The Taming of the Chloroplast

A fascinating study [1] has recently underscored the hypothesis that our mitochondria, the power packs of our cells, share an ancient kinship with a particularly nasty disease, typhus. Put plainly, the same bacterium may have been the granddaddy of each. This result surprisingly implies that we’re all partly bacterial, and not only in a genetic sense but also structurally. In the last post (“Frankenstein’s Batteries“), I covered the story of how a forced cohabitation with our one-celled ancestors could have made the originally disease-causing bacterium change its stripes and give rise to the essential mitochondria that now power our cells. Dedicated components of our cells (organelles) have been acquired via the process of endosymbiosis, in which one organism lives within the body of another in order to gain access to benefits such as a reliable source of nutrients or protection from the elements.

But many people, especially if they have been courted by the ideology of creationism or intelligent design, might respond: “Fascinating story, but too bad you don’t have evidence of intermediate stages of the process. All you have are fully parasitic microbes and fully integrated organelles, right? Can you point to any living candidates of in-between stages?” To this question, an over-enthusiastic biologist — not unlike myself — would bristle with excitement and answer: “Glad you asked! Let’s rectify this problem and fill the alleged gaps with some colorful living examples.”

So let’s look at some weird and wonderful examples of living intermediate stages in the taming of another organelle, the chloroplast. But first, let’s consider how chloroplasts appear to have evolved, and the evidence for their evolutionary origin.

Cells of the moss Plagiomnium affine, showing the numerous brilliant green disk-shaped chloroplasts inside each cell. (Image: Kristian Peters -- Fabelfroh)

Plants and Algae: Hunters-Turned-Farmers

Plant and algae cells have mitochondria, the same as we do. (Recall, from the last post, that mitochondria are the power plants in our cells, churning out useful energy by ‘burning’ the food molecules that we ingest.) But the ancestors of plants had an even better idea than did our animal cells’ ancestors. (Of course, you need to read “idea” in a figurative sense only — cells have no conscious volition or thought processes.) Plants’ ancestors acquired an improved version of an energy generating device — a chloroplast — by engulfing cyanobacteria, a photosynthetic group of bacteria that are also known as “blue-green algae”. The chloroplast differs from the mitochondrion in that it appears to have arisen not from the invasion of a host cell by a parasite, but from a predator playing with its food before digesting it. Nevertheless, it’s a splendid example of endosymbiosis.

In those early days, plant cells’ ancestors did not possess the green color that they do today. Whatever green hues they did sport probably came from the cyanobacteria that they ate, and it lasted for the short time before they proceeded to digest the cells, pigments and all. Cyanobacteria are good sources of food because they are full of chemical energy. Cyanobacteria use the green pigment chlorophyll (in collaboration with red, orange and yellow pigments called carotenoids) to convert, or transduce, solar energy from the sun into useful chemical energy. They do this by cocking the hammer, as it were, on high-powered molecules such as adenosine triphosphate, or ATP. But they also store some of the energy from light in the energetic chemical bonds within sugar molecules. This way, they not only get abundant free energy from the sun, but are also able to shelf some of it in a stable form that their mitochondria convert into ATP later at night, when the sun is not around. Their solar-powered habit made cyanobacteria palatable to other types of cells in their environment — predatory cells. These predators feasted on cyanobacteria for countless millions of years. But then a revolutionary event occurred. It may have gone something like this:

A predatory eukaryotic cell slurped up cyanobacteria from the warm surface of a pond, lake or ocean, engulfing them by phagocytosis — i.e. wrapping a membrane around them and then pumping digestive enzymes into the membrane to dismantle the cyanobacteria. The simple digested molecules were then fed into mitochondria, which turned them into energy (ATP) for the cell. But the cyanobacteria continued to make sugar by photosynthesis for a short time before they were digested in the phagocytosis membrane. Some of this sugar leaked out into the surrounding cell, and for a short time before digestion, the predatory cell enjoyed photosynthetically-manufactured food, courtesy of the cyanobacterium’s last gasps. Some cells refrained from digesting their captured cyanobacteria because it turns out that if they stockpiled a whole lot of these membrane-coated cyanobacterial ‘candies’ and let them continue to live while restraining their rate of reproduction, then the predators (now hosts) could soak up so much sugar from their cyanobacterial captives that they didn’t even need to expend energy to ingest more cyanobacteria. They could just bake in the sun all day long and let their cyanobacterial vending machines pump out sugar for their mitochondria to convert into energy.

And so the chloroplast was born, a membrane-enclosed organelle in plant and algal cells that carries out photosynthesis. Of course, cells did not make any conscious decisions to refrain from digesting cyanobacteria. But when several ways of life are available to an organism, the more economically prudent option (with a high ratio of benefit to cost) results in more offspring, making this way of life ever more prevalent in the population if it can be inherited genetically. Retention of living cyanobacteria offered the great opportunity to abandon the expensive business of hunting at the small cost of foregoing the energy from digesting the whole cyanobacterial cell. It was a little like the transition that our own human ancestors made thousands of years ago: farming presented a good return on the investment of giving up hunting.

Cross-section of a generic chloroplast, the organelle in which photosynthesis occurs in plants and algae. Its structure and genome is very similar to that of ancestral cyanobacteria. (Image: Miguelsierra)

Evidence for Cyanobacterial Ancestry of Chloroplasts

As for mitochondria, there’s evidence of a bacterial origin for chloroplasts. Like mitochondria, chloroplasts possess their own DNA (called the plastome), which is a circular loop, more like that in bacteria than in the eukaryotic host cell. This DNA is severely reduced, containing only about 5% as many genes as free-living cyanobacteria, but the genes that are present are similar to those of their cyanobacterial ancestors. And the missing DNA? Amazingly, much of it has been transferred from the chloroplast to the host’s own chromosomes in the nucleus. This extensive genetic cross-wiring illustrates that stable endosymbiosis has caused an impressive amount of the labour of living to be divided between the host and its photosynthetic guest.

Farming photosynthetic organisms by engulfing them and then holding them captive to soak up their sugary cell products is such a good strategy for survival that there is evidence that it has taken place multiple times in the past in different groups of cells. Molecular biologists can recognize at least two genetic lines of chloroplasts, meaning that cyanobacteria were engulfed and successfully ‘domesticated’ on at least two separate occasions (in the Archaeoplastida, which includes plants and algae on the one hand, and in the amoeboid cell Paulinella on the other hand). Furthermore, within the main Archaeoplastida genetic line, we see evidence of not only primary endosymbiosis (establishing chloroplasts by engulfing naked cyanobacteria), but also secondary endosymbiosis. This means that some algae, such as Vaucheria, appear to have engulfed an algae that had in turn engulfed a cyanobacterium ages ago. The whole arrangement now resembles Russian nesting dolls, with the original cyanobacterial descendent wrapped in four concentric membranes corresponding to the two membranes of the chloroplast nested within the cell membrane of its primary host and wrapped in the feeding membrane of its secondary host. In some cases (e.g. cryptomonads), the original nucleus of the engulfed algal cell is still found squashed between the membranes of the chloroplast.

An evolutionary tree showing the relatedness of different lineages of chloroplasts in living groups of organisms. Generally, each major lineage originates from a unique event of endosymbiosis, the establishment of a stable association between a host and either a cyanobacterium or an algae that already harbours a chloroplast. (Image: Nova)

Almost a Chloroplast: Intermediate Stages in Evolution

But there’s a catch: if this predator-gone-plant way of life was so attractive that it arose more than once, then we should expect to see it happening today as well. We should see some intermediate stage of chloroplast taming going on. Evolution doesn’t normally just work once and then stop. Predatory cells that feed on photosynthetic cells should still be embarking on similar collaborative business ventures with their food. So where are they? They’re all around us, it turns out.

A Fungus Took a ‘Lichen’ to Some Algae…

Lichens are a weird chimaeric life form with an almost absurdly robust ability to survive under extreme conditions, such as the soil-free surface of wind-lashed rocks on the peaks of mountains, tomb stones,  tree trunks, old rusting automobiles, soil, sand, etc. They derive their versatility partly from their compound nature: lichens consist of a durable fungus (normally a heterotroph, which gets its food from digesting other organisms) whose internal cells are modified into finger-like formations that clasp single cells of cyanobacteria or green algae (like a long-fingered basketball player holding a ball between dribbles), and forcing the membranes of the algae to leak out some of the sugars that it produces. The lichen is thus effectively a photosynthetic fungus, powered by the sun.

A lichen called Xanthoparmelia growing on basalt, a volcanic rock, on O'ahu, Hawaii. The shape of the creature is determined by the fungus, and the subtle green color is due to algae held captive under the upper cortex (skin-like layer) of the fungus. The color is only faintly green because light does not penetrate as easily through the lichen's cortex as it does through the cells of a plant leaf, so most of the color is due to the fungal portion of the creature. Lichens are more obviously green when they are wet, partly because their tissues are more transmissive to light under those conditions. (Image: Eric Guinther)

Lichens are interesting in that the algae do not grow inside the fungus cells (unlike a plant, which has cell-bound chloroplasts), but are held within the body of the many-celled fungus nonetheless. The relatively primitive nature of the association is also underscored by the fact that the algal or cyanobacterial cells have to be captured from the environment each time that the fungus portion reproduces from spores. However, it may be hard to find the algae that it needs to survive in some of the wretched environments in which it lives, and the lichen may die out if it needed to catch its food-producing algae each time it reproduced. So the lichen solves the problem by also being able to reproduce by fragmentation, and by releasing little balls of fungal cells that are already clasping algal cells.

Corals and Anemones: Alternative Green Energy on the Reef

Animals are usually pretty good at getting around and hunting for their food. But say you’re an animal without legs or a brain — not unlike a coral or sea anemone in the ocean. This predicament makes hunting for your food pretty difficult, and you’re forced to rely on laying in wait for snacks to come bumbling along and to get close enough for you to ensnare them in your tentacles. So you’d better hope (also a trifle difficult without a brain) that you live in a heavily populated lagoon, with lots of “accidental” feeding opportunities. It wouldn’t be a bad idea to have a backup plan in case your neighborhood experienced a drop in property value and stopped attracting tourists.

Two examples of mutualism, an interaction between species that mutually benefits each. In the first example, the clownfish hides from its enemies among the poisonous tentacles of the anemone (to which it has evolved a defense) while the anemone derives both nutrients from the fish's wastes and protection against anemone-eating butterfly fish (which the clownfish drives off). In the second example, the tentacles of the anemone are green because of the endosymbiotic algae that live in its cells, providing the host cell with photosynthetically produced sugars in exchange for a stable habitat in which to live, free of grazing. In effect, the algae serve the animal in the same way that chloroplasts serve a plant, and only part of an anemone's food consists of other animals that it consumes. This is why bleaching of corals (the loss of the endosymbiotic algae) is so damaging to reefs; it starves them of solar-generated food. (Image: Janderk)

In an energy crisis, going green is advisable. Unlike a great deal of conservative politicians, many comparatively highly evolved corals and anemones have embraced precisely this strategy. They have solved the compound problem of an unpredictable food supply and a sessile lifestyle by hosting algae within their own cells and harvesting the chemical energy that their windowsill gardens provide. The bizarre result is an effectively photosynthetic animal. If you’ve ever looked into an aquarium and seen a green colored coral, or an anemone waving verdant tentacles, it’s the endosymbiotic algae that are responsible for this hue.

Coral polyps (the animal units of colonies that form the large corals with which we are familiar), tinged green by their dinoflagellate algal endosymbionts. (Image: Nbarakey)

Endosymbiotic algae in corals much more closely resemble cloroplasts than do the algae in lichens. Not only do they reside within cells than between them, but they can also be transmitted to the next coral generation in egg cells, circumventing the need for the animal to acquire its algal cells from its environment. But although the algal cells are more integrated into the coral’s system than those found in lichens, they are still not quite chloroplasts. The association between corals and algae is not as tightly coevolved as the plant/chloroplast association, in which many of the genes for controlling reproduction have been surrendered by the cyanobacterium (now a chloroplast) to the plant’s chromosomes. The algae can survive perfectly well independently of the coral (perhaps even better, leading to the suggestion that the coral actually parasitizes the algae), and corals can both collect populations of algae from their environment and release algae from their cells.

Algal cells are prevented from multiplying out of control and bursting the cell like a virus by (1) digestion of excess cells, (2) production of chemicals that prevent the algal cells from multiplying, or (3) the above-mentioned release of algae from coral cells [2]. In fact, it’s a malfunction of this ability of corals to release their endosymbiotic algae that leads to the serious problem of coral bleaching on reefs. An upset of their environment by factors such as warm ocean temperatures can cause the release of so many algal cells that the corals starve.

Coral bleaching due to the expulsion of endosymbiotic algae. Normal coral on the right, its greenish hue due to the algae in its cells; bleached coral on the right after ejecting its complement of photosynthetic cells. (Image: NOAA)

The Disposable Solar Batteries of Dinoflagellates

Many other types of life forms also acquire algae from their environment and use them as power sources. They include not just animals, but also single-celled predators. Dinoflagellates are one such group of unicells, oddly shaped creatures that look like plated military helmets plastered together. Not all species of dinoflagellates harbour endosymbiotic algae, and even those that do can expel them and shift back to a predatory lifestyle. In this sense, dinoflagellates use algae like disposable batteries, and the impermanent nature of the interaction underscores the incompleteness of evolution toward a stable association. In a bizarre twist of fate, dinoflagellates are sometimes also enslaved as endosymbionts by certain corals.

A typical dinoflagellate cell (Peridiniella danica), which is oddly shaped due to its cell wall forming grooves along which lie their two characteristic whiplike flagella, with which they propel themselves through the water. (Image: Crassiopeia)

Hatena arenicola: The Jekyll and Hyde Microbe

Among the tiny single-celled creatures that keep captive algae to freeload on their photosynthetic products is an odd creature called Hatena, a scientific name which means “enigma” in Japanese — an apt name [3]. It represents one of the best examples of an association that is transitional between free-living species and an obligately joined union, because of several modifications to each partner that facilitate their association.

Each cell of Hatena harbours only a single large endosymbiotic cell of the algae called Nephroselmis. This algae possesses its own dedicated chloroplast (so recall that we’re dealing with secondary endosymbiosis here), but once the Hatena acquires the algae, the chloroplast is severely enlarged, and other cell components, such as mitochondria, Golgi body, cytoskeleton, and the internal membrane system are degraded. These are major modifications that maximize the efficiency of the algae as a solar-energy converter, reducing those parts that it would only need when living on its own.

Oddly, when Hatena divides, one daughter cell keeps the algal cell and remains photosynthetic, living a life like a plant, while the other daughter cell turns predatory because it has lost its solar power generator. Hatena switches identities like Dr. Jekyll and Mr. Hyde. The predatory alter-ego then grows a special feeding apparatus that allows it to acquire a new Nephroselmis algae from its environment, starting the endosymbiosis anew. Once the algae is acquired, the feeding apparatus is lost.

It is this amazing array of special adaptations toward a conjoined existence that makes the HatenaNephroselmis association such a wonderful example of an evolutionary transitional form probably undergoing selection toward permanent integration. It sheds light on one particular route that such evolution can take.

‘Kleptoplasty’ in Sea Slugs: Evolution by Purse-Snatching

Among animals that have gone the solar-powered way of plants, sea slugs in the group called Opisthobranchia have gone a step further even than Hatena in the reduction of the unneeded parts of their endosymbiotic algae [4]. Sea slugs normally use a rough, sand-paper-like row of teeth called a radula to scrape a meal of algae off the sea floor. However, the Eastern Emerald Elysia sea slug (Elysia chlorotica) sees the algae Vaucheria as more than a quick meal. It sees it for what matters most: its chloroplasts alone. But Vaucheria is a long, filamentous algae, with perhaps a little too much wrapping around the chloroplasts to practically hold onto the whole algae. No problem — Elysia simply performs a bit of purse snatching. It pierces the long cells of Vaucheria with its radula, and then sucks out the contents as if from a straw. It digests the contents of the Vaucheria cell, but stops short at the chloroplasts, which it claims for itself and maintains in its digestive tract cells in a functional state while the chloroplasts last.

The sea slug known as the Eastern Emerald Elysia (Elysia chlorotica), colored green by its kleptoplasts, stolen chloroplasts from the algae Vaucheria. (Image: Mary Paert)

This felony is called kleptoplasty, which literally means “stealing plastids” (a plastid is a membrane-bound organelle, such as a chloroplast). The chloroplasts lend Elysia a bright green color, hence its common name. Check out the original paper describing this interaction, “The making of a photosynthetic animal”, by Mary Rumpho and collaborators. Even if you do not read the technical parts of the manuscript, it’s very much worth a look to see the spectacular color photos of Elysia and other animals that use endosymbiotic algae for photosynthesis.

But the chloroplasts of Vaucheria are optimized for Vaucheria alone. Therefore, although they multiply inside cells of Vaucheria, the chloroplasts are unable to do so in the foreign environment of the sea slug’s cells, and they ultimately die. Still, they last for the entire 10-month life span of the sea slug, even though they are not transmitted to its offspring. How is this possible? Amazingly, studies have shown that Elysia has stolen not only chloroplasts from Vaucheria, but also some of its genes [4]! Some of the genes required for chloroplast maintenance are now found on the chromosomes of the sea slug, which greatly increases the ability of the sea slug to cultivate its stolen kleptoplasts. This is one of those rare examples of horizontal gene transfer between an animal and a microorganism. I covered horizontal gene transfer in more detail in a previous post, “Evolution’s Usual Suspects: 1. Plagiarizing Wizards“.

So Elysia is a photosynthetic animal that truly possesses chloroplasts, and even goes as far as to possess some of the genes necessary to maintain chloroplasts that cannot survive outside of their host. However, the association is not completely stable, for sufficient genes are not present for maintenance of reproducing populations of chloroplasts in its cells, so Elysia is not entirely photosynthetic.

An interesting side note about the stolen chloroplasts of Elysia: in a way, they are an example of tertiary endosymbiosis. The chloroplasts are highly modified red algae (with cyanobacterial chloroplasts of their own), which were in turn enslaved by Vaucheria, but were then enslaved yet again by Elysia. Poor red algae-derived chloroplasts — they are freed from one instance of metabolic slavery only to be enslaved afresh.

A Deep Sea Grand Theft Mystery Solved

Perhaps the most convoluted and colorful story of borrowed biological components hails from the deep sea, in the tale about the tiny but monstrous looking and equally intimidatingly-named Black Loose-jaw Dragonfish (Malacosteus niger). These bizarre creatures, like many other deep-sea fish, are bioluminescent, generating their own light through a biochemical reaction (more on this in a later post). They do this both to communicate with each other (e.g. find mates) and to illuminate their prey so that they can hunt more efficiently. Most of the light they generate is blue in color, and the eyes of deep sea animals are sensitive to such blue light. Bioluminescence in the deep sea is convenient, but it also therefore makes fish visible to their enemies, so it’s a risky superpower to possess.

The enigmatic Black Loose-jawed Dragonfish (Malacosteus niger), which installs light-sensitive pigments into its eyes that are derived from photosynthetic bacteria via copepods. (Image: Rafael Bañón)

However, dragonfish are unique among deep-sea fish in that they also generate red light, to which other fish — including their enemies — are blind, so they can escape their predators and more effectively illuminate their prey. But to be able to use red light, they must also be able to see it, and for that they have evolved a remarkable apparatus.

Their eyes contain a light-sensitive pigment that is not their own, but was stolen twice, once from a copepod (tiny plankton related to lobsters) and once from a photosynthetic bacterium [5]. (Recall that we can see light because the retinas of our eyes possess special compounds called pigments, which slightly change their molecular configuration when they are excited by light, and this excitation is transmitted to our nerves and ultimately our brains.) The special pigment in the eyes of dragonfish is derived from pigments called bacteriochlorophyll c and d. Bacteriochlorophyll c and d are actually photosynthetic pigments used to convert light to chemical energy (like plants use chlorophyll) by an ancient group of bacteria called green sulfur bacteria. Green sulfur bacteria are holdovers from a time over 2 billion years ago, when the earth’s atmosphere lacked free oxygen. So the pigment used by the fish to detect light is stolen from a bacterium that manufactures it to harness the energy in light.

But, the deep-sea dragonfish does not eat the bacteria directly. (You may think it obvious, for photosynthetic bacteria should not be found in the dark deep-sea, but green sulfur bacteria have in fact been isolated from hydrothermal vent communities in the deep-sea [6].) Instead, the dragonfish eat planktonic copepods, which in turn have eaten the bacteria and have retained the pigments in their bodies. This is like a thief stealing a stolen article from another thief. True, the dragonfish story does not quite qualify as endosymbiosis (no living components of another organism are harboured in the dragonfish’s cells), but it does serve to illustrate that the light-sensitive pigments of photosynthesis are valuable enough to encourage such grand theft between diverse creatures. Photosynthesis is one of the greatest inventions of life on earth, and I’ll cover more about it in a later post.

There are many, many other strange and awe-inspiring stories of endosymbiosis among earth’s living systems, but I will stop here to avoid writing a full-length book on the subject. Hopefully, however, this account has helped to inspire my readers to further investigate the ample trail of bread crumbs left by evolution in the form of endosymbioses.

References

1. 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. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 cladeScientific Reports, 2011; 1 DOI: 10.1038/srep00013

2. Titlyanov EZ, Titlyanov TV, Leletkin VA, Tsukahara J, van Woesik R, Yamazato K. (1996) Degredation of zooxanthellae and regulation of their density in hermatypic corals. Marine Ecology Progress Series. 139: 167-178. (FREE DOWNLOAD)

3. Okamoto, Noriko; Inouye, Isao (October 2006). Hatena arenicola gen. et sp. nov., a katablepharid undergoing probable plastid acquisitionProtist 157(4): 401–19. doi:10.1016/j.protis.2006.05.011.

4. Rumpho M, Pelletreau KN, Moustafa A, Bhattacharya D. (2011) The making of a photosynthetic animalThe Journal of Experimental Biology 214:303-311 (FREE DOWNLOAD)

5. Douglas RH, Mullineaux CW, Partridge JC. (2000) Long-wave sensitivity in deep-sea stomiid dragonfish with far-red bioluminescence: evidence for a dietary origin of the chlorophyll-derived retinal photosensitizer of Malacosteus niger. Philosophical Transactions of the Royal Society of London, Series B. 355: 1269-1272. (FREE DOWNLOAD)

6. Beatty JT, Overmann J, Lince MT, Manske AK, Lang AS, Blankenship RE, Van Dover CL, Martinson TA, Plumley FG. (2005) An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal ventProceedings of the National Academy of Sciences of the United States of America 102 (26): 9306–10. doi:10.1073/pnas.0503674102 (FREE DOWNLOAD)

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Frankenstein’s Batteries

Endosymbiosis: Bread Crumb Superhighway

As life ambles along evolutionarily, it leaves behind bread crumbs of evidence that we can use to retrace its route. As bread crumb trails go, the one left by the process of endosymbiosis is a veritable multilane superhighway. Endosymbiosis (from “endo”, meaning “inside”, and “symbiosis”, meaning “living in close association”) refers to the weird condition of one creature taking up residence inside another. The signature of evolution is scrawled layer upon layer, not only in gene sequences but also in cellular structures. We can even catch transitional compound organisms — chimaeric Frankensteinian constructs of surprising beauty — in the act of formation. As a biologist, this is one of my favourite topics of study. It’s one of those classic areas of science that is rife with fascinating and intricate stories of cooperation and collaboration that leave one’s jaw agape in wonder, whether one is a biologist or not.

Endosymbiosis helps us to understand who we are at the most basic level. Over the last few posts, I’ve been tracing the unexpectedly tangled branches of the tree of life up which we’ve climbed to our current perch. But as we’ve seen, the tree of life does more than just branch out with time (e.g. causing us to wave a genetic goodbye to our chimpanzee cousins about 6 or 7 million years ago). Some of its branches also meet and fuse, causing genetic material from different species to blend by various means. This blending makes a web perhaps a better analogy than a tree for the geneology of life on earth.

A quick recap of some of the methods of genetic blending: In the first post of this series (Cavemen in Your Genes), we saw how recent research yielded genetic evidence that we hybridized with another species of human called Neaderthals about 60,000 years ago. I then delved into the process of horizontal gene transfer in the next post (Evolution’s Usual Suspects: 1. Plagiarizing Wizards), describing how bacteria swap their genes and sometimes stick them in plant or animal (including our own) genomes. In the third post (Evolution’s Usual Suspects: 2. Hijackers in Rehab) we saw how entire ‘life’ forms (viruses) have uploaded themselves into our chromosomes millions of years ago and now reside permanently among our genes as lengths of DNA called endogenous retroviruses.

And now we come to (in my opinion) the most spectacular story of the set: endosymbiosis, in which organisms fuse at the level of their bodies, not just their genetic material. The roots of this process are billions of years in the past, but it still continues today. Endosymbiosis fundamentally altered our ancestors’ cellular structures. Endosymbiosis can therefore generate macroevolution at the grand scale that proponents of creationism erroneously claim is absent.

All of the previous cases of genetic fusion that I’ve discussed play out entirely on the stage of our chromosomes. Foreign genetic material is pasted between our genes and therefore alters our identity a little. But our cells still look the same after the alteration. The story of endosymbiosis, by contrast, takes some of the action outside the cell’s nucleus, into the cytoplasm. The resulting changes to the cell can be seen not only through the microscope, but often by the naked eye as well. The associated changes in physiology are even more profound.

Mitochondria: The Coppertop League

Think back on how satisfying it is to drink in a lungful of brisk spring air and to go jogging. Do you know why you can do this? The answer lies in a population of infinitesimally small particles swarming in our cells. Called mitochondria, these roughly bratwurst-shaped intracellular organelles (integrated structures within our cells that perform dedicated tasks) are the power plants of our cells. Small as they are (only about a micrometer in size, or a millionth of a meter — the size of bacteria), mitochondria contain the means to run the chemistry by which our food is struck with oxygen to liberate the energy stored within the organic food molecules (such as glucose). This process is called aerobic respiration. The extensive energy that it can wring from glucose using oxygen is what makes it possible for us to go to cafes, write blogs, work out, and generally be as active as we are. This is because it takes an enormous amount of energy to maintain the level of activity in our cells. We are very much attached to our precious mitochondria for survival.

Cross-sectional diagram of a mitochondrion. (Image: LadyofHats)

Amazingly, although mitochondria are now an integral part of our cells, recent research indicates that they originally descended from bacteria that took up residence in our cells in the hazy past before our unicellular ancestors decided that bunching up into groups of cells was a good idea [1].

How can this be?

Mitochondria not only look like bacteria, but they also reproduce on their own in our cells — not under the direction of the nucleus, just like an independent life form. To facilitate this, they have their own protein manufacturing systems (ribosomes) and their own DNA. Both their ribosomes and their DNA are of a distinctly bacterial type, which is substantially different from that found inside our cells but outside of the mitochondria. (The difference has to do with the size of ribosomes, the shape of the chromosome, and a number of other things.) Now, molecular biologists have the ability to isolate and read the genetic code sequence of this mitochondrial DNA (commonly abbreviated mtDNA). When they compare this mtDNA sequence to all catalogued DNA sequences from other life forms on earth (a lot have been catalogued), do you know which organisms they are most similar to?

Not humans, not by a long shot.

Rather, the mtDNA sequence is most similar to a group of bacteria that includes Rickettsia, better known as the disease agents that cause epidemic typhus and Rocky Mountain spotted fever [1]. This result may sound absurd at first, but it’s astoundingly sensible from an evolutionary perspective. Why?

Consider this: of all the organisms to which mtDNA could be similar, isn’t it curious that it most closely resembles a parasitic group of bacteria that can only survive inside the cells of their hosts? Rickettsia is a nasty pathogen that is difficult for the immune system to detect and destroy because it enters and dwells within our cells when we are infected by it. This parasite is so well adapted to surviving within host cells that it has lost some of its genes, relying on its host cells to make up for its short comings.

But this gene trimming prevents it from growing and reproducing outside of the host cells. In fact, microbiologists can only grow cultures of Rickettsia inside living cultures of host cells, such as chicken embryos. To infect cells, it enters them by biochemically inducing or forcing the cells to swallow them, by a process called phagocytosis (literally, “cell eating”). It’s very similar to how an amoeba engulfs its food, by forming a dent in the cell surface that expands inward around the Rickettsia and pinches off inside the cell to form a bubble or vesicle that encloses the Rickettsia cell. However, once inside, the Rickettsia evades digestion and instead purloins a meal at the host cell’s own table.

Microscopic view of cells of the species Rickettsia rickettsii (stained magenta) living inside a pair of larger eukaryotic cells (note the large blue-stained nucleus in both cells). (Image: CDC)

So we now have the elements for a hypothesis on how mitochondria evolved. A parasitic ancestral bacterium similar to Rickettsia could force its way into the cells of another species, most likely an archaean organism similar to Thermoplasma [2, 3]. The parasite was already predisposed to reside only within these host cells, freeloading on the predictable supply of nutrients that the host cell accumulated for itself.

Now, recall from my previous post (Evolution’s Usual Suspects: 2. Hijackers in Rehab) the discussion about the evolution of avirulence, where we explored how a particularly nasty or virulent disease agent can evolve by natural selection to become less virulent over many generations. This occurs because the less harm that the parasite does to its host, the less resistance it experiences from the host, and the more easily it can maintain the infection, thereby increasing its chance to reproduce itself and spread through the host population. This sort of evolution is especially likely to occur when there is a strong bond between the host and parasite: what befalls the host also befalls its guest.

The increasing dependence of the parasite on the host led to the loss of some genes from the parasite’s already depauperate genome (Rickettsia has the smallest genome of any bacterium — only about 1.1 milllion units or base pairs, compared to over 3 billion in humans). In fact, this loss of genes included those genes needed for a basic type of metabolism that we accomplish in our cells, called glycolysis. But this meant that the parasite was no longer able to survive outside of our cells.

Why would this kind of deleterious gene loss occur? Basically, the parasite became ‘lazy’ in a sense: since it could rely on the host for food procurement and pretreatment, there was no need to expend energy to maintain its own genes against damage, because they were redundant as far as the host’s metabolic capabilities were concerned. Traits that are not highly beneficial for survival and reproductive success tend to be lost from the gene pool over time. But because this loss of DNA prevented the parasite from ever leaving the host to infect another cell, the parasitic bacterium was now permanently stuck within its host. At this point, it had better behave nicely toward its host if it was to survive.

In such a strongly dependent situation, natural selection often favours the survival of organisms that mutually benefit each other (a condition known as mutualism, which can arise in several different ways that I won’t go into now). Again, this is because their fates are so intertwined that survival and successful competition is best guaranteed by working together. If you were tied to your enemy by a steel wire, you wouldn’t try to push them off a cliff, would you?

This kind of evolutionary pressure resulted in parasites that rewarded the parasite-host duo with enhancement of an activity that the aerobic (oxygen-‘breathing’) bacterial parasite was already good at: energy production by ‘burning’ food with oxygen. The most successful of their descendants made more and more energy and exported it to the host, which used it to compete more successfully by hunting down food with greater efficiency, escaping enemies more successfully, and becoming overall more supercharged and awesome. Hence, mitochondria evolved into the energy producing centers of our cells. But their close genetic relatedness to Rickettsia is evidence that they shared a common ancestor with a parasitic bacterium.

This idea was popularized by evolutionary biologist Lynn Margulis in the Serial Endosymbiosis Theory to explain the origin of organelles in cells. Over time, the close association of one creature living within the other’s cells (the condition called endosymbiosis) selected for ever-diminished virulence of the parasite and increasing interdependence of each organism on the other.

The evolution of mitochondria is a funky example of evolution moulding the descendents of a disease organism into an essential partner for survival. It also produced a brand new type of cell (a eukaryote, which contains internal organelles and a nucleus surrounded by membranes) that was qualitatively different from its predecessors (prokaryotes, such as bacteria, which are more homogeneous internally). So, in essence, we are composed partly of huge populations of bacterial batteries, to which we owe our lives and energy levels. Kind of humbling, no?

References

1. 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. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 cladeScientific Reports, 2011; 1 DOI: 10.1038/srep00013

2. Yutin N, Wolf MY, Koonin EV (2009) The origins of phagocytosis and eukaryogenesisBiology Direct. 4: 9-34 (FREE DOWNLOAD)

3. Poole AM, Neumann N (2011) Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis.Research in Microbiology. 162: 71-76 (FREE DOWNLOAD)

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A Remarkable Pregnant Plesiosaur

Taking a quick break from the ‘origins of our genome’ series, because…

Today, Drs. Luis Chiappe and Robin O’Keefe publish a paper about an exciting fossil find from the Cretaceous oceans of Kansas, 78 million years ago (yes, Kansas was then covered by an ocean of water, not crops). It describes the spectacularly preserved and articulated remains of a Polycotylus latippinus (a short necked plesiosaur, a type of marine reptile with four flippers), but the most exciting aspect of the find is that the animal was pregnant when it died, and the embryo is preserved within the mother’s skeleton [1].

Restoration of Polycotylus giving live birth. (Image: Julius T. Csotonyi)

Why do we suspect it wasn’t the animal’s last meal? The shapes of the bones are consistent with those of other Polycotylus individuals, and were neither fully formed, nor fully ossified (turned from cartilage to bone), which is characteristic of embryos.

Most excitingly, the young creature was over 30% of the length of the adult (6 versus 15 feet, or 1.8 versus 5 m), offering the first strong evidence that plesiosaurs gave birth to live young, since this size is far too large to have fit in a reasonable sized egg. Plesiosaurs had occasionally been restored as emerging onto the shore to lay eggs like sea turtles, but evidence to the contrary had been lacking until now.

I have illustrated what a diver might have seen, had one been around in the Cretaceous, during the live birth of the Polycotylus, had the embryo been carried to term (image above). Notice the relatively large size of the young compared to the mother. Such big babies are characteristic of many social animals, leading to the hypothesis that plesiosaurs may have formed social groups, much as modern dolphins travel in pods. Indeed, plesiosaurs are great examples of convergent evolution (i.e., the phenomenon of relatively distantly related organisms acquiring similar shapes or life styles due to experiencing similar types of selection pressures); not only do they have a body plan reminiscent of cetaceans (whales and dolphins), but their gestation patterns and (possible) prosociality also make them resemble marine mammals more than reptiles.

Other extinct marine reptiles, such as ichthyosaurs, have been known to give birth to live young. For example, fossils of Stenopterygius quadriscissus have been found containing the bones of embryos. In this way, some of the groups of extinct marine reptiles differ from most modern reptiles, including sea turtles. Although we usually associate live birth with mammals (which I discussed briefly in my last post), the bearing of live young (viviparity) appears to have evolved multiple times in other groups of animals. This includes reptiles, most species of which lay eggs (a condition known as oviparity). Retention of embryos in the mother increases the probability of survival of young compared to the vulnerable state of development in eggs, which are unable to escape and are more likely to become damaged.

Still, Polycotylus is not the earliest pregnant vertebrate animal known from the fossil record. Amazingly, two species of early fish from the Devonian Period (members of an extinct group known as placoderms) have been found with young within their bodies [2, 3]. The 380-million-year-old fossil of Materpiscis attenboroughi even contained the preserved remains of the umbilical cord [2].

Meanwhile, Polycotylus is not in Kansas anymore. The beautifully prepared specimen now resides in the new Dinosaur Hall of the Natural History Museum of Los Angeles County. Readers of this blog may recognize this museum as one whose opening I featured in a previous blog, “The New Face of Museums“.

References

1. F. R. O’Keefe, L. M. Chiappe. Viviparity and K-Selected Life History in a Mesozoic Marine Plesiosaur (Reptilia, Sauropterygia)Science, 2011; 333 (6044): 870 DOI:10.1126/science.1205689

2. Long et al. Live birth in the Devonian periodNature, 2008; 453 (7195): 650 DOI: 10.1038/nature06966

3. John A. Long, Kate Trinajstic, Zerina Johanson. Devonian arthrodire embryos and the origin of internal fertilization in vertebratesNature, 2009; 457 (7233): 1124 DOI: 10.1038/nature07732

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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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