I recently returned from the San Juan Islands, where my sister-in-law is studying how anthropogenic noise affects the calling behavior of killer whales (orcas). I got to spend many hours watching killer whales merely hundreds of yards away or less, as they surfaced to breathe, breeched, and slapped their pectoral and caudal fins against the sea. A microphone below the waves let us hear their squeaky vocalizations. The population is so well studied that every individual whale can be visually recognized by the local experts based on the dorsal fin and the white dorsal patch.

The San Juans are one of the few places where you can be virtually guaranteed to see whales any day of the year, because of the unique behavior of these particular animals. While other “transient” killer whales are out roaming the open ocean hunting marine mammals, the “resident” killer whales in the San Juans stay near the islands and catch salmon. Hunting is a learned behavior in these highly social animals, so there are effectively two distinct killer whale cultures: the wolflike transients and the piscivorous residents. Even when transients visit the Straight of Juan de Fuca, the two whale societies have nothing to do with each other, and apparently rarely mate.

As an evolutionary biologist, I am intrigued by these cultural differences promoting genetic differentiation. It’s tempting to speculate that these cultural differences could lead to speciation, but in the case of the orcas this seems unlikely. Even in our own species, which is more culturally diverse than any other, cultural speciation has never occurred. Throughout history, when two different cultures encountered each other, at least some individuals have been willing to have sex with someone from the other group. Thus, no human group, no matter how culturally isolated, is a distinct species. For orcas, cultural speciation is even more unlikely, since young orcas are raised entirely by their mother and her family, and don’t even know their father. Thus, a young hybrid doesn’t have to suffer lower fitness by straddling two lifestyles; instead, it learns the hunting behaviors of its mother regardless of the population its father came from. As a result, an adult orca has nothing to lose by mating with an orca from another population. On the other hand, might residents avoid the whale-killing transients out of fear for their own safety, and thus shun them as mates? As a reproductive isolating mechanism, this is unheard of, but it’s still possible, I suppose. Molecular evidence shows that residents and transients have different mitochondrial lineages (as expected in a matriarchal species), but are only moderately different at neutral nuclear markers, consistent with occasional male-mediated gene flow between populations (Hoelzel et al. 2007). These groups are not yet different species, but I wonder what could happen far into the future…

If these whale survive far into the future, that is. The resident whales are threatened by several factors. Sitting at the top of the food chain, they accumulate massive amounts of toxic chemicals, espeicaly PCBs and PBDEs, from their food. The food itself, salmon, is declining due to overfishing. Finally, the tiny population size of the residents puts them at risk for inbreeding depression and stochastic extinction. Unfortunately, we don’t have a good legal mechanism for saving them. The specialized culture of the residents should be preserved, but because these whales are not a different species, and because the global numbers of killer whales are still high, they aren’t really the type of entity that the Endangered Species Act is supposed to target. Either we need a law that protects endangered non-human cultures, or else the local human community needs to recognize the ecotourism value of these whales and step up to protect them on their own.

Hoelzel AR, Hey J, Dahlheim ME, Nicholson C, Burkanov V, Black N. 2007. Evolution of Population Structure in a Highly Social Top Predator, the Killer Whale. Molecular Biology and Evolution 24(6):1407-1415

SC has been quiet for a month, we know. It’s a busy summer us. This week, for the second year in a row, I attended the annual meeting of the Society for Molecular Biology and Evolution. This time the conference was in Halifax, Nova Scotia. I saw many outstanding talks and posters on a range of topics in evolutionary genetics: models of codon substitution that account for selection on synonymous sites or tertiary protein structure; evidence for adaptive evolution in mammalian globins, fish antifreeze proteins, and mollusk reproductive proteins; analyses suggesting that positive selective sweeps might be major drivers of genomic evolution; studies of adaptive variation maintained by natural selection in several different taxa; evolutionary forces governing gene duplication; etc. If you understood all of that, you might want to think about joining the Society.

One of the highlights of the meeting was getting to meet some of the other scientist bloggers, whose work so often provides a welcome distraction from whatever I am supposed to be doing. Photographic evidence of this historical encounter can be found here.

Now I’m at Vanderbilt University in Tennessee, where I’m about to spend a couple of weeks learning that there’s more to studying molecular evolution than just catching frogs and looking at their DNA sequences. Updates to follow, hopefully.

Meanwhile, Ivan is somewhere off in the wilderness catching frogs. Like I said, it’s a busy summer.

I just realized that no one appears to have ever used the phrase “conservation immunogenetics.” I searched Google and the Web of Science for the phrase and found no hits. Time to fix that. I hereby coin the phrase “conservation immunogenetics,” defined as follows: the study of how variation at disease resistance genes affects the long-term survival of a species, and the application of this knowledge to the conservation of biodiversity.

The field of conservation immunogenetics is over 15 years old, even if no one has called it that before. In 1991, Austin Hughes published a paper arguing that vertebrate captive breeding programs should prioritize the maintenance of variation at the major histocompatibility complex (MHC). His proposal was too oversimplified to be practical, and was criticized (not all MHC alleles are necessarily important, and certainly other types of genes are just as important as MHC). Nevertheless, it seems clear that species with low variation at immunity genes have a higher risk of extinction, and it is theoretically possible to identify important adaptive genetic variants that ought to be conserved. A sophisticated approach is needed, and the goal of conservation immunogenetics is learn enough to able to locate and save adaptive immunogenetic diversity within species. Conservation immunogenetics is not just restricted to captive breeding programs. For example, wild populations with unique heritable disease resistance capabilities should be special targets of conservation efforts.

Let me know if you have seen a previous example of this phrase. Otherwise, you heard it here first, folks. I’m not founding a new branch of biology, I’m just giving it a name.

Suppose I sequence one of your genes, and then I sequence the same gene from me, and from a chimpanzee. Are you going to be more genetically similar to me or to the chimp? Obviously, assuming you are a human, you’ll be more similar to me at most genes. But not necessarily every gene. If I pick the right spot in the genome, the chimp might look like a close cousin compared to a distant relative such as myself. Even though the ancestors of chimps and humans parted ways millions of years ago, we still haven’t finished sorting out all of our genetic material into two independent branches of the evolutionary tree. Behold the bizarre phenomenon of trans-species polymorphism.

As any good investor knows, a diversified portfolio can reduce risk. The same is true for certain immunity genes. Genes of the major histocompatibility complex (MHC) help vertebrates to recognize invading germs and parasites so the immune system can start fighting back. At any given MHC genetic locus, just like for every gene, you have two variants (alleles): one from your mother and one from your father. Organisms with two very different MHC alleles can recognize more pathogens than organisms with two identical alleles, so they survive better. There’s even some evidence that animals (including humans) prefer mates who smell like they have different MHC genotypes, so their offspring will have two different alleles (yes, they’ve actually done these studies in humans by having people smell sweaty t-shirts worn by someone of the opposite sex. In theory, if you know the MHC genotype of that special someone, you could douse yourself with sweat from someone of a really different MHC genotype, and get lucky this Valentine’s Day. In theory.).

Anyway, as a result, natural selection has favored a vast diversity of MHC alleles in the gene pool of most vertebrate species. At most “normal” genes, new variants occasionally appear and replace the older variants, whether by natural selection or by random chance (genetic drift). Not so with MHC, because no one allele is as good as two different alleles. So different allelic lineages hang around a very long time, even through speciation events. The MHC diversity that existed in the most common ancestor of human and chimps is still with us, floating around the gene pools of both species.

And not it’s just us. Trans-species polymorphism has been documented in several different vertebrate groups. MHC genes are not the only genes showing trans-species polymorphism, either. One way of defining “species” is that a species is a group of organisms who are all each other’s closest relatives throughout their genomes (the so-called “phylogenetic species concept”). Trans-species polymorphism shows that this in not an entirely accurate to define species, since humans and chimps are clearly distinct species. We’re just maybe not as distinct as you might assume.

How much DNA do you have in your body? A DNA base pair has a length of a little less than one nanometer (a billionth of a meter). There are approximately three billion DNA base pairs in the human genome, and since we are diploid organisms, each cell actually contains six billion base pairs. Therefore, if you took all the DNA in a human cell and stretched it out, it would reach a few meters. Now, there are about 10 trillion cells in the human body. So, all the DNA in your body, if laid end to end, would reach from the Earth to the Sun a hundred times! Yes, you read that correctly. Yes, that is a long freaking way!

Now, how much DNA does a salamander have?

Let’s take the mudpuppy, Necturus maculosus. Mudpuppies are aquatic salamanders from eastern North America that retain their external gills throughout life. I’ve caught them in Cayuga Lake in upstate New York by wading through the shallows near shore at night while shining a flashlight down into the water. Mudpuppies grow to be over 40 centimeters long. These little guys have about 30 times as much DNA in every cell as a person has: about 180 billion DNA base pairs. I don’t really know how many cells a mudpuppy has, but I estimate that they weigh about a pound. Cells with large genomes tend to be larger, so so the number of cells per pound is probably less in a mudpuppy than in a human. Given their weight and cell density, let’s say that a mudpuppy has about 1/300 as many cells as an adult human. This is a very rough estimate, but it will do for our purposes. So, if you stretched out this salamander’s entire DNA library, it would also reach to the sun multiple times, but probably less than your DNA library (more like 10 times).

Let’s try another salamander example. The Japanese giant salamander, Andrias japonicus, can weigh over 100 pounds. It has about half the DNA per cell that a mudpuppy has: “only” about 90 billion DNA base pairs. But since it’s so large, and since its cells are intermediate in size between those of humans and those of mudpuppys, a giant salamander probably has nearly as many cells as an adult human. If so, the sum total of this critter’s DNA would reach from the Earth to the sun more times than your DNA would… maybe as many as 1000 times!

Why do we have so much DNA? And why do salamanders have bigger genomes than we do? After all, humans appear more complex than salamanders, so it would seem that we would need more genes… but even humans shouldn’t need genomes so large that they can be measured in astromical units. For years, biologists were puzzled by this conundrum, called the “C-value paradox.” The solution seems to be that most of the genome is junk. Both salamanders and humans have lots of DNA, but most of that DNA doesn’t actually do anything, and you could build a highly organized animal using much less DNA. Of course, this still doesn’t explain why the junk DNA exists at all. This question is not yet entirely resolved. One idea is that junk DNA is very slightly deleterious; in species with large population sizes, natural selection is able to weed out the junk, but in species with small population sizes, natural selection isn’t strong enough to stop junk from accumulating. Both salamanders and primates have relatively small effective population sizes compared to, say, most species of bacteria. Junk DNA has built up in vertebrates over millions of years, and perhaps salamanders have just ended up with more of it due to chance.

I study genes that code for antimicrobial peptides, or AMPs. What are these AMPs, and why are they so interesting that I would spend 5-6 precious years of young adulthood doing research on them?

A peptide is a small protein molecule. Yes, protein, just like it says on the nutrition label on your bag of beef jerky. An antimicrobial peptide is able to kill bacteria and other germs by poking holes in the germ’s cell membrane. All animals, even humans, produce AMPs, and they seem to be pretty widespread among plants and other eukaryotes, too. Most people I talk to can understand the potential application of an antimicrobial substance. We all like to be able to kill germs at times, since otherwise they are liable to kill us. The development of antibiotics has been a medical miracle, but we’re living on borrowed time, since many bacteria species are rapidly evolving resistance to whatever antibiotics we throw at them. We will soon need a whole new arsenal. Are AMPs the solution? Well, maybe. There are a lot of practical issues involved in actually using them as medicine. If you swallowed them, these small protein molecules would suffer the same fate as your beef jerky: get digested. But maybe someone can design a new antibiotic based on an AMP molecule but without the easily breakable peptide bonds…

There’s a conservation angle, too. As we’ve discussed at SC several times before, infectious diseases can threaten wildlife. It’s important to understand the genetic basis for immunity in lots of species, so they can be managed to ensure that they have sufficient genetic variation to resist disease threats. In other words, if there are several variants of an immune system gene, don’t let one variant get fixed in the species, because a new disease might come along that can overcome that variant. In reality, of course, humans are only willing to spend so much effort to monitor and manage wildlife. Some charismatic megafauna receive special help through captive breeding programs that might incorporate data on immunity genes. The fates of most species, though, will not be much affected by how much we know about variation in disease resistance among individuals. So, while I hope that conservationists will be able to use my research results, there’s only a small chance that what I do will make a direct difference to endangered animals. A larger, indirect effect might be through education. If more people learn about amazing and potentially useful molecules like AMPs, they might be less willing to extirpate endangered species and the AMPs they produce.

The main reason I study AMPs is because they are a terrific model system for discovering how adaptive evolution occurs at the molecular level. Moreso than for most other genes, AMP evolution is rapid and frequently driven by positive natural selection. In other words, new variants are always appearing that confer higher fitness to the organism, and these replace the old variants. Why this happens isn’t entirely clear, but it could be that germs quickly evolve resistance to a particular AMP, prompting the evolution of a new one in an endless molecular dance. It’s easy to measure the antimicrobial abilities of different AMPs in the lab, and this functional data can be integrated with observations of evolutionary patterns. Adaptive evolution is the reason we are who we are and nature is the way it is. I want to use AMPs to help figure out how the whole process works. And then, who knows? The beauty of basic research, which often goes unappreciated, is that you can never tell what applications your results might lead to. Could Watson and Crick have predicted that their basic research on an obscure acid would lead to genetic counseling? If we learn enough about the fundamental forces of our world, such as natural selection, we’ll be able to move forward in ways currently unimaginable.

The fossil record for amphibians is fairly spotty, apparently, and hasn’t provided much data for scientists to answer questions about what has happened to amphibians during the Earth’s major extinction events (e.g. at the ends of the Permian and Cretaceous). If worldwide extinctions are associated with major changes in climate, the expectation is that amphibians should have been hit hard in the past, due to their sensitivities to temperature, chemicals in the environment, etc. Modern day climate change is thought to be an important factor in the acceleration of amphibian extinctions. Have amphibian lineages diversified gradually since the good ol’ Permian, or, as we might expect given the delicate nature of amphibians, are the groups existing today the descendants of a lucky few lineages that survived the last global extinction event? If you were to consult the amphibian fossil record for an answer, you would have a tough time finding one.

Molecular Phylogenetics to the rescue! A recent study published in PNAS used DNA sequences from representatives of most of the extant amphibian taxa to show that, when paired with the available fossil data, the molecular data tell a story of amphibian extinctions and subsequent diversification over the last several hundred million years. Mass extinctions in amphibians have occurred at roughly the same times as the extinctions of amniote vertebrates. Some amphibian groups went through adaptive radiations–sort of like what happened to mammals after the dinosaurs bit it. The most diverse and widespread groups today are mostly those that underwent rapid diversification toward the end of the Cretaceous: the Natatanura (including “true frogs” in the genus Rana), the Nobleobatrachia (including toads and treefrogs), Microhylid frogs, Plethodontid salamanders, and Salamandrid salamanders. Sorry for the sesquipedalian taxonomic jargon.

What species or lineages of modern amphibians will make it through the current extinction crisis? Hopefully most of them, if anything can be done about the depressing trend of habitat destruction and global warming. From a long-term, evolutionary perspective it seems likely that a handful of amphibian lineages will survive and diversify in the future. If I were placing bets, I would put my money on bullfrogs (Rana catesbeina), cane toads (Bufo marinus), and maybe the Pacific treefrog (Pseudacris regilla). These plucky species seem to do pretty well despite the efforts of humans to either eradicate them outright or modify their habitats beyond recognition. There are probably other pest-like amphibians around the world that for one reason or another are well-suited to coping with environmental change. I hope that the global experiment to see which amphibian lineages are capable of surviving this latest, human-caused catastrophe never takes place. Wait… I guess it’s already begun, hasn’t it? Crap!

How genetically diverse is the human species? How genetically different are we from other species? You might think that scientists could spit out simple, single-number answers to these questions. However, measuring genetic variation and divergence is not as straightforward as it might seem.

To assess the genetic difference between two individuals, you could just align related DNA sequences from their two genomes, and calculate the percentage of nucleotide letters that differ between them. This is analogous to aligning two English phrases:

“Mary had a little lamb. Its fleece was white as snow. And everywhere that Mary went, the lamb was sure to go.”
“Mary had a little lamb. Its fleece was white as snot. And everywhere that Mary went, the lamb was sure to go.”

The above two phrases are 99% identical, due to a single typo (mutation). So, you might conclude that the books (genomes) in which you found these phrases are also 99% identical. But in reality, genomes don’t align so nicely. Chunks of DNA get copied and deleted pretty often, so you might find something like this:

“Mary had a little lamb. Its fleece was white as snow. And everywhere that Mary went, the lamb was sure to go.”
“Mary had a little lamb. Its fleece was white as snow. And everywhere that Mary went, the lamb had a little lamb was sure to go.”

These phrases also differ by single “mutation,” but this time it’s a copy-and-paste mutation, so the phrases are only about 92% identical.

Since “copy-and-paste” mutations can cause bigger changes than “typo” mutations, they are responsible for more genetic variation and divergence. According to a paper that just came out in the journal Nature, 12% of the human genome is variable in terms of the number of copies of DNA sections. In contrast, less than 1% of the genome is variable in terms of “typo” differences (called single nucleotide polymorphisms, or SNPs). So most of the genetic variation in our species is due to copy number, and it would be misleading to use the percentage of nucleotide letters that differ among sequences as an absolute measure of diversity. Similarly, you may have heard the oft-repeated factoid that humans and chimps are only 1% genetically different. This is true if you’re just talking about typos, but in terms of copying-and-pasting the difference is substantially greater. Many of the important adaptive phenotypic differences within and between species are probably due to differences in the copy number of chromosomal regions. Aligning related sequences and looking for typos is easy, but that method might miss most of the variation.

An entertaining thought occurred to me a few days ago. I was actually thinking long and hard about my own research when, for whatever reason, the idea for this blog post just popped into my head. Basically, I believe that a useful comparison for our current political situation in Iraq is that of the adaptive landscape from the field of evolution. You may be wondering to yourself, what exactly is an adaptive landscape? To the best of my limited abilities, an adaptive landscape is basically a representation of particular combinations of genotypes (or phenotypes) and their respective fitnesses. In three dimensions one can imagine a landscape peppered by particular combinations of genotypes with correspondingly variable levels of fitness.

By no means do I claim to be an expert in adaptive landscapes, but I have been able to glean a few useful characteristics from various sources. First, one can become stuck on a local peak even if it is not the highest peak in the adaptive landscape. This is because, as you can see from this figure, that in order to get to another peak one would have to traverse an area with significantly lower fitness. To move off of a peak, some sort of “push” has to occur such as drift in conjunction with selection (See Wright’s shifting balance theory). Another property of adaptive landscapes is that when you run into a “hill” you will climb it (i.e., you will not go around it) because even a slight increase in fitness is better than staying on the plane of low fitness. The evolutionary implications are certainly very interesting and useful, but how about its political implications? One could imagine an adaptive landscape for the current situation in Iraq, for example. Instead of genotypes controlling the x,y position on a plane, imagine that the position of a peak is controlled by types of government. The height of the peak is no longer fitness, but rather some sort of measure of political/humanitarian well being. In this example we will consider political stability as a proxy for fitness. Below, I have inserted a high quality figure depicting such an adaptive landscape – created by yours truly in a sophisticated program known as Microsoft Paint.

One can see that Iraq under Saddam Hussein was at a medium level of political stability (“fitness” ) for the region. However, the vast majority of peaks on the landscape are in fact of lower fitness. This is due to the political instability and trying socioeconomic factors of the region. Note that this representation of an adaptive landscape is only one snapshot in time, however, the true adaptive landscape is perpetually dynamic. Also note that there are in fact several peaks with higher fitness throughout the landscape. These peaks represent governmental regimes where George Bush and the current administration imagined that we would end up after this endeavor. Such peaks have been named “democracy” and “free society.” Does this mean that such regimes are the only kind that can lead to high levels of general well-being? Absolutely not, however, for reasons of convenience I will stick to the general parlance that is currently being thrown around in the political arena. If one were to take a probabilistic (and hence realistic) view of this landscape, we would have been able to see that we were/are much more likely to end up on a peak of lower fitness – such as “Islamofascism” or “Talibanism”. This is for two reasons: 1.) There are far more peaks of lower fitness than higher fitness and 2.) the widths (or circumferences for 3 dimensions) of the peaks with higher fitness are much smaller than those with lower peak heights. This is due to the greater difficulty (or smaller number of combinations of genotypes) in achieving this type of political system. The main point of this exercise is to demonstrate that in order to get to a peak of higher fitness we need to be able to see this adaptive landscape so that we know what direction to travel. Even if we could see the true adaptive landscape could we actually control our direction? So where are we right now on this landscape? Well, ever since Operation Iraqi Freedom, the peak of medium political stability that was “Iraq under Saddam” has been completely wiped off the face of the landscape. I believe we are currently wandering around aimlessly on the plane. What peak we will hit only remains to be seen, however, the options are not looking good.

To what other scenarios could this adaptive landscape be applied? The simplest ideas are to change the z axis from political stability to other measures of interest. Ideas that spring to mind are general happiness, religious fanaticism, and economic measures (e.g., GDP). The shape of the surface would be different for each idea. Of course, the adaptive landscape metaphor could be extended to completely different situations. Relationships spring to mind (x axis: you, y axis: your partner, z axis: happiness). The secret to love, therefore, is to not get stuck on a local optimum, but to keep searching the adaptive landscape until you find your global optimum. However, at this juncture, Wright would probably be shaking his head disapprovingly at me…

Our lab is in the news! Some of the people who work with Ivan and me just published a paper in the journal Conservation Biology (Mike Blouin is our advisor, and the other authors do research in our lab or are affiliated with it). Their paper shows that maintaining steelhead in hatcheries for several generations reduces their fitness in the wild, such that these hatchery fish can’t be considered equivalent to wild fish. The dataset is truly impressive. For years, every fish that has passed over a dam on the Hood River has been recorded and sampled for tissue. Using DNA markers, our colleagues were able to construct a nearly complete pedigree, of “family tree,” for the entire population, and show how many descendents each fish produced. Wild fish contribute much more to subsequent generations than do hatchery stock. Essentially, the hatchery stock have been domesticated; they have evolved to survive well in a hatchery, and are losing some of their adaptations for life in the wild. However, if fish are taken into hatcheries fresh from the wild, instead of being recycled through the hatchery year after year, they still have high fitness. Thus, hatcheries can help declining fish populations but they cannot solve the problem alone. We need wild habitats where fish can thrive indefinitely. The story has been picked up by the Associated Press and can be read on Yahoo News, and our lab has made the front pages of local papers.

This is the kind of result that makes everyone happy. Environmentalists can bolster their claim that hatcheries have been harmful to fish populations, while those who favor hatcheries can point out that hatcheries are useful if we just manage them correctly. The AP has chosen the headline, “Modern hatcheries aid wild salmon,” which is an interesting choice of words. Compare that to the headline of the Oregonian yesterday, “Hatchery fish fail to thrive in the wild,” which sounds like the exact opposite conclusion. What the study has shown is that it all depends on how you run your hatchery.