fact, it’s a marvel that they are so devoid of genetic disorders that result from inbreeding. On the contrary, naked mole rats hold the title of the longest-lived rodents, with a life-span of 28 years! Their unusually stable genetic makeup is currently being investigated; the humble naked mole-rat is the latest addition to the list of animals whose genes have been fully sequenced.

Naked mole rats huddling in an artificially constructed burrow. (Photo: Edward Russell)

What could have driven a mammal to develop a complex eusocial structure so similar to distantly related ants? The answer actually embodies a nice example of the predictive power of evolutionary theory. Prior to the discovery of naked mole rats, a biologist by the name of Richard Alexander used ecological principles to predict that a hypothetical eusocial mammal should evolve from a colonial subterranean rodent exploiting a widely distributed food source from an expandable underground nest [1]. His description nearly perfectly matched the nature of the eusocial naked mole-rats that were discovered soon thereafter.

What spurred Alexander to make such a prediction? Recall the literary description of wild nature as “red in tooth and claw”. This adage alludes to the selfishness that is predicted to evolve in creatures by natural selection. The better an individual can compete for resources, the more resources it can acquire and the higher will be its fitness. If the traits that lead to this increased competitiveness are genetically encoded, then they may be passed on to the creature’s offspring. Its greater access to resources means that it can afford to produce more offspring. This will lead to an increase in the proportion of ‘competition-enhancing’ genes in the population from one generation to the next.

Unfortunately, there’s an all-too-popular misconception that continues to circulate: it’s the idea that increased competitiveness can only arise from the selfishness of individuals. This oversimplified interpretation has led to the erroneous belief (usually by proponents of creationism or intelligent design) that evolution can’t explain the existence of cooperation or the apparent presence of a “moral code” in humans. How could just about every human society on earth possess an innate knowledge of what constitutes right and wrong, if it wasn’t instilled in us by a creator? Since many animals do not hesitate to kill each other (also a bit of an oversimplification), why do we seem to realize that killing or stealing is wrong? Surely this is evidence that these altruistic tendencies were bestowed on us divinely, right?

Mole rats, had they the facility of speech, would beg to differ. They (and myriad other animals) demonstrate that a species can achieve competitiveness by the evolution of cooperation rather than selfish fighting among individuals, essentially extending the unit of selfishness to the group rather than the individual. (Remember that squinty-eyed view of the ant nest as an amoeba? Yes, think along the lines of a superorganism, and you’re on the right track.) The key factors in the case of mole-rats turn out to be (1) relatedness and (2) the distribution of food sources. (Keep these factors in mind for human evolution too…)

African savannah. (Photo: Marco Schmidt)

Remember that the mole rats in a colony are extremely closely related to each other. Their colonies are large families consisting of many, many siblings, just like ants. Now, aside from the occasional sibling rivalry that crops up in families, brothers and sisters tend to get along quite well, and usually favour each other over strangers when it comes to food and fortune. Why? Ecologists explain this by pointing out that siblings share a large proportion of their genes, for they all acquired their genetic material from the same two parents. Thus, if you help your brother or sister to gather resources (and therefore to better afford to have kids), you are helping to pass along a portion of your own genetic code almost as well as if you have children of your own. Exercising a set of strategies that help one’s relatives survive (even at a small cost to one’s own fitness) is referred to as “kin selection”. So really, evolutionary theory predicts that a closely related group should express some cooperative behaviour to each other. And, the more similar the genetic makeup of individuals, the more likely they are to promote the survival of their own genes by helping each other; so the closer the familial relationship, the higher the predicted degree of cooperation. (We tend to help our brothers and sisters more readily than our second cousins.) The extremely low genetic diversity among mole rats helps to explain their excessively high cooperative behaviour (remember, the workers are sterile, foregoing reproduction entirely in order to gather food and maintain the burrows).

OK, so why live in family groups at all? If selfish individuals are just as likely to succeed as selfish family groups, then why should individuals band together at all? After all, cooperation does require one to give up some of one’s own resources. Well, have you observed how families stick together most strongly in the face of adversity or lean times? Mole rat societies demonstrate wonderfully well how a patchy distribution of food can stimulate cooperative behaviour. Naked mole rats live in arid regions of Africa that receive little rain. They feed on tubers (enlarged portions of roots that are rich in nutrients, serving as storage structures for plants in harsh environments), which are widely spaced due to the paucity of nutrients and water for plant growth in these deserts. Although a single tuber could last an individual mole rat for a long time, a single mole rat would have a very hard time finding another tuber before succumbing to hunger and death. It would be very advantageous for this mole rat to be able to be in many places at once while searching for its next meal in order to cover more ground. The best way for it to do this is to make many copies of itself and share the burden of the search among its copies. That’s very close to what naked mole rats do. They set up cohesive colonies and produce a lot of extremely closely related offspring that can broaden the search and increase the chance of finding tubers. Kin selection then encourages them to cooperate by sharing their finds rather than keeping it for themselves. In some ways, then, you can almost see the closely knit colony as a “superorganism”, a kind of extension of the individual to increase survival by spreading the workload to overcome some of the environment’s unpredictability.

So then, harsh environments with scarce and difficult-to-find resources can promote the emergence of cooperative groups, and kin selection helps to increase the cohesive bond of these groups. This phenomenon is taken to the extreme in mole rats, but how does it relate to human evolution and the rise of our cooperative tendencies or our apparently innate sense of right and wrong? The following ideas have been presented by many investigators prior to this explanation, but the argument goes something like this:

An early hominin, Ardipithecus ramidus. (Image: Julius T. Csotonyi)

Like mole rats, our ancestors also arose in Africa. The arid savannah presented an environment in which food was widely dispersed, giving groups of hominids a better chance of survival than solitary individuals [2]. Group living also made more eyes and ears available for detection of predators, further increasing chances for survival through cooperative vigilance and alarm-calling. It became evolutionarily advantageous for early hominids to exhibit cooperative behaviour, and for the group to frown on behaviour that was destructive to this strategy (e.g. killing others of the group, stealing resources, etc.). Interestingly, these are the very same strategies that make up what many of us refer to as human morality. Groups exhibiting more extensive cooperation would have had a better chance of surviving, and would therefore have passed on their genes more numerously to the next generation. Thus any genes that promoted altruistic behaviour would have increased in proportion from one generation to the next, setting the basis for the evolution of behaviours that we label as morally right.

So there we have it. From mole rats to morality. I have certainly skipped over many details in human behavioural evolution, including the influence of society on behaviour in non-genetic ways. I’ve also left out many mechanisms by which cooperation can evolve, either within or between species, and the evolution and persistence of cheating, but those are the subjects of another fascinating story… For now, my intent was to briefly describe one plausible explanation for the emergence of cooperative behaviour in humans by invoking natural selection and by comparison to the mole rat model. Who knew that mole rats had so much to teach us of the evolutionary routes taken by our own ancestors?

References

1. PW Sherman, JUM Jarvis and RD Alexander. (1991) The Biology of the Naked Mole-rat, Princeton University Press, Princeton, New Jersey

2. Jeffrey A. Kurland and Stephen J. Beckerman. (2009) Optimal Foraging and Hominid Evolution: Labor and Reciprocity (pages 73–93) DOI: 10.1525/aa.1985.87.1.02a00070

Links

Mole rats

http://animals.nationalgeographic.com/animals/mammals/naked-mole-rat/

http://www.sandiegozoo.org/animalbytes/t-naked_mole-rat.html

http://www.livescience.com/6219-naked-mole-rats-secrets-revealed.html

Evolution of cooperation and prosociality

http://www-personal.umich.edu/~axe/research/Axelrod%20and%20Hamilton%20EC%201981.pdf

http://www.nytimes.com/2007/09/18/science/18mora.html?pagewanted=1

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Birds of a Feather

To kick off this blog, I wish my fellow Canucks a happy Canada Day this July 1!

So have you heard? Life is getting increasingly set-in-stone (pardon the pun) for us paleoartists, as paleontologists continue their relentless chipping and chiselling at our artistic license regarding the colors of dinosaurs. Last year, Li et al. (2010) and Zhang et al. (2010) used an ingenious technique to decode the actual colors that the feathered dinosaurs Anchiornis huxleyi and Sinosauropteryx prima sported. By examining the shape and distribution of microscopic (originally pigment-bearing) structures called melanosomes fossilized within the exquisitely preserved plumage of this tiny four-winged troodontid dinosaur, they were able to show that the patterns exhibited by the melanosomes were similar to patterns found in living birds (the probable descendents of a common ancestor with Anchiornis and Sinosauropteryx). Because these patterns correlate with feather color in extant avian species, the investigators were able to map out the actual color patterns of Anchiornis: grey with alternating white strips on the wings, a russet crest and russet markings on the cheeks. This compelled me to update my previously red-colored illustration of the animal, yielding the following:

Anchiornis huxleyi, sporting realistic colors.

Now, a different team of researchers (Wogelius et al., 2011) has applied a brand new technique to shed light on the plumage coloration of the 100-million-year-old early Chinese bird, Confuciusornis sanctus. They reported today in Science Express that x-ray fluorescence images acquired of the magnificently preserved avalian dinosaur fossil reveal the presence of traces of copper in organometallic compounds derived from the pigment eumelanin, which is responsible for dark coloration in skin, fur and feathers. The technique allowed mapping of the distribution of eumelanin over the entire fossil, revealing that Confuciusornis possessed light colored wings and a dark head, neck and tail.

Remarkable discoveries such as this one underscore not only the sheer amount of information preserved within some fossils, but also the ingenuity of paleontologists faced with the task of reconstructing the biology of organisms whose remains have lain sandwiched between sedimentary rock layers for dozens to hundreds of millions of years. Until now, only feathered dinosaurs have been color-mapped, but this is mainly because the analysis was based on the morphological examination of melanosomes within feathers. However, the integument of scaly-skinned animals is also extremely well-preserved in some specimens, and paleontologists such as Phillip Manning are hard at work to determine whether the thin veneer of organic material that sometimes accompanies the skin impressions can be used to infer the original distribution of pigments in life. For example, it will be interesting to determine whether techniques such as synchrotron rapid scanning x-ray fluorescence (SRS-XRF) will yield color patterns on scaly skin impressions of dinosaurs like the mummified Edmontosaurus annectens specimen nicknamed ‘Dakota’. For now, paleoartists wield a measure of artistic license in assigning color patterns to non-feathered dinosaurs, but if recent advances in paleontological analytical techniques are any indication, the relative creative freedom of these days may soon go the way of the dinosaur.

References

Quanguo Li, Ke-Qin Gao, Jakob Vinther, Matthew D. Shawkey, Julia A. Clarke, Liliana D’alba, Qingjin Meng, Derek E. G. Briggs, Long Miao, Richard O. Prum. Plumage Color Patterns of an Extinct Dinosaur. Science, Online February 4, 2010 DOI: 10.1126/science.1186290

R. A. Wogelius, P. L. Manning, H. E. Barden, N. P. Edwards, S. M. Webb, W. I. Sellers, K. G. Taylor, P. L. Larson, P. Dodson, H. You, L. Da-Qing, U. Bergmann. Trace Metals as Biomarkers for Eumelanin Pigment in the Fossil Record. Science, 2011; DOI: 10.1126/science.1205748

Fucheng Zhang, Stuart L. Kearns, Patrick J. Orr, Michael J. Benton, Zhonghe Zhou, Diane Johnson, Xing Xu, and Xiaolin Wang. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature, 27 January 2010

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