A Blog by Carl Zimmer

The Mystery of Kangaroo Adoptions

When you spend six years watching kangaroos, you start to see some strange things. From 2008 to 2013, Wendy King, a doctoral student at the University of Queensland, and her colleagues studied wild grey kangaroos in a national park in Victoria, Australia. All told, King and her colleagues studied 615 animals–194 adult females, and 326 juveniles, known as joeys. The first time King and her colleagues captured each kangaroo, they took a number of measurements and then marked it so they could recognize it later. From time to time, they’d find a juvenile kangaroo in the pouch of a different mother. Sometimes it would climb out, but then it would climb back into the new pouch, getting milk and protection from the adult female for months, until it was ready to live on its own.

In other words, these kangaroos had been adopted.

A marked kangaroo and her adopted joey. King et al PLOS One 2015 http://bit.ly/1dxRljP Photo by Camille Le Gall-Payne
A marked kangaroo and her adopted joey. King et al PLOS One 2015 http://bit.ly/1dxRljP

Scientists have observed adoption in occurring 120 species of mammals. Other species that are harder to study may be adopting, too. As for kangaroos, scientists have long known that if they put a joey in an unrelated female’s pouch, she will sometimes keep it. But King and her colleagues have now discovered that kangaroos will voluntarily adopt joeys in the wild. All told, they found that 11 of the 326 juveniles were adopted over their five-year study–a rate of about three percent. Given the commitment adoption demands from a mammal mother–a kangaroo mother needs a full year to raise a single joey to weaning–this discovery cries out for an explanation.

Over the years, researchers have proposed a number of different explanations for adoption. Some have suggested that mammals adopt young offspring of their relatives because they are genetically similar. By rearing the offspring of their kin, this argument goes, adoptive parents can ensure that some of their own genes get passed down to future generations.

According to another explanation, unrelated adults may adopt each other’s young because this kind of quid-pro-quo benefits everyone involved. And according to a third explanation, young adults adopt orphaned juveniles as a kind of apprenticeship. They learn some important lessons about how to raise young animals, which they can apply later to raising their own offspring.

These explanations share something in common. They all take adoption to have an evolutionary benefit. In the long run, the genes that make animals willing to adopt become more common thanks to natural selection.

But in the case of kangaroos–and perhaps other species, too–evolution may have instead have made a mess of things. Adoption may not be an adaptation. It may be a maladaptation.

To understand why some kangaroos adopted joeys, King and her colleagues looked for evidence that adoption provides an evolutionary benefit. They found that adoptive mothers didn’t pick out closely related juveniles to adopt. That finding weighs against kinship as an explanation.

King and her colleagues also didn’t find evidence to support the adoption-as-practice explanation. For one thing, only one out of eleven adoptive mothers was a young female that hadn’t yet had joeys of her own. In fact, some of the mothers swapped their babies.

Remarkably, King and her colleagues never observed an orphaned juvenile being adopted. In some cases, a mother adopting one joey would, in the process, abandon her own. These abandoned joeys were not then taken up by another adult female. Instead, they disappeared, presumably killed by foxes or other predators in the park.

All in all, adoption seems like a pretty bad move for mothers and joeys alike. King and her colleagues propose that adoptions happen not because natural selection favors it, but because kangaroos aren’t very good at recognizing their own joeys.

When a joey climbs out of its mother’s pouch and then tries to hop back in, its mother gives it a sniff. If the joey doesn’t smell like it belongs to her, she will push it away. King and her colleagues propose that in an emergency–such as when a predator turns up, prompting joeys to rush into pouches and adults to hop away–mothers may not have time for this inspection. An unrelated joey may leap in their pouch and stay there as the mother flees for safety. Once in the pouch, the joey will take on the same odor as her own offspring had. Now it will pass the sniff test–and become officially adopted.

One observation that King and her colleagues made supports this explanation: adoptions happened more often when the kangaroo population was high. When a mother is surrounded by a big crowd of joeys, there may be more opportunities for an unrelated joey to leap into her pouch.

I asked Kirsty MacLeod, a biologist at the University of Cambridge, what she thought about the new study. She found the evidence compelling, if bizarre. “It’s pretty weird,” she said. “It makes very little evolutionary sense to stop investing in your own young, and instead divert all your resources to another offspring, especially one that isn’t related to you.”

MacLeod thinks King is probably right that kangaroos adopt by accident during a crisis. “But that doesn’t necessarily mean it’s intrinsically nonadaptive,” she added.

Grabbing the closest joey in an emergency may be a good strategy for kangaroo mothers, since the closest joey will probably be her own. “It’s likely better to take that chance (and one out of ten times, face the consequence of raising another female’s young),” said MacLeod, “than to risk separation and offspring death, a catastrophe for a mother that spends over a year rearing a joey.”

It would be a mistake to draw a lot of lessons from this study about human nature. It’s true that humans adopt children, too. But the causes behind human adoption demand attention to the human experience–which, among other things, does not involve putting babies in pouches. But there are other lessons to take from this research. When trying to make sense of the weirdness of animal behavior, it’s a good idea to consider the possibility that it exists because of its evolutionary benefit. But it’s also worth wondering if you’re dealing with evolution’s imperfection.

A Blog by Carl Zimmer

Bamboo Mathematicians

In the late 1960s, a species of bamboo called Phyllostachys bambusoides–commonly known as the Chinese Mainland Bamboo or Japanese Timber Bamboo–burst into flower. The species originated in China, was introduced to Japan, and later into the United States and other countries. And when I say it flowered, I mean it flowered everywhere. Forests of the plant burst into bloom in synchrony, despite being separated by thousands of miles. If, like me, you missed it, you will probably not live to see it happen again. The flowers released pollen into the wind, and the fertilized plants then produced seeds that fell to the ground. The magnificent bamboo plants, which can grow 72 feet tall, then all promptly died. Their seeds later sprouted and sent up new plants. The new generation is now close to fifty years old and has yet to grow a single flower. They won’t flower till about 2090.

We can say this with certainty this because Chinese scholars have kept such careful records for such a long time. In 999 A.D. they recorded a flowering of Chinese Mainland Bamboo. It was probably an astonishing sight, since no one alive at the time had ever seen the species flower before. The bamboo plants died, their seeds sprouted, and the forests did not flower again till 1114. After the species was imported to Japan, the Japanese recorded flowers in the early 1700s, and then again in 1844 to 1847. The flowering in the late 1960s was just the next burst of a 120-year cycle.

An 1885 illustration of Chusquea abietifolia, with a 32-year flowering cycle. Gray Herbarium Library, Harvard University Herbaria
An 1885 illustration of Chusquea abietifolia, with a 32-year flowering cycle. Gray Herbarium Library, Harvard University Herbaria

This remarkable cycle would be fascinating enough on its own. But it turns out a number of other species of bamboo grow flowers on cycles lasting decades, too. A species called Bambusa bambos flowers every 32 years, for example. Phyllostachys nigra f. henonis takes 60 years.

Three biologists at Harvard got puzzled by these cycles and recently set out to find an explanation for how they evolved. In the journal Ecology Letters, they offer up a tantalizing hypothesis: bamboo cycles have reached their remarkable lengths through some simple arithmetic.

Like all scientists, these biologists (Carl Veller, Martin Nowak, and Charles Davis) stand on the shoulders of giants. Or one giant in particular–the ecologist Daniel Janzen, who over the years has cast off a huge number of creative, influential ideas with unsettling ease.

In the mid-1970s Janzen came up with an explanation for why bamboo plants would flower in synchrony. He noted that rats, birds, pigs, and other animals devour colossal numbers of bamboo seeds. Each gobbled-up seed represents the loss of a potential offspring. If there are enough seed-predators, and they are hungry enough, they can wipe out a bamboo plant’s entire set of seeds.

Bamboo plants might fare better, Janzen argued, if they flowered at the same time. They would overwhelm their enemies with food. Even if they gorged themselves to bursting, they would still leave some seeds untouched. Those surviving seeds would then have enough time to grow into plants that could defend themselves with tough fibers and bitter chemicals.

Once bamboos fell into flowering lockstep, it would be hard for them to slide out. If a few bamboo plants flowered a few years too early, animals would feast on their seeds, and their out-of-sync genes would fail to make it into future generations.

Other scientists have found support for Janzen’s idea. Swamping enemies with seeds really does lower the overall harm that seed-eaters cause to each individual plant. But Veller and his colleagues still had questions. How did the bamboo plants get into those beneficial flower cycles to begin with? And how did various species end up with such long–and such different–flowering rhythms?

The scientists developed a mathematical model based on what’s known about bamboo biology. They started out with a bamboo forest in which almost all the plants flower annually, as some bamboo species do.

But the population also contained some mutants. They had mutations in their flower-timing genes, so that they needed two years to flower instead of one. Some of the two-year mutants flowered in even years, while others flowered in odd years. Spending two years between flowering instead of one could have some advantages for bamboo plants. The plants could have more time to gather more energy from sunlight, which they could use to make more seeds, or give their seeds more defenses against predators.

As more of the forest becomes two-year plants, there are fewer plants releasing their seeds every year. Eventually, Veller and his colleagues found, a year arrives when the annual bamboo plants can’t produce enough seeds to survive the onslaught of animals. In one fell swoop, they’re wiped out. If it’s an odd year, then the odd-year two-year plants can get wiped out, too. If it’s an even year, the even-yeared plants take the fall. Either way, the whole forest gets abruptly synchronized into flowering every two years.

It’s also possible that the forest wouldn’t just have two-year mutants, but mutants that took three years or more to flower. Veller and his colleagues found that in their mathematical model, bamboo plants with longer flowering cycles could also take over. Exactly which cycle won out was partly a matter of chance, because how many seeds bamboo plants successfully produce in a given year can fluctuate due to the weather and other unpredictable conditions. Whichever cycle emerges as the dominant one, the whole forest then evolves to stay synchronized. Any outliers flowering out of sync get wiped out, just as Janzen had proposed.

There is one exception, though: a mutant bamboo plant can evolve a new cycle that’s a multiple of the original one. Imagine that a two-year bamboo turns into a four-year one. Every year it flowers, it’s protected by the two-year plants flowering at the same time. And it’s got an advantage over them: it can spend the extra time making more seeds.

Even though the four-year flowers need twice as long to produce their seeds, the scientists found, under some conditions they can still become increasingly common over a few centuries. Eventually, the whole forest will lock onto the four-year cycle.

But bamboo can’t evolve the other way, the scientists found. If a four-year forest produces a two-year mutant, it will flower half the time in years when it has no protection from predators. The only direction it can go is towards longer cycles. If a four-year forest produces an eight-year mutant, it can have the same advantage that the four-year plants originally had: well-protected time.

Veller and his colleagues realized that they could test this model. Over millions of years, they reasoned, species should have multiplied their flowering cycles. It’s likely that they could only multiply the cycles by a small number rather than a big one. Shifting from a two-year cycle to a two-thousand-year cycle would require some drastic changes to a bamboo plant’s biology. Therefore, the years in a bamboo’s cycle should be the product of small numbers multiplied together.

The mathematics of bamboo offers some promising support. Phyllostachys bambusoides has a cycle of 120 years, for example, which equals 5 x 3 x 2 x 2 x 2. Phyllostachys nigra f. henonis takes 60 years, which is 5 x 3 x 2 x 2. And the 32 year cycle of Bambusa bambos equals 2 x 2 x 2 x 2 x 2.

Veller et al 2015 Ecology Letters
Veller et al 2015 Ecology Letters

The scientists found more support when they looked at how bamboo species have evolved. Here’s an evolutionary tree of Phyllostachys bambusoides and its close relatives. It’s possible that their common ancestor had a five-year cycle, and then the cycle multiplied by small factors along each branch of the tree.

But could this just be a kind of meaningless bamboo numerology? Is it just a coincidence that these species display such elegant multiplications? Veller and his colleagues carried out a statistical test on bamboo species with well-documented flowering cycles. They found that the cycles are tightly clustered around numbers that can be factored into small prime numbers. It’s a pattern that you would not expect from chance. In fact, they argue, this test offers very strong evidence for multiplication (for stat junkies: p=0.0041).

There is plenty of opportunity to put this model to the test. A lot of species of bamboo have long flowering cycles that no one has measured very carefully. Scientists could see how newly studied cycles fit into Veller’s model. If scientists find a new species of Phyllostachys that’s got a 23 year cycle, for example, it would be mathematically impossible for it to have evolved from a five-year ancestor. One thing’s for sure, though. If this model requires scientists to sit around watching bamboo, waiting for it to flower, this is going to take a few generations of scientists to settle.

A Blog by Carl Zimmer

Can Scientists Turn Birds Back Into Dinosaur Ancestors?

We know they evolved from dinosaurs about 150 million years ago, but it remains to be discovered precisely how the DNA of ground-running dinosaurs changed–a transformation that turned arms into wings, produced aerodynamic feathers, and created a beak. It’s possible that some clues to those genetic changes can be found in living birds themselves. By blocking some of the recently evolved steps in the development of bird embryos, we might be able to get birds to grow some dinosaur anatomy.

A team of researchers recently used this approach to understand how dinosaur snouts turned into bird beaks. Beaks are really just insanely extravagant versions of little bones called premaxillae. (You’ve got a pair just behind your front teeth.) The researchers blocked some proteins produced on the face of chicken embryos and found that the chickens failed to make beaks. Instead, their premaxillae became an unfused pair of bones–a lot like you might find in living beakless relatives of birds, such as alligators. Here, a normal chicken skull is on the left, an altered one is in the middle, and an alligator is on the right.

Bhullar et al, Evolution 2015
Bhullar et al, Evolution 2015

As I write in my column today in the New York Times, some researchers remain skeptical that these chickens are really developing the beakless heads of their ancestors–that they’ve run evolution in reverse, in effect. More precise experiments on chicken DNA could confirm that this is what indeed happening.

Some people may find this exciting because it could presage the coming of dino-chickens. But no one has any idea of how long it would take to figure out how to reverse the rest of a bird’s body. A chicken with nothing more than a snout, by this measure, is profoundly underwhelming.

But for those who are interested in how evolution actually happened, it’s already very thought-provoking. For example, the scientists picked out two proteins to block specifically to turn beaks into snouts. To their surprise, this procedure simultaneously changed other bones in the skulls of the birds, turning them back to dinosaur-like shapes.

When birds evolved beaks, other parts of their head was also undergoing some evolutionary changes. The palate bones in the roof of their mouth became very thin, serving mainly to transmit forces from muscles at the back of the head to the beak. When the scientists blocked proteins in chicken embryo faces, they changed the palate bones as well as the beak. This figure, which looks up at the palate from underneath, shows what happened:

Bhullar et al 2015 Evolution
Bhullar et al 2015 Evolution

Scientists have long known that a single gene can have several effects on an animal. This multi-tasking is called pleiotropy. The new experiment hints that the bird beak didn’t evolve simply through a series of little steps, each having a single effect on bird heads. Instead, birds might have taken some bigger evolutionary leaps.

A Blog by Carl Zimmer

Sitting on a Cliff Vs. Falling Off a Cliff

The Steller’s sea cow is gone. This mega-manatee swam the North Pacific for millions of years, and then in the 1700s humans hunted them to extinction. Today on the front page of the New York Times, I write about a warning from a team of scientists that if we keep on doing what we’re doing now–industrializing the ocean and pouring carbon dioxide into the atmosphere in greater and greater amounts–a lot of other marine animal species will go the way of the Steller’s sea cow.

Yet this story is actually a fairly hopeful one. The scientists compared the pace of extinctions at sea to those on land and found that the oceans are basically where the land was in 1800–with relatively few extinctions yet, on the verge of massive changes to the habitat that could wreak much bigger havoc. The oceans still have a capacity to recover, if we choose to let them.

It’s hard to strike that balance, but it’s important. By coincidence, a group of marine biologists has just published a provocative opinion piece calling for more skepticism about “ocean calamities”–the claim that the oceans are getting hit with some global shock of one sort or another. (You can read the piece in Bioscience for free.) They complain that too often scientists see a small-scale change in one region of the ocean and blow it up to a global catastrophe. The scientists pick apart some of these cases, such as the belief that jellyfish are taking over the planet. The strongest evidence for their rise turned out to be a natural increase of one population of jellyfish that is part of a natural cycle.

That doesn’t mean that thee are no ocean calamities. The scientists see strong evidence for devastation from overfishing, for example. And that doesn’t mean that dangers that don’t seem to have had big impacts yet won’t have them in the future (see ocean acidification). But leaping to the apocalypse based on limited or ambiguous evidence is bad science and bad policy, the scientists argue:

We conclude that a robust audit of ocean calamities, probing into each of them much deeper than the few examples provided here, is imperative to weeding out the equivocal or unsupported calamities, which will confer hope to society that the oceans may not be entirely in a state of near collapse and which will provide confidence that the efforts by managers and policymakers targeting the most pressing issues may still deliver a healthier ocean for the future.

I wanted to check in with the authors of the Bioscience piece about the new study I wrote about for the Times. If they thought this new study was an egregious case of calamity-mongering, I needed to know that, and I would make it clear in my piece.

But that’s not what I found. When I spoke to Robinson Fulweiler, a marine biologist at Boston University, she said, “I was really excited to read their paper, and I actually felt good about their conclusions.” She thought the scientists did a good job of gauging what’s happened to the oceans so far, the risks they face in the future, and–importantly–the steps that we can take, armed with our knowledge of the situation.

When we’re contending with our effects on the planet, it may be tempting to go limp and say we’re all doomed, or to wave it off as some huge delusion. But the reality of the oceans calls for a different response altogether.

A Blog by Carl Zimmer

Your Inner Feather

Feathers are like eyes or or hands. They’re so complex, so impressive in their adaptations, so good at getting a job done, that it can be hard at first to believe they evolved. Feathers today are only found on birds, which use them to do things like fly, control their body temperature, and show off for potential mates. The closest living relatives of birds–alligators and crocodiles–are not exactly known for their plumage. At least among living things, the glory of feathers is an all-or-nothing affair.

But the more we get to know feathers, the more we can appreciate how they evolved. The general rule is that complex things–be they feathers, hands, or eyes–take a very long time to evolve. As I wrote in National Geographic in 2011, the fossil record has gone a very long way in helping us to understand how feathers took on the form we see today. Birds evolved from dinosaur ancestors, and those ancestors already had feathers. Feathers started out as simple filaments, turning to fuzz, and then diversifying into a lot of different forms–including the ones that eventually let birds take to the air.

A sampling of feathered dinosaurs and early birds. Xing Lida/National Geographic
A sampling of feathered dinosaurs and early birds. Xing Lida/National Geographic

Now a new study in the journal Molecular Biology and Evolution offers an even deeper look into the history of feathers. Instead of looking at fossils, the scientists look at the genetic recipe for feathers written in the DNA of birds. It turns out that a lot of that recipe already existed hundreds of millions of years before anything vaguely resembling a feather existed on Earth. In fact, you, my fine unfeathered friend, have most of the genetic information required for making feathers, too.

Scott Edwards, a Harvard ornithologist, and his colleagues couldn’t have carried out this study even a few years ago, because scientists have only recently figured out a lot of the details of how feathers develop. Bird embryos starts out featherless. But in their skin, they develop lots of tiny blobs of cells known as placodes in which cells are switching on genes in a distinctive pattern. The reason that certain genes switch on in the placodes and others don’t is that genes have little on-off switches near them. If a particular combination of proteins lands on a gene’s switch, the gene will start making a protein of its own.

Ng et al 2012.  PLoS Genet 8(7): e1002748
The development of a feather. The middle figure is a cross-section of the primordial feather shown on the left. Source: Ng et al 2012. PLoS Genet 8(7): e1002748

At first, the cells in the placodes multiply quickly. Then they start grow into shafts, which then split open to form feathers. Depending on the bird, and on the spot on the bird’s body where it grows, the feather may split into a downy plume, or into a paddle-shaped flight feather, or into an ornamental tail feather. Along the way, the cells differentiate, producing different combinations of proteins. The cells that make up the central shaft of the feather are stiffened with certain types of keratin, for example, while cells that are in the more delicate regions of the feather produce more flexible forms of the protein from different genes. Clusters of cells produce pigment molecules to give the feather colors and patterns. Every cell has an entire genome, which means it has all the genes for making any part of the feather. But its switches ensure that it only uses a certain combination of those genes.

Frizzled chicken. Photo by Alisha Vargas via Creative Commons https://flic.kr/p/7XmQqu
Frizzled chicken. Photo by Alisha Vargas via Creative Commons https://flic.kr/p/7XmQqu

Edwards and his colleagues combed the scientific literature for genes that are important for feather development. Scientists have studied frizzled chickens, for example, identified the mutation for the breed’s frizzles, and thereby identified a gene essential for developing feathers. All told, Edwards and his colleagues found 193 feather genes this way. Their list included 67 that encode variations of keratin, and 126 that help establish the pattern of feathers.

Next, the scientists searched for the switches that control those genes. This isn’t so easy. The switches are short stretches of DNA, often nestled deep inside much longer stretches of DNA that are just gibberish. What’s more, genes have distinctive segments that let you know you’re looking at a gene. The switches are much harder to distinguish from the gibberish.

The scientists used several strategies to zero in on the switches. They took advantage of the fact that most switches for a gene are close to the gene itself. So they only searched in the neighborhood of the 167 feather genes. They also took advantage of the fact that switches evolve relatively little, because most mutations will be harmful to them. So the scientists compared the DNA around feather genes in several different species and sought out the stretches that were noticeably similar from one species to the next. Using these two strategies, the scientists discovered a staggering 13,307 feather gene switches (technically known as conserved nonexonic elements, or CNEEs for short).

Next, the scientists asked when each part of this feather cookbook evolved. If they found a gene or a switch only in the DNA of birds, then they could be confident that it had evolved after the ancestors of birds split off from the ancestors of alligators and crocodiles. But if they found a gene or a switch in birds and alligators and crocodiles, then it must have evolved earlier, in their common ancestor.

(You may be asking, how did these new genes evolve? The short answer is that they can evolve through the duplication of old genes, or the transformation of genetic gibberish–a k a noncoding DNA. If you want to get more details, watch this TED-Ed video I wrote the script for.)

To see how far back the evolution of feather genes went, the scientists compared birds to a wide range of vertebrates, including humans, turtles, and pufferfish. They found that the instructions for making feathers got their start a long, long time before feathers themselves (see the tree at the bottom of the post or embiggen it here). The genes that establish the basic pattern of placodes already existed in the common ancestor of living fish and birds (and us)–in other words, about half a billion years ago. Even more feather genes evolved as our common ancestors climbed ashore and walked around on land 350 million years ago. Many switches for feather genes also emerged during this period, too.

About 300 million years ago, our ancestors began to lay hard-shelled eggs. Those early animals would give rise to mammals, reptiles, and birds (collectively known as amniotes, named for the amniotic egg). Edwards and his colleagues found that the first amniotes already had the entire complement of feather patterning genes. That means you, as an amniote, have them too.

Later, the early amniotes split away into their major lineages. The lineage that includes alligators, birds, and extinct dinosaurs–called archosaurs–originated about 250 million years ago. Edwards and his colleagues detected many new keratin genes evolving during the origin of archosaurs, along with 86 percent of their 13,000 or so feather gene switches.

It would not be another 100 million years or so before the oldest known birds flew. And yet just about everything you need to make a feather, genetically speaking, was already in place.

It may seem strange to consider the fact that you, as a mammal, have all the known genes required to pattern a feather, and yet you do not look like Big Bird. The reason for this discrepancy is that genes can do different jobs. Depending on where and when they make their proteins, they can build different kinds of anatomy. But it didn’t take much rewiring of genetic switches to turn the scaly skin of early reptiles into feathers. Indeed, the deep history of feathers could explain why paleontologists are finding so much evidence of simple feather-like filaments not just in dinosaurs, but in their close relatives like pterosaurs. Evolution was tinkering with the same toolkit.

Edwards and his colleagues noticed something else intriguing in the genomes of birds. They found a lot of switches that were not near feather genes, but were unique to birds. When the scientists looked for the nearest genes, they noticed that many of the genes help birds grow. They control the size of bird bodies, for example, or the size of their limbs.

This is an intriguing finding, because the fossil record reveals that as dinosaurs evolved into birds, their bodies shrank, while their arms got long for their size. The shift made it possible for birds to generate a lot of lift with big wings, which only had to keep a small body aloft.

Edwards and his colleagues may have found the molecular signature of that change. If they’re right, the cookbook for feathers is very old, but it took the evolution of a new kind of body for birds to use their feathers to fly.

From Lowe et al 2014
From Lowe et al 2014 (Click to embiggen)

With apologies to Neil Shubin for riffing on his title.

A Blog by Carl Zimmer

What Slipped Disks Tell Us About 700 Million Years of Evolution

From Zimmer and Emlen, Evolution: Making Sense of Life
From Zimmer and Emlen, Evolution: Making Sense of Life

There’s a unity to life. Sometimes it’s plain to see, but very often it lurks underneath a distraction of differences. And a  new study shows that there’s even a hidden unity between our slipped disks and the muscles in a squirming worm.

Scientists call this unity “homology.” The British anatomist Richard Owen coined the term in 1843, sixteen years before Charles Darwin published The Origin of Species.  Owen defined homology as “the same organ in different animals under every variety of form and function.” For example, a human arm, a seal flipper, and a bat wing all have the same basic skeletal layout. They consist of a single long bone, a bending joint, two more long bones, a cluster of small bones, and a set of five digits. The size and shape of each bone may differ, but the pattern is the same regardless of how mammals use their limbs–to swim, to fly, or to wield a hammer.

Darwin argued that homology was the result of evolution. The common ancestor of humans, seals, bats, and other mammals had a limb which became stretched and squashed in various contortions. And over the past 150 years, paleontologists have found a wealth of  fossils that help document how the tiny paws of Mesozoic mammals diversified into the many forms found in mammals today.

But Darwin wasn’t just out to explain the evolution of mammals. He saw a kinship across the entire living world. And that’s where things got complicated. Anatomists in Darwin’s day could find no clear counterparts to many of the traits in our own bodies in distantly related animals.

It turns out the homology is there, but you just need the right eyeglasses to see it.

Recently, Detlev Arendt, a biologist at the European Molecular Biology Laboratory, and his colleagues investigated the evolution of an important but  overlooked feature in our bodies, known as the notochord. It’s a stiff rod of cartilage that develops in human embryos, running down their back. Later, as the spine develops, the notochord transforms into the disks that cushion the vertebrae (and sometimes slip later in life, causing much grief).

Other mammals also develop a notochord as embryos. And so do birds, reptiles, amphibians, and fish. Even our closest invertebrate relatives, such as lancelets, have notochords. All animals with a notochord belong to the same group, known as the chordates.

Unlike most vertebrates, lancelets keep their notochord into adulthood, using it to stiffen their bodies when they swim. Early chordate fossils also have a lancelet-like anatomy. So it’s likely that 550 million years ago, the notochord evolved in chordates first, and then the skeleton evolved later. In fish, the spine took over the body-stiffening job, but the notochord still had other work left to do.  In the vertebrate embryo, the notochord releases chemical signals that tell the surrounding cells whether they should become nerves, blood vessels, or other tissues.

Arendt and his colleagues wondered how the notochord first evolved. Squid don’t have a notochord. Neither do clams, or cockroaches, or tarantulas. The notochord, in other words, seems to be unique to chordates. So where did it come from? Did it emerge right at the dawn of chordates, or did it have deeper origins?

The scientists decided to tackle these questions by looking at the genes in notochord cells. In a developing vertebrate embryo, notochord cells switch on a unique combination of genes. The scientists wondered if the genetic signature of a notochord cell might be lurking in animals that have no notochord.

They started their search in ragworms, ocean-dwelling relatives of the more familiar earthworms. Worms (or to be more precise, annelids) are an ancient lineage that split off from our own ancestors long before the notochord evolved. There’s nothing in their squishy bodies that you would mistake for a notochord.

The axochord. Colors correspond to activity of genes listed in the figure. Lauri et al, Science 2014
The axochord. Colors correspond to activity of genes listed in the figure. Lauri et al, Science 2014

Arendt and his colleagues added chemicals to ragworm larvae to make cells glow if they were using notochord genes. The larvae lit up like Christmas trees.

The cells using notochord genes formed a strip running from the head to the tail of the ragworm larvae–in much the same arrangement as our own notochord. When the rag worm larvae matured, the scientists found, the strip developed into a cord of muscle.

The worms need this cord–which the scientists dubbed the axochord–to move around. When the scientists destroyed the axochord with a laser, the ragworms could no longer swim. And once Arendt and his colleagues discovered the axochord in ragworms, they looked for it in other animals that lack a notochord. They found signs of axochords in a number of other invertebrates.

The marine worm Platynereis has a muscle (red) which develops in the same place and has the same genetic signature as the notochord (blue) that develops into our spinal discs. Credit: Kalliopi Monoyios
The marine worm Platynereis has a muscle (red) which develops in the same place and has the same genetic signature as the notochord (blue) that develops into our spinal discs. Credit: Kalliopi Monoyios

This study  reveals the homology of notochords and axochords, but it also does something more. It  helps us go back in time. Ragworms and humans share a common ancestor, along with other animals that have brains, heads, tails, and distinct left and right sides. Collectively all these animals are known as bilaterians. The emergence of bilaterians some 700 million years ago was a tremendous evolutionary event, giving rise to a huge diversity of animal forms and even changing the chemistry of the oceans and atmosphere.

Evolutionary biologists would love to know what the first bilaterians looked like, and to understand how they gave rise to such different animals today. One of the biggest surprises in the history of biology has been the discovery that bilaterians share a deep homology in the genes that build their bodies. Fly eyes and human eyes may look different, for example, but the same network of genes helps build both kinds. Or take the front and back of our bodies. In us (and other chordates), the main nerve cord runs down the back and our digestive tract runs down the front. In a fly or in many other bilaterians, the arrangement is vice-versa. But all bilaterians use the same genes to tell the two sides apart.

These discoveries let scientists develop hypotheses about what the first bilaterians looked like. They may have already had a head, tail, brain, and eye-like senses for example. And the new study hints that they may have had a precursor of our notochord. Our own cartilage notochord turns out to be a peculiar variation on the bilaterian body plan. Other bilaterians have an axochord–basically, a notochord made of muscle. So it’s possible that 700 million years ago, our first bilaterian ancestors had an axochord made of muscle, which they might have used to swim. The descendants of these first bilaterians diverged into many body forms. In a few lineages, Arendt and his colleagues argue, the axochord was transformed into structures that look dramatically different today. We belong to one of those lineages.

The new study suggests that the signals that our notochord cells received changed slightly, switching from muscle to cartilage. This is actually easier than it may sound, since embryonic stem cells are incredibly versatile. In fact, we can fall victim today to such anatomical mix-ups. Last year, for example, I wrote a story for The Atlantic about a rare disease called FOP that switches muscles to cartilage, which then turns to bone. It takes a single mutation to produce this disease.

Only 1 in 2 million people get FOP. Slipped disks are a far more common disorder. As many as a third of people may end up with a disk bulging out of place. That’s the kind of risk you run when your ancestors’ notochord evolves into spine cushions, and then, much later, your ancestors start walking around upright. If you ever find yourself laid up in bed because your notochord fails you, try distracting yourself by reflecting on its long evolutionary history reaching back over half a billion years, and the unity it shares with worms wriggling through the sea.

(Here’s a video showing the axochord in 3-D)

(Update: changed title to better reflect story)

A Blog by Carl Zimmer

The Erotic Endurance of Whale Hips

Buried deep within the body of a whale, underneath the heaps of muscles and tendons, lie some little, lonely bones. They are whale hips–and they are one of the stranger examples of evolution’s transforming power. Perhaps kinkier is a better word.

Some 54 million years ago, the ancestors of whales and dolphins were four-legged mammals. Their anatomy was well-adapted for moving around on land, including their hips. Here, for example, is an ancient member of the whale lineage, called Indohyus. The hip bones of these early whale relatives had scoops where the balls of their femurs could be tucked away. They had shelves where leg muscles could anchor. While the hips themselves were made up of a cluster of bones, they were fused together, and they were also joined tightly to the spine. Those firm connections allowed the animal to hold its body up against gravity, and use the forces generated by its legs to propel its body forward.

Indohyus reconstruction. Thewissen et al. Nature 2007. 450, 1190-1194
Indohyus reconstruction. Thewissen et al. Nature 2007. 450, 1190-1194

Over the course of about ten million years, the ancestors of today’s whales moved into the water. They evolved seal-like bodies with stout limbs; later, their forelegs became flippers and their hind legs dwindled away. They lost their fur and their nostrils migrated from the tip of their head to above their eyes, where it became a blow hole. (I wrote about this transition in my book At the Water’s Edge.)

By 40 million years ago, the walking whales were long gone. In their place were species like Dorudon atrox. As you can see from this diagram, its body looks a lot like a living whale. And like a living whale, its hips have shrunk and become separate from its spine. Unlike today’s whales, however, Dorudon still had well-developed hind legs–albeit tiny ones.

Dorudon. From M. Uhen, Annu. Rev. Earth Planet. Sci. 2010. 38:189–219
Dorudon. From M. Uhen, Annu. Rev. Earth Planet. Sci. 2010. 38:189–219

Within a few million years, those leg bones were pretty much gone, too. The diagram below shows a series of hip bones from the whale lineage, going from terrestrial species (Indohyus and Pakicetus) to more aquatic ones (Ambulocetus) to totally aquatic (Basilosaurus, which looked a lot like Dorudon) to living whales.

Whale pelvic bones. From Thewissen et al 2009, Bioscience. dx.doi.org/10.1007/s12052-009-0135-2
Whale pelvic bones. From Thewissen et al 2009, Bioscience. dx.doi.org/10.1007/s12052-009-0135-2

All that remained were a tiny set of hip bones. They lay far away from the rest of the skeleton. They no longer fused to each other, and they no longer had the distinctive scoops and shelves that used to be essential for walking.
When we see whale hips at the end of this long evolutionary history, they make more sense. They are vestiges of the terrestrial history of whales. But the fact that they still linger is also puzzling. If hips were adaptations for a vanished life, then why haven’t they vanished altogether?

A new study in the journal Evolution helps to answer that question. Far from being abandoned by evolution, whale hips are still evolving today. While they may not be essential for walking, they still matter a lot to whales. (A quick editorial note: this post gets NSFW from here on out.)

To see why, we have to go back to those hips of land mammals. They are important for walking on land, but they serve other purposes, too. Among other things, they anchor muscles that control the sex organs. If these muscles are anesthetized in men, for example, they have a hard time gaining an erection.

As whale hips stopped mattering to walking, they didn’t stop mattering to having sex. In male whales, the pelvis controls the penis with an especially elaborate set of muscles. In some whale and dolphin species, these muscles make the penis  downright prehensile.

Dines et al, Evolution in press
Dines et al, Evolution in press

Jim Dines of the Natural History Museum of Los Angeles and his colleagues have recently been studying how the sex life of whales drives the evolution of their hips. If a male animal can fertilize more eggs than other males, his genes may become more common over the generations. This process–known as sexual selection–can lead to all sorts of baroque adaptations in animals. Dines and his colleagues wondered if whale hips are also experiencing sexual selection.

Sexual selection gets stronger as the competition between males gets more intense. In some species, males fight battle for the opportunity to mate with females, and they often evolve big weapons like horns or oversized claws. In some species, the competition takes place inside the females, because a single female may mate with several males. Any strategy that lets one male’s sperm do better than another’s may become more common.

Females can make sexual selection even more intense. In some species, they have evolved elaborate reproductive organs that let them choose which male’s sperm she will fertilize her eggs with. Those female adaptations may drive the evolution of even more elaborate male organs that can overcome them.

One of the best ways to see sexual selection in action is to compare different species. As I wrote on the Loom a few years back, different species of ducks and other water fowl have huge penises and equally huge reproductive tracts. The longer the penis, the more maze-like the reproductive tract. This pattern suggests the birds are trapped in a sexual arms race.

Another way for males to increase their success is to produce more sperm, so as to overwhelm the competition. Scientists have tested this possibility by comparing primate species where males compete a lot with each other to species where there is very little competition–in other words, where the primates are monogamous. They’ve found that in the more promiscuous species, males have bigger testicles. (We humans have moderately large testicles, suggesting we’ve experienced moderate sperm competition.)

Dines and his colleagues decided to take a similar approach to whales and dolphins. They studied pelvic bones from 29 different species, and compared their dimensions to their mating systems. Some of the species the scientists looked at, like the franciscana dolphin, are monogamous. Other species are more promiscuous. Marine biologists once observed two male Northern Right whales mating with a female at the same time, for example.

A pattern emerged from their analysis–the kind of pattern you’d expect from sexual selection’s fingerprints. The more promiscuous a species was, the bigger its pelvis bones tended to be. The scientists also found that as whales evolved to become more promiscuous, their pelvic bones changed shape. These changes weren’t part of some general change to their skeleton, however. The ribs near the hips didn’t show the same patterns of size and shape change.

Dines and his colleagues can’t say what the change in the shape and size of pelvic bone does to a whale. That would require a level of intimate observation of whale sex that is simply impossible. But they have been able to get some clues by looking at other parts of male whale sexual anatomy. The whales with big hip bones also tended to have big testicles and big penises. This pattern may mean that hip bones are evolving as part of a bigger system. Whales with more competition may be using bigger hip bones to control a longer penis to deliver more sperm to females. (The new study only considers how whale hips may be selected in males. That doesn’t necessarily mean they have no function in female whales, which have hips too. Or perhaps they are the female equivalent of male nipples, carried along for the ride. For now, the subject is too mysterious for scientists to say anything firm about it.)

“Far from being mere relics of a terrestrial past,” Dines and his colleagues conclude, “cetacean pelvic bones are targets of sexual selection.” In fact, the only reason that we can still see these strange vestiges may be that they still matter to evolution, and in the most intimate way imaginable.

[Update: Added sentences about hips in females.]

A Blog by Carl Zimmer

The Tree of Smells

Animals have been smelling for hundreds of millions of years, but the evolution of that sense is difficult to trace. You can’t ask an elephant to describe the fragrance of an acacia tree, for example, nor can you ask a lion if it gets the same feeling from a whiff of the same plant.

So scientists have to gather indirect clues to how different species use their noses. One way is to run simple tests on animals, seeing if they show an ability to tell different odors apart. Elephants, for example, can tell the difference between the smells of as many as 30 different members of their extended family.

Another way to track the evolution of smelling is to dissect the molecules that do the smelling in different species. Inside our noses, nerve endings are studded with receptors that can grab different odor molecules.  All mammals build variations on the same basic structure, known as an olfactory receptor. But they may have hundreds of different kinds of receptors in their noses, each encoded by a different gene. The structure of each kind of receptor determines the kind of molecules it can grab–and the signal it can send to the brain.

Recently, scientists at the University of Tokyo compared 20,000 olfactory receptor genes from 13 species of mammals. In some cases, such as elephants, they were the first to make such a catalog. In other cases, such as cows and mice, they identified olfactory receptor genes that had gone overlooked till now.

One striking result of the study was that elephants have a lot of different olfactory receptors. They have 1948 receptor genes, the highest ever recorded for a species. Dogs have less than half, with 811. And humans have 396.

Does that mean that elephants have evolved to become five times better at smelling than we are? There’s not a simple relationship between olfactory receptor genes and the sense of smell. And the evolution of smell is a lot more than just a list of numbers.

New olfactory receptors don’t just come out of the blue. They emerge from a special kind of mutation. Sometimes when cells are duplicating their genes, they accidentally make an extra copy of a stretch of DNA. Where there was once a single olfactory receptor gene, there are now two identical copies. Mutations can then alter the sequence of one of the genes, and thus change the structure of the receptor.

But mutations can also rob mammals of olfactory receptors. They can disable a gene, so that neurons can’t use it to make the corresponding receptor. In some cases, they accidentally delete the gene altogether.

What’s most interesting about the new study from Tokyo is that the scientists were able to reconstruct 100 million years of smell evolution in a single tree. They could recognize related versions of the same gene in different species, and use that information to trace when new genes arose and when they disappeared.

Here’s the tree, and I’ll explain it below.

Niiumura et al http://genome.cshlp.org/content/early/2014/07/16/gr.169532.113
Niiumura et al http://genome.cshlp.org/content/early/2014/07/16/gr.169532.113

The common ancestor of all these species lived about 100 million years ago. Based on their shared genes, the scientists determined that that ancestral mammal had 781 genes–almost twice as many as we have today, and less than half of what elephants have.

The blue circles show how many genes the common ancestors of today’s mammals had at each node in the tree. The numbers along each of the branches show how many new genes were gained, and how many were lost.

The lineage that led to elephants certainly gained a lot of new genes–1335 all told. But so did a lot of other lineages. If you trace the tree from the base to rats, you’ll find that they gained 884 new genes. But they also lost a lot of genes along the way, too, so that now they have only 1207 genes.

But elephants lost genes, too–168 all told. Even if elephants do have an amazing sense of smell (something we just don’t know), that wasn’t simply the result of adding new genes. Some genes may have been useless to them–ones that remain useful in other species. But we don’t know why they lost the genes they did.

There are other weird features of this tree. As you move down the tree from the common ancestor to rats, for example, you can see that their ancestors had a net gain of genes for their first 10 million years or so, followed by at least 20 million years of losses, followed in turn by a major gain of genes. No one can say why they had these ups and downs.

Our own evolutionary story has mysteries of its own. There’s no question that we humans are pathetic in the olfactory receptor gene department. Many scientists have speculated that our primate ancestors shifted to relying more on vision for finding food and attracting mates. With a gain of vision came a loss of smell, the argument goes. But we can’t go too far in dismissing smell from our evolution. After all, as my fellow Phenom Ed Yong wrote this spring, we can still smell trillions of different smells. For some reason, other apes and monkeys have ended up with fewer olfactory receptor genes than we still have. It’s especially intriguing to consider all the genes we gained even as our collection of receptors shrank. We have 18 kinds of olfactory receptors that are found in no other mammals, not even chimpanzees, our closest living relatives. What on Earth do we use them for?

This tree represents everything we know about the evolution of these genes in mammals. But there are some 5000 other species of mammals on Earth, and adding their branches would reveal a lot more. As you can see in this figure, elephants are only distantly related to rodents, primates and the other species that have been studied so far. As a result, they sit on a long lonely branch in this tree. In reality, elephants have plenty of living relatives, such as manatees and hyraxes. It would be interesting to see if their huge set of genes grew gradually, or exploded after they gained their trunks.

Meanwhile, our own stubby branch raises questions of its own. Did Neanderthals have the identical set of olfactory receptor genes as we do? How would a rose smell to a Neanderthal, I wonder?


A Blog by Carl Zimmer

Young Animals and Old, Old Plants

Last Friday, I was a guest on the radio show Science Friday with photographer Rachel Sussman. We talked about her new book, The Oldest Living Things in the World, for which I wrote the introduction. You can listen here. (And you can read my whole introduction to Sussman’s book here.)

I talked on the show about some of the ideas that scientists are exploring about why some species live for a long time and some don’t. What’s intriguing me a lot right now is how old some plants can get. There are a few animal species can reach a very ripe age, such as clams that live for five hundred years. But Sussman’s book is dominated by plants–by ancient trees and shrubs and such–that can live for many thousands of years.

Scientists can’t offer a simple, straightforward answer to why plants can get so much older than animals. But they have gathered a lot of intriguing evidence that may lead them to one. For one thing, the biology of aging is different in some important respects in animals and plants, as Howard Thomas of Aberswyth Aberystwyth University in Scotland  Wales explained last year in the journal New Phytologist.

As we animals get older, things go wrong. For example, as our cells divide, their DNA sometimes mutates. This can cause the cells to malfunction or even turn cancerous. This burden of mutations only gets greater the older we get. We can try to fix this damage–repairing DNA, killing off defective cells, and so on–but that takes a lot of energy, energy that animals could otherwise use for other purposes, like reproducing.

Plants don’t seem to have to deal with these challenges. Trees that are 4700 years old don’t have more mutations in their cells than much younger plants. It’s possible that they lack those mutations because a kind of evolutionary struggle taking in the tissues of old plants. If some cells suffer mutations, other cells that are in better shape will take over and continue to grow healthy tissue.

Thomas also suggests that plants aren’t trapped in a trade-off between repairing their cells and growing like animals are. That’s because animals have to eat their food, while plants manufacture theirs from the sun and the air. They’ve got a lot more energy to work with.

The very bodies of plants may also give them an opportunity to grow very old, while ours do not. An animal is made up of two kinds of cells: somatic cells that make up most of the bodies, and a small collection germ cells (sperm or eggs) that can give rise to a new animal. That division gets established early in the development of an animal embryo and never changes. Plants don’t have such a stark division between somatic and germ cells. As they grow, they add new modules, each of which may produce germ cells (hence, a cherry tree is covered in blossoms, rather than just one blossom). Some of those modules may get stressed and even die, but the other modules can survive and continue to grow.

Recently a team of scientists from Ghent University in Belgium pointed out in Trends in Cell Biology that plants are different from animals in another respect: their stem cells.

Stem cells, which grow in both animals and plants, have the potential to grow into new tissue. In animals, they can maintain a healthy, young body. If they stop rejuvenating muscle, skin, and other tissue, an animal becomes old.  (See my post this week for more details).

Plants have stem cells, too, which are concentrated where the plants are putting on new growth, such as their stems and root tips. But they also have what you might call stem cells for stem cells. Known as quiescent cells, they form a tiny patch in the middle of a cluster of stem cells. They grow very slowly, and each time a quiescent cell splits in two, one of the new cells becomes a true stem cell. That new stem cell divides rapidly into still more  stem cells, which in turn can develop int a root or a leaf or some other part of a plant. But the other cell from that original division is yet another quiescent cell, which remains behind in reserve.

Quiescent cells appear to be vital to plants. If scientists remove all the quiescent cells from a root, for example, some of the stem cells in the root will turn into new quiescent cells. It’s possible, the Belgian scientists write, that they are also crucial to the ability of plants to keep rejuvenating  for a long time. They can create a supply of stem cells for millennia.

After thousands of years, in other words, a bristlecone pine may still be young at heart.

Llareta, an ancient shrub. From the Oldest Living Things in the World, by Rachel Sussman
Llareta, an ancient shrub. From the Oldest Living Things in the World, by Rachel Sussman