One of the more interesting challenges in biology is to explain the genetic basis of important traits in a given species, and how the trait arose. There are always evolutionary origins, we assume, but they can be difficult to work out. A classic example is teeth: we depend on them for eating and survival. Teeth are hard, repetitive structures, produced by a wave of repeated use of the genetic mechanisms that produce each one. But our earliest vertebrate ancestors didn't have teeth, or jaws for that matter. What they did have at an early stage in vertebrate evolution, was scales--hard repetitive structures over their bodies.
A long-standing issue is where teeth came from developmentally, and whether teeth are a recruitment of scale-generating genetic mechanisms. While the issues are a bit technical, one of the leaders in work on this area from a genetic point of view is Dr Kazuhiko Kawasaki, a senior research scientist in our own group here at Penn State. We asked Kazz if we could post his up-to-date exploration of this issue, and he kindly agreed. Here it is:
Contributed by Kazuhiko Kawasaki
The Developmental and Evolutionary Origins of the Tooth
Among the most important innovations in the evolution of vertebrates is the tooth, which enabled active feeding. It has long been thought that oral teeth arose from scales on the skin surface, based on the similarities in these two structures in the shark (1). However, an extinct jawless vertebrate, called Loganellia scotica, was found to have scales on the body and tooth-like structures (called denticles) in the oropharyngeal cavity (the back of the mouth). Analysis of these structures led to a new hypothesis: oral teeth originated by co-opting the developmental control used in the oropharyngeal denticles (2). The former theory, that teeth originated from external scales, is called the 'outside-in' hypothesis, whereas the latter, that oral teeth came from oralpharyngeal teeth, the 'inside-out' hypothesis. The tooth and the denticle both develop between two primary tissue layers in the early embryo, epithelium and neural-crest-derived ectomesenchyme; hence a critical difference in these two hypotheses is the tissue origin of the epithelium, either ectoderm (scales) or endoderm (oropharyngeal denticles). In what tissue do these structures originate?
Teeth (left) and scales (right) of the nurse shark.
Until recently, the epithelium involved in oral tooth development was thought to be derived from ectoderm that is located near the border with endoderm. Soukup et al. updated this premise using a transgenic Mexican axolotl that produces green fluorescent proteins (GFP) in the whole body (3). They transplanted GFP producing ectoderm to a normal animal and injected a red dye into endoderm of the transplanted animal at an early developmental stage. The result was that some teeth are labeled in green, others in red, and still others in both green and red, showing that teeth are of ectodermal, endodermal, or a mixed ecto/endodermal origin. Based on this result, the authors suggested "a dominant role for the neural crest mesenchyme over epithelia in tooth initiation and, from an evolutionary point of view, that an essential factor in the evolution of teeth was the odontogenic capacity of neural crest cells, regardless of possible 'outside-in' or 'inside-out' influx of the epithelium".
While the developmental and molecular data demonstrate the essentially identical nature of ectodermal and endodermal teeth, the result does not answer the question about the evolutionary origin. Yet, this study appears to have triggered many subsequent studies, and the outside-in, inside-out, and other modified theories have been proposed as a result (4, 5). A recent analysis showed a gap in the phylogenetic distribution (that is, among different vertebrate lineages) of the internal denticles in Loganellia and oral teeth in jawed vertebrates. Thus, the morphological similarities in these two structures are likely the result of convergence, unrelated evolution of the same trait, refuting the evidence that supports the inside-out hypothesis (6). Further, tooth-like scales were discovered in the cheek and the lip of an Early Devonian jawed vertebrate, suggesting "the existence of a field of gene expression near the mouth margin in which scales could be transformed into teeth" (7). These scales and teeth share a similar structure, and probably used common genetic machinery for mineralization. It is also likely that this transformation was caused by a slight change in the gene regulatory network, responding to a signal from neural crest cells, if the tissue origin does not strictly determine the fate of epithelium.
A Naturepaper,and a Nature News story about it, widely covered in the news (e.g., here), concerns the mating patterns of 2 million year old Australopithecines (human ancestors, or related side-branch(es)) and their mating patterns, as inferred from mineral analysis of teeth.
Fossilized teeth of early human ancestors bear signs that females left their families when they came of age, whereas males stayed close to home.
A chemical analysis of australopithecine fossils ranging between roughly 1.8 million and 2.2 million years old from two South African caves finds that teeth thought to belong to females are more likely to have incorporated minerals from a distant region during formation than those from males.
In non-human primate societies, it is typical for adolescent males to get into conflict with adult males in the local group or troop, and be kicked out. They then have to break into neighboring groups to find mates. In most 'primitive' human societies, it is the female exogamy that is most common. That is, females must find a mate in a different--usually nearby adjoining--local village or population, often also specified by some sort of social or kinship relationship (clan, type of cousin, etc.).
Here's a summary of the interpretation being given to the paper (in part by the authors, but extended greatly in the usual way by the melodramatic media--and, as usual, by Nature). This study of Australopithicene specimens in Southern Africa reports that male teeth all seem to share the same molecular signature of dietary intake when young that is consistent with residence in the local area where they were found. But the females show molecular signatures of distant locations. This suggests to the authors that there was female exogamy at that time. Whether or not these Australopithecines were direct human ancestors, the authors infer that they showed that the typical human mating pattern had begun to evolve.
But hold on. In fact, the samples were small.The inference was made based on current assessment of the morphology of Australopithecine specimens that this was a single, sexually dimorphic species. If that is so, then relatively small teeth would be from females, and larger teeth from males. But of course this is an assummption. Dental molecular composition was compared between small and large teeth, assuming they represented males and females. Other animal fossils were used as comparison, assuming taxa that today have particular ranges had them back then. Molecular evidence in males was that it seemed similar to local-remaining species, and the nature of the environment was measured by molecular data from current species--modern plants and animals within 50 km of the Australos' sites. And the evidence was statistical, that is, 'at least 50%' of the females were non-local by the authors' criteria, while only 11% of the males were. The statistical significance was marginal (p=0.49), and given the kinds of data manipulation one does with such indirect inference, and the prior assumptions made, is rather weak. But the authors then found that there were more non-local small hominins than non-local small-range mammals, with p=0.028 (somewhat more statistically significant) but no such distinction for non-local large hominins and non-local small-range mammals, again suggesting that the small hominins were relatively non-local.
This is interesting but must be viewed as circumstantial and rather weak evidence. An important question is how, in this case, the inference could have been made about population structure since usually not only do the individuals come from nearby demes--not more than 50 km away?--but they keep exchanging every generation, and essentially every, not just some, male or female in a group has to follow the same rules. Also, we must accept that these specimens were essentially contemporary, but of course fossil dating is not so precise as a rule. Unless the environmental patterns varied very locally how could one determine origins? The authors didn't, so far as we see in the paper, identify by molecular means where the females came from--only that their signature was 'non-local'.
Still, this is of some potential interest, This is especially so if the different environments were far apart, to understand how contemporaries--mates--know of each other's group and travel so far to meet each other? Such things, if true, would be interesting to understand! In sparse settlement areas, with hunter-gatherer population densities (in humans ~1 person per 10 square km), distances could be traveled on foot that could exceed 50km, at least in principle for modern hunter-gatherers. So, even if we reject the authors' assumptions, it is interesting to ask what explains their findings. And if we accept them, again, we have interesting things to think about.
Note that these 'people' were not 'people' in the modern sense, as we only came on the scene around 100,000 years ago, not 2 million. And they were not 'cavemen' and 'cavewomen' as the hyperbolic telegenic press so typically categorizes anyone not living in New York or London today.
The last week of November I was hit with hemorrhagic E. coli.* I think my body pretty well expelled the bug on its own, but a strong dose of two different antibiotics made sure it was real dead.
Many people who’ve taken Cipro have experienced that notoriously unpleasant taste in their mouths. The flavor is difficult to describe, but ever since I finished taking the medicine, I’ve continued to have a foul tasting mouth and a foul mouth (ba dum bum bum). My dogs love the makeover (which was amusing for about five seconds), but I can’t bear to ask my husband if he’s noticed a difference. (Ego, 1: Scientific rigor, 0.)
Is this new taste a signal that my mouth’s ecosystem is different? My mind (I take no credit for this) imagines that the antibiotics killed off more micro-critters than just the E. coli and those that better survived are now more prevalent compared to their ancestors. Maybe the species that currently dominates my mouth, or its products, tastes different from the bacterial composition that I had before.
Since this shift in balance would have happened abruptly during the Cipro killing spree, it makes sense that my taste receptors are detecting it now – my brain would have ignorantly ignored a slow bacterial change just like it couldn’t detect my transformation from 2 cells to 32-year-old.
I’ve been popping mints, gargling, and flossing like a lumberjack, for a month now and this whole oral fiasco is why I was naturally drawn to this recent article,“The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity.”
Bacteria. Adaptation. Oral Cavity. This is totally going to be about me! See, first I happened to watch Food Inc., in which they discuss hemorrhagic E. coli while I was recovering from hemorrhagic E. coli, and now just as there’s a bacterial coup in my oral cavity, I stumble upon new research on oral bacteria!** Is it going to identify the species that differentially survived antibiotics, ran rampant in my mouth, and ruined my breath?***
Well, it turns out that this article is not at all about me or my dilemma - despite the common themes which you'll read about below, I can't solve my bad breath mystery by simply reading about oral bacteria. But it’s still a good read for people with oral cavities, people with cavities in their oral cavities, people who are afraid of getting cavities, and people who are fascinated with evolution. It’s especially poignant if you’ve got a sweet tooth that has taken command of your life for the past few weeks like mine has.****
We’ve all got like 900 species of microbiota in our “oral biofilm.” Some of those species are more similar to what’s down the hatch than others. The genus Bifidobacterium is one group that has species living from the lips all the way down to the colon, and also in the vagina (although the article doesn't mention the vaginal species, only my brief internet search said so). You may recognize the genus Bifidobacterium because many of its species are considered “probiotics” and they are included in foods and food supplements to help with digestion, sometimes under the term “Bifidus.”
Most species in this genus are your friends. They’ve teamed up with your body so that they get what they want out of the food that you eat while at the same time they're helping you get what you need out of the food that you eat. It’s a win-win situation and all these microbiotic critters running around inside you (well, more like clinging desperately to your epithelial linings) are why you are more cells of them than you are cells of you.
Like many microbiota in your mouth, B. dentium (the focal species of the paper we're talking about here) is great at metabolizing carbohydrates and approximately 14% of the genes in its entire genome code for proteins that are involved in this process. How does this compare to human genes for metabolizing carbohydrates? I don’t know, but I’m guessing we have relatively fewer genes that are involved in carbohydrate metabolism and that by teaming up with other species which are essentially born to do this, our own system can afford to slack, functionally speaking. It’s a beautiful relationship. But it comes with some costs.
For example, although B. dentium helps with our digestive functions, it has evolved in such a way that it’s no longer just a friend. It’s also a pathogen!
B. dentium is by far the most popular Bifidobacterium to be associated with cavities on tooth crowns in both children and adults and those on the roots of adult teeth. By producing acid, it lowers the pH enough to cause teeth to demineralize. And it’s so good at surviving in this highly acidic environment that it that it can make a living like this, on our rotting holiday cookie-smothered teeth.
The whole genome sequence revealed that the intergenic regions of the B. dentium genome have more nucleotide differences than the protein-coding regions. Sound familiar? (Everything boils down to human vs. chimp, doesn’t it?)
The results of these differences found in the genome of B. dentium are (1) it can withstand low pH conditions (as mentioned above), (2) it can metabolize a wider range of stuff that we eat compared to what its cousins in the colon can metabolize (which makes sense considering the smorgasbord presented to B. dentium vs. what metaphorical crumbs make it down to the colon) and it can even live off our own saliva, and (3) it seems to be able to resist biocide better than its relatives (which was tested by growing B. dentium in mouthwash which sounds completely unethical).
Regarding that third point, B. dentium has a relative abundance of what are called “two-component systems (2CSs)” which are instances where protein-coding genes are essentially flanked by regulator genes, and this seems to be a surprise to the authors based on what is known about other bifidobacterial genomes. The implications of these numerous 2CSs are that they may be indicative of B. dentium’s “ability to sense dynamic environmental cues and to modulate appropriate physiological responses.” Perhaps this is what enables them to differentially survive despite our attempts to murder them with mouthwash (or, heh heh, during E. coli-cide? Hmmm?). Or at least, perhaps this is what enables them to not just tolerate but thrive in fluctuating habitat acidity. And what's even more exciting is that these adaptations may be linked.
Naturally we’re left to wonder: How long ago or recently did B. dentium originate? Did our behavior induce B. dentium to adapt this way through our diet and/or through our dental hygiene? Is it smart to ingest commercially sold probiotics if they contain species that can evolve to be opportunistic pathogens like B. dentium did or, worse, if they actually contain the pathogenicB. dentium and we just don’t know it?
Because it's the holidays, should we just forget about it and eat all the cookies and sweets that we want because we can't stop the evolution of our oral microbiota?
I like that idea. More cookies, please, and pass the biocide and the floss, thanks.
Starred Footnotes:
*No, hemorrhagic E. coli is not why I’ve been gone since mid November (apart from dropping comments on Anne and Ken’s posts). University life has kept me sufficiently busy and generally abloggish. But getting hemorrhagic E. coli certainly didn’t help. No, I don’t know where it came from. And no, I didn’t go to this doctor for treatment (amicably sarcastic emoticon).
** I believe this is what Oprah calls “The Secret.”
***Please do not take this opportunity to tell me that my breath was already ruined.
**** I used to think that a gold tooth was a sweet tooth and that it could actually taste sweets better than enamel teeth. This is because my uncle has a gold tooth and a sweet tooth, so naturally a 5-year-old me who had never seen or heard of either of those things thought that they were one in the same, and thought that a sweet tooth was a pretty neat trait to have. For much of my childhood I was incredibly jealous of every person I saw sporting a gold tooth.
I dare say that all paleontologists, including myself, drool over papers like this one recently published in PLoS Genetics, because, as the authors write, it “provides manifest evidence for the predictive power of Darwin’s theory."
Instead of looking at the genes behind new or modified existing traits, the authors looked at the genes for traits that have disappeared. Most lost or vanishing traits that come to mind are comprised of soft tissues that do not preserve well in the fossil record (e.g. cave fish eyes), but thanks to the steadfast properties of enamel, tooth loss and enamel loss can be examined both genetically and in the fossil record. That means the evolutionary scenarios for the evolution of enamel loss and tooth loss can be rendered in much higher resolution, if you will, than those for soft tissue traits.
Tubulidentata (aardvarks), Pholidota (pangolins), Cetacea (whales, porpoises, and dolphins), and Xenarthra (armadillos, sloths and anteaters) are four groups of mammals with toothless and/or enamelless taxa. They also have pretty decent fossil records, especially when it comes to teeth. What’s more, mutations in known mammalian genes (e.g. enamelin’s gene ENAM) that are involved in enamel formation are known to – wait for it – cause defects in enamel.
This is a perfect opportunity to bring fossils and DNA together.
Do these mammals in question show degeneration, like a pseudogene, at ENAM? Yes, various kinds.
Do the nature of those changes support the phylogenetic hypotheses made by comparative anatomy and the fossil record? Yes, mostly (e.g. enamel may have been lost independently in different armadillo lineages).
