Despite living in the carotid artery of Northeast traffic, I still share my property with a particularly prehistoric kind of wildlife. Each spring, monstrous snapping turtles emerge from the salt marshes and rip up our garden to lay eggs. Then in late summer the baby turtles hatch and crawl out of the mulch to head for the water again.
This was the scene outside our front door (I highly recommend setting the movie to full-screen). The baby snapping turtles, each the size of a jumbo chicken egg, crawled to the light one by one and clambered onto our stone steps. As this video demonstrates, baby snapping turtles deal with these unexpected situations without much hesitation. They climb to the edge of their world and keep going.
I got this tattoo after finishing my PhD at the University of Utah working on the ecology of southern right whales that visit the coast of Peninsula Valdes (northern Patagonia), Argentina. The tattoo depicts a Surface Active Group (SAG). SAGs are usually thought as mating groups or whales in apparent courtship behavior. At Peninsula Valdes the SAGs that we normally see are much smaller with only a handful of whales, but the energy displayed by these animals is just as impressive as the large groups seen in other populations or species. The tattoo is actually a modification of Figure 1 in Kraus and Hatch (2001) showing a SAG of North Atlantic right whales. I think once you see them from close proximity you can appreciate how powerful and gentle at the same time these huge animals can be.
Here are a few numbers about DNA–some big ones, and then some very small ones.
The human genome contains about 3.2 billion base pairs. Last year, scientists at the University of Leceister printed the sequence out in 130 massive reference-book-sized volumes for a museum exhibit. From start to finish, they would take nearly a century to read.
A typical gene is made up of a few thousand bases. The human genome contains about 21,000 genes that encode proteins. There are other genes in the human genome that encode molecules known as RNA, but how many of those RNA molecules actually do anything useful in the cell is a matter of intense debate. A lot of the human genome is made of neither protein- or RNA-coding genes. Much (maybe most) of it is made up of dead genes and parasite-like stretches of DNA that do little more than making copies of themselves.
As I wrote recently in the New York Times, 3.2 billion base pairs and 21,000 genes are not essential requirements for something to stay alive. E. coli is doing very well, thank you, with a genome about 4.6 million base pairs. That’s .14% the size of our genome. Depending on the strain, the microbe has around 4100 protein-genes. That’s about a fifth the number of protein-coding genes that we carry. The high ratio of genes to genome size in E. coli is the result of its stripped-down, efficient genetics. Mutations that chop out non-functional DNA spread a lot faster in microbes than in animals.
E. coli, in turn, has proven to be positively gargantuan, genetically speaking, compared to some other species. As scientists explore more of the microbial world, they find species with smaller genomes. In my column for the Times, I wrote about the record-holding tiny genome, belonging to a microbe called Tremblaya. Its genome is a mere 139,000 base pairs. That’s .004% the size of our genome. You could print the entire sequence in a single slim paperback you could slip in your pocket. And in that sleek genome are just 120 protein-coding genes–.6% of our own collection of protein-coding genes.
Whenever I report on such record-breakers, I try to stress that they are only breaking records at that moment. Tremblaya has the smallest genome known. Or, I should now say, it had the smallest genome known last month.
This month in the journal Genome Biology and Evolution, Gordon Bennett and Nancy Moran describe a new record holder, called Nasuia deltocephalinicola. It has a genome of just 112,000 base pairs. Imagine taking that slim novella and ripping off the last chapter. Ironically, Nasuia packs in more genes into its DNA than Tremblaya–137 protein-coding genes, Bennett and Moran estimate.
What’s really striking about all these current and former record-holders for small genomes is that they all live in a single exotic ecological niche. Without exception, they can be found inside plant-feeding insects. Tremblaya lives in mealy bugs, for example, while Nasuia lives in a leafhopper (Macrosteles quadrilineatus).
Inside those hosts, these microbes carry out chemical reactions on the food that the insects eat. The insects feed on sap and other fluids from plants, which contains few nutrients. But the bacteria can use the compounds floating in the fluid to build amino acids, which the insects can then assemble into proteins.
Leafhoppers, cicadas, sharpshooters, and other related insect species carry related versions of the same stripped-down bacteria. By drawing their evolutionary trees, Bennett and Moran have found that the insects got into a symbiotic relationship with the microbes over 260 million years ago. I’ve reproduced their tree below for those who want some gory details. The blue lines show Nasuia and related lineages of microbes. The insects also acquired another species of bacteria, known as Sulcia. Together, these two microbes split the work for millions of years. (In some insects, fungi also jumped into the mix.)
The ancestors of Nasuia started out as free-living microbes that had genomes on par with E. coli. But once they got inside a host, they were able to lose DNA without paying a price. The insects gave them a stable home, building special organs to shelter them, and they even pass down the bacteria to their offspring. The bacteria cast aside many genes that might otherwise seem essential, such as a number of genes involved in generating energy. All they needed to do was continue to provide a service, by synthesizing some amino acids.
Nasuia holds the record now, but probably not for long. There are many other species of insects left to investigate. Moran had John McCutcheon of the University of Montana have done some back-of-the-envelope calculations to figure out how much smaller the genomes of those symbionts can get. All known insect symbionts share 82 genes in common. It’s possible those genes are absolutely required to survive as a symbiont. But a symbiont also needs to provide a benefit to its host, or its host will likely get rid of it. It takes at least 11 genes to synthesize a single amino acid. Those 93 genes, McCutcheon and Moran estimate, could fit in a genome as small as 70,000 base pairs.
It’s funny that these bacteria allow us to probe one of the most basic questions about life: how simple life can get and yet still qualify as being alive? While those who make fun of science for a living may consider such research a waste of time, studying these stripped-down organisms is also about as practical as science can get. The leafhoppers that house Nasuia, for example, are a nightmare for farmers, causing damage to a wide range of vegetables by spreading fungi and bacteria. Yet they would be helpless if not for their exquisitely simple lodgers. If we can understand how they survive with such tiny genomes, we may be able to stop them from enabling their hosts.
The Stanford biologist Stephen Palumbi wrote an excellent book some years ago called The Evolution Explosion, in which he argued that humans have become a powerful force in the evolution of life. We’ve altered the whole planet, so that now many species are traveling on new evolutionary trajectories. (For more, here’s a review of the book I wrote for the New York Times Book Review.)
Over the years since Palumbi’s book came out, scientists have documented more examples of our effect. This week, I was intrigued to come across a new study that we may be even altering the brains of animals. It’s the subject of my new Matter column for the New York Times. It’s only a preliminary study, of course, but it does raise some fascinating questions about the mental challenges animals now face as they navigate a human-dominated world. Check it out.
When Charles Darwin developed his theory of evolution, he resigned himself to only seeing its effects. Evolution happened so slowly, he was convinced, that we couldn’t see life changing from one generation to the next by a mechanism such as natural selection. So he found other ways to amass evidence for evolution.
He pointed out, for instance, that natural selection was a logical–even inescapable–fact of life. Individuals varied in their traits. Some of those variations influenced how many offspring they had. And those traits could also be passed down to offspring. Under such conditions, natural selection just happens.
Darwin also looked back over the history of life and showed how powerfully evolution could explain its large-scale patterns. He couldn’t account for every jot and tittle over the past four billion years, of course. But he could, for example, account for how groups of species shared sets of traits: because they descended from a common ancestor that lived millions of years ago.
Starting in the mid-1900s, however, evolutionary biologists  began documenting measurable evolution over the course of years, not millennia. As chronicled by Jonathan Weiner in The Beak of the Finch, for example, Peter and Rosemary Grant have measured changes in the beaks of Darwin’s finches over the past four decades.
Microbes–which breed much faster than animals and acquire mutations at a faster rate–are also opening new lines of research into evolution. Scientists like Richard Lenski and Paul Turner are tracking the evolution of bacteria and viruses over a matter of weeks, or even days.
This week in my “Matter” column for the New York Times, I took a look at a new study on experimental evolution. Bacteria living in Petri dishes evolved extra tails, which allowed them to swim faster and take over their populations. The experiment is fascinating in many ways–from its potential applications to medicine to what it says about the predictability of evolution. Plus, it comes with cool videos.
While the response to my column has been generally enthusiastic (thanks), I have gotten some negative comments that echo an old refrain I often hear when I write about experimental evolution. Basically: they’re still bacteria.
Opponents of evolution often like to decree what evolution really is. That way, when scientists study evolution, they can declare, “That’s not evolution.”
Nevathir, for example, claims that that what happened in this experiment is just “pattern formation,” which apparently refers to how dogs give birth to puppies that have different color patterns. (That’s not actually called pattern formation, but I have to guess here.)
Puppies get different color patterns because (among other reasons) they inherit different combinations of genes from their parents. The experiments I wrote about this week are not “pattern formation” in this sense of the phrase. They started with genetically identical bacteria, which divided, producing identical clones except when new mutations arose. Those mutations were then passed down to their descendants. Mutations to one gene in particular led to the emergence of “hyperswarmers.” Hyperswarmers were genetically programmed to make more tails, which allowed them to swim faster than their ancestors. And they quickly drove slower bacteria extinct as they came to dominate the population.
That is evolution–evolution in under a week, in fact.
V. Hugo asks what new traits were created. Apparently acquiring a number of new tails is not a new trait, in the same way that a mutation in people can lead to the development of an extra finger on the hand. And apparently changes can only be called evolution if they involved the evolution of a new trait.
It’s very hard for me to see how evolving from a single tail to up to half a dozen tails–all of which work together rather than getting tangled up with each other–is not a new trait. But even if we go along with V. Hugo this far, his sort of argument still fails, because it’s not an argument at all. He’s just creating a personal definition of evolution in order to scoff at scientific research.ÂThe origin of new traits is part of evolution, but so is the spread of beneficial mutations due to natural selection.
I suspect that Nevathir and V. Hugo aren’t satisfied with this experiment because it isn’t a large-scale episodes of evolution–the split between species, for example, or the origin of an eye or a hand. (I’m guessing here, but it’s a guess educated on many previous such comments.) Large-scale episodes take time, typically stretching across thousands or millions of years. The scientists who study bacteria over the course of a few weeks don’t expect to witness such transformations. Instead, they are finding that they can dissect the mechanisms of evolution. They can even document the emergence of new genes, as mutations accidentally duplicate stretches of DNA, which can then begin to take on new functions.
And then there’s the “They’re-still-bacteria” remark. I hear variations of this refrain many times, which makes me assume that it gives opponents of evolution great comfort. Bacteria are one “kind” of life form, and since these experiments don’t show them evolving into another “kind”–like a dog–then they reveal nothing.
Such a remark isn’t just wrong-headed about evolution, though. It reveals a misunderstanding of bacteria. Bacteria originated about 3.5 billion years ago and have been diversifying into many different forms ever since. Some bacteria float in the ocean, turning sunlight into carbon. Others breathe iron. Others make squid glow. Watching bacteria evolve in a Petri dish helps us to understand not just evolution in general, but bacteria in all their particulars.
