I’ve updated yesterday’s cat evolution post with some tough comments from an expert on cat fossils. Check it out.

Rick Perry’s on board! And no postmodern vagueness for him. He’s here to tell us that intelligent design is a “valid scientific theory.” That’s right, governor. Just check out all the work on intelligent design going on in the biology department at your state’s fine university. Um…wait…it’s there somewhere. Just let me figure out how to work this search function…

(Hat tip to Panda’s Thumb.)

As the proud owner of a fine cat, Tino, I’m happy to join the ritual of cat-blogging. I was inspired after reading a new study that sorts out Tino’s kinship with other cats. Now I know that a cheetah is more closely related to Tino than it is to a leopard (right and left, respectively).

The evolution of cats has been a tough nut to crack. While it’s no great mental feat to tell the difference between Tino and a tiger, it’s not so easy to figure out exactly which species are most closely related to domesticated cats and which are more distant relatives. The oldest cat-like fossils date back 35 million years ago, and since then they’ve rapidly evolved into many lineages that have spread across all the continents save Antarctica. When evolution moves fast, it is hard to reconstruct its path. Making things harder is the fact that cat lineages have repeatedly evolved into similar forms to take advantage of similar ecological niches.

This pattern isn’t unique to cats. Mammals with placentas (including cats, dogs, bears, bats, cows, primates, and rodents) underwent a massive evolutionary explosion, driven in large part by the extinction of big dinosaurs 65 million years ago. The evolutionary picture of this entire group has long been blurry. Over the past few years, a network of scientists have forced that picture into focus by gathering gene sequences from a wide range of mammal species and comparing them with statistical methods that can only be carried out on big computers. The major branches of the mammal tree are much clearer now.

The researchers (who come mainly from the Laboratory of Genomic Diversity at the National Cancer Institute) have now turned their attention to some of the branches on the mammal tree–such as cats. They looked at 22,789 base pairs of DNA from all living cat species. They used several different methods, based on the different ways in which DNA can evolve. Among the most common mutations are changes to single base pairs. The researchers calculated the most likely course evolution had taken to produce these sorts of mutations in the various lineages of living cats. Less common are mutations that move large chunks of genetic material from one part of the genome to another. When a group of species share the same massive mutation, scientists become more confident that they share a close common ancestor. And finally, by looking at the fossil record of cats and other mammals, the scientists constructed a molecular clock that they used to calculate when the lineages branched off from each other.

The scientists were able to reconstruct the evolutionary tree of cats with a great deal of statistical confidence. Their results are published in this week’s Science (link to come here). I’ve put the illustrations from the paper at the bottom for those who like to revel in the gorey details. What’s particularly neat about the paper is that it offers a hypothesis for how cats spread around the world. The researchers came up with this hypothesis by looking at where cats are today, and then mapping their locations onto the evolutionary tree.

The common ancestor of all living cats, according to their results, lived in Asia about ten million years ago. This cat’s descendants split into two branches. One led to lions, jaguars, tigers, leapards, snow leopards, and cloud leopards. The other branch gave rise to all other cats. These early cats remained in Asia until 8.5 million years ago, when new lineages moved into the New World and Africa. The New World immigrants gave rise to bobcats, couggars, lynxes, ocelots, bobcats, and other species found in the Western Hemisphere today. The African migrants were the ancestors of today’s servals and other small cat species.

But cats have a way of wandering. The ancestors of domestic cats moved back from North America back into Asia around 6.5 million years ago. Lynxes moved back as well about 2 million years ago, spreading west until they reached Spain. The ancestors of today’s mountain lions in the New World also produced another lineage that moved back into Asia and eventually wound up in Africa, where it became today’s cheetahs. Other big cats moved into Africa at around the same time–the cousins of tigers and snow leopards in Asia moved through the Sinai peninsula and evolved into African lions. But close cousins of the lions moved into the New World, evolving into jaguars.

It’s a cool study, but I was struck by the fact that all seven authors are geneticists, without a single paleontologist in their ranks. That’s pretty typical these days. Geneticists are busy publishing evolutionary research as they get their hands on vast new supplies of data. When they do glance at the fossil evidence, they mainly do so to calibrate their molecular clocks. But paleontologists have dug up lots of fossil cats all over the world, all of which have something to say about the evolution of these creatures. How, I wonder, do they fit into the pictures below?

Still, this DNA evidence is important for suggesting just how fast cats could migrate, and how splendidly they could adapt to all sorts of new niches, from the cliffs of the Himalayas to the canopy of South American cloud forests to the Sahara. Conservation biologists are rightly concerned about the introduction of cats to Australia and remote islands, where they’re wiping out endangered animals. But it turns out they’ve had plenty of practice at being invasive species, without help from us.

Update: 1/6 2 pm: I contacted an expert on cat fossils, Blaire Van Valkenburgh of UCLA, for her thoughts on the paper. She just replied. While she is impressed by the cat tree, she’s not so pleased with the way they use it to interpret the migrations of cats without consdering the fossils.

“The problem of ignoring extinct species and their potential influence on the tree produced is huge,” she writes, ” and they can only get away with it because it is impossible to get DNA from such ancient material. Their biogeographic hypotheses are provocative, but not at all convincing. One of my main problems with the paper is the lack of a causal explanation between sea-level shifts and cat speciation rates. In one case, they point out that an increase in within-lineage divergence is associated with higher than present sea levels (6.4-2.9 ma) and then in another case, they point out that rapid speciation is associated with lower sea levels (3.1-0.70. So what is the driving mechanism? I think they would have been wiser to look for associations between global cooling and drying as well as grassland expansion to explain some of these patterns.”

By the way, the paper is now online.

I have an article in tomorrow’s New York Times on a provocative theory about our origins. Humans, other animals, plants, fungi, and protozoans are all eukaryotes. We all share a distinctive genome compared to other organisms (prokaryotes, which include bacteria and archaea). Our genes are more versatile: they can be switched on an off in more complex patterns than in prokaryotes, and one gene can make many different proteins, depending on which parts of the gene our cells look at. Some scientists would like to say that this distinctiveness must be the product of natural selection. But Michael Lynch, a biologist at Indiana University, is here to remind us that natural selection is not the whole story when it comes to evolution. By this he doesn’t mean that the rest of the story involves aliens manufacturing everything we don’t yet understand. He means genetic drift and neutral evolution–processes that dont’ get much attention in the popular press. In writing this article, I figured out why: they’re hard to write about. There are few good metaphors in easy reach for these processes, so you’re left swinging around blunt weapons of statistics. Yet ultimately this is very provocative stuff: it suggests that a great deal at the core of our biological existence emerged in large part thanks to flukes of probability, not thanks to the fine craftsmanship of the blind watchmaker known as natural selection.

The new paper is here. You need a subscription to read it. But a paper Lynch published earlier this year that describes one piece of the puzzle is free.

Update, 1/4 10:30: I’ve posted the full text on carlzimmer.com here.

Update, 1/4 10:40 am: John Travis, deputy news editor at Science comments that he’s surprised that the article did not include comments from other scientists. Actually, it originally did, but in the merciless squeeze to fit on the newspaper page, those quotes had to come out. I contacted four experts in the field, and three had high praise for Lynch’s ideas and one remained skeptical. It’s certainly a controversial idea, since so many efforts in the past to explain the eukaryote genome have proposed that its features emerged as adaptations favored by natural selection.

I’ll be in Ann Arbor for a talk on January 14 at the natural history museum in conjunction with the opening of the “Explore Evolution” exhibit there. I’ll talk about reporting on new research in evolutionary biology. Here are the details.

Two of the most important stages in hominid evolution were the origin of the entire hominid branch some six to seven million years ago and the first movement of hominids out of their African birthplace. This week we now get a new look at both.

On the cover of Nature, the editors splashed the first reconstruction of Sahelanthropus, the oldest known hominid. The scientists who made the reconstruction used new material they found in the Sahara, adding to the material they described in their first report in 2002. There had been some argument over whether Sahelanthropus was an early hominid that looked a lot like other apes, or an ape that had a passing resemblance to hominids. The authors argue the former. They also claim that their new reconstruction provides new evidence that Sahelanthropus may have been bipedal. MSNBC reports that other scientists would prefer to see a nice pelvis or femur before accepting that claim.

Meanwhile, via John Hawks, National Geographic has a lovely display of some of the oldest hominids fossils found outside of Africa. Found in Georgia, they were initially assigned to Homo erectus, which is known to have spread all the way to Indonesia by 1.8 million years ago. But Homo erectus was a tall hominid with a big brain and a relatively flat face. The Georgia hominids, as you can see in NG’s new reconstructions, were tiny and reminiscent of earlier hominids back in Africa. Which raises the possibility, which I’ve discussed before, that the "hobbits" recently found in Indonesia (Homo floresiensis) might have been the relicts of a pre-Homo erectus migration of little folks out of Africa. (NG also has an article on the hobbits this month, by the discoverers.)

Unfortunately, there’s also bad new about hominids these days–the hobbit bones, which were "borrowed" last fall, are a mess.

UPDATE: Minutes later…Man, Nature is hominid crazy this week. I totally missed another paper in this issue on a new skull from the Georgia hominids. What’s most interesting about this indvidual was that it was old and toothless. It somehow survived for a long time after losing its teeth, which suggests it got a lot of help from its fellow hominids. Old age and extended family bonds are usually considered to have evolved later in hominid evolution, but this old gum-sucker suggests otherwise.

I’m guessing it’s only a matter of time before this guy gets a show on cable. Bryan Fry is a biologist at the University of Melbourne in Australia, and he spends a lot of his time doing this sort of thing–messing with animals you really really shouldn’t mess with. In addition to being telegenic, he rattles off those delicious Australian phrases, like, "No drama, mate." (Translation: No problem.)

While Fry is comfortable milking a king cobra in a jungle, he also has a lab-jockey side, using genomic technology to dredge up vast numbers of new snake venom genes. In tomorrow’s issue of the New York Times, I have an article about Fry’s latest research. He has offered a rough draft of the history of venoms–a 60 million year tale of gene recruitment and gene duplications and high-speed evolution. Understanding this history is a crucial part of Fry’s long-term goal of turning venoms into new drugs–a tradition that has already given rise to billions of dollars of sales each year and many lives saved. That may put him off-limits for IMAX movies, but television seems inevitable.

Spring is finally slinking into the northeast, and the backyard wildlife here is shaking off the winter torpor. Our oldest daughter, Charlotte, is now old enough to be curious about this biological exuberence. She likes to tell stories about little subterranean families of earthworm mommies and grub daddies, cram grapes in her cheeks in imitation of the chipmunks, and ask again and again about where the birds spend Christmas. This is, of course, hog heaven for a geeky science-writer father like myself, but there is one subject that I hope she doesn’t ask me about: how the garden snails have babies. Because then I would have to explain about the love darts.

Garden snails, and many other related species of snails, are hermaphrodites, equipped both with a penis that can deliver sperm to other males and with eggs that can be fertilized by the sperm of others. Two hermaphroditic snails can fertilize each other, or just play the role of male or female. Snail mating is a slow, languorous process, but it also involves some heavy weaponry. Before delivering their sperm, many species (including garden snails) fire nasty-looking darts made of calcium carbonate into the flesh of their mate. In the 1970s, scientists sugested that this was a gift to help the recipient raise its fertilized eggs. But it turns out that snails don’t incorporate the calcium in the dart into their bodies. Instead, love darts turn out to deliver hormones that manipulate a snail’s reproductive organs.

Evolutionary biologists have hypothesized that this love dart evolved due to a sexual arms race. When a snail receives some sperm, it can gain some evolutionary advantage if it can choose whether to use it or not. By choosing the best sperm, a snail can produce the best offspring. But it might be in the evolutionary interest of sperm-delivering snails to rob their mates of their ability to choose. And love darts appear to do just that. Their hormones prevent a snail from destroying sperm with digestive enzymes, so that firing a love dart leads to more eggs being fertilized.

Recently Joris Koene of Vrije University in the Netherlands Hinrich Schulenberg of Tuebingen University in Germany set out to see how this evolutionary arms race has played out over millions of years. They analyzed DNA from 51 different snail species that produce love darts, which allowed them to work out how the snails are related to one another. They then compared the darts produced by each species, along with other aspects of their reproduction, such as how fast the sperm could swim and the shape of the pocket that receives the sperm.

Koene and Schulenberg found that love darts are indeed part of a grand sexual arms race. Love darts have evolved many times, initially as simple cones but then turning into elaborate harpoons in some lineages. (The picture at the end of this post shows eight love darts, in side view and cross section.) In the same species in which these ornate weapons have evolved, snails have also evolved more powerful tactics for delivering their sperm, including increasingly complex glands where the darts and hormones are produced. These aggressive tactics have evolved, it seems, in response to the evolution of female choice. Species with elaborate love darts also have spermatophore-receving organs that have long, maze-like tunnels through which the sperm have to travel. By forcing sperm to travel further, the snails can cut down the increased survival of the sperm thanks to the dart-delivered hormones.

Sexual conflict has been proposed as a driving force in the evolution of many species, and this new research (which is published free online today at BMC Evolutionary Biology) supports the idea that hermaphrodites are not immune to it. What’s particularly cool about the paper is that all these attacks and counter-attacks co-vary. That is, species with more blades on their love darts tend to have longer rerpoductive tracts and more elaborate hormone-producing glands and so on. Only by comparing dozens of species were they able to find this sort of a relationship.

My wife always tells me that as a science writer, I ought to be well-prepared to give our children the talk about the birds and the bees. But I’m not sure the love darts would send quite the right message.

I’ll be a guest tonight at 7 PM EST on NPR’s talk show On Point, talking about the new wave of dinosaur science. Jack Horner will be on as well, delivering the dirt about his mind-blowing discovery of soft tissue from a T. rex. Should be interesting.

Update, 3/29/05 9:30 am: The show is now archived here. The links to the real player and windows media feeds are at the top of the page.

Today Gregor Mendel is a towering hero of biology, and yet during his own lifetime his ideas about heredity were greeted with deafening silence. In hindsight, it’s easy to blame his obscurity on his peers, and to say that they were simply unable to grasp his discoveries. But that’s not entirely true. Mendel got his ideas about heredity by experimenting on pea plants. If he crossed a plant with wrinkled peas with one with smooth peas, for example, the next generation produced only smooth peas. But when Mendel bred the hybrids, some of the following generation produced wrinkled peas again. Mendel argued that each parent must pass down factors to its offspring which didn’t merge with the factors from the other parent. For some reason, a plant only produced wrinkled peas if it inherited two wrinkle-factors.

Hoping to draw some attention to his research, Mendel wrote to Karl von Nageli, a prominent German botanist. Von Nageli was slow to respond, and when he did, he suggested that Mendel try to get the same results from hawkweed (Hieracium), the plant that von Nageli had studied for decades. Mendel tried and failed. It’s impossible to say whether von Nageli would have helped spread the word about Mendel’s work if the hawkweed experiments had worked out, but their failure couldn’t have helped.

After Mendel’s death, a new generation of biologists discovered his work and, with the insights they had gathered from their own work, they realized he had actually been onto something. Pea plants really do pass on factors–genes–to their offspring, and sometimes the genes affect the appearance of the plants and sometimes they don’t. Mendelian heredity, as it came to be known, was instrumental in the rise of the new science of genetics, and today practically every high school biology class features charts showing how dominant and recessive alleles are passed down from one generation to the next. Mendelian heredity also helped explain how new mutations could spread through a population–the first step in evolutionary change.

But what about that hawkweed? It turns out that usually Hieracium reproduces very differently than peas. A mature Hieracium does not need to mate with another plant. It does not even need to fertilize itself. Instead, it simply produces clones of itself. If Nageli had happened to have studied a plant that reproduced like peas, Mendel would have had more luck.

Hawkweed raises an important question–one that is particularly important this morning. Does it tells us that Mendel was wrong? Should teachers throw their Mendelian charts into the fire? No. Mendel found a pattern that is widespread in nature, but not a universal law. Most animals are pretty obedient to Mendel’s rule, as are many plants. Many algae and other protozoans also have Mendelian heredity, although many don’t. Many clone themselves. And among bacteria and archaea, which make up most of the diversity of life, Mendelian heredity is missing altogether. Bacteria and archaea often clone themselves, trade genes, and in some cases the microbes even merge together into a giant mass of DNA that then gives rise to spores.

Today in Nature, scientists found another exception to Mendelian heredity. They studied a plant called Arabidopsis (also known as cress) much as Mendel did, tracing genes from one generation to the next. They crossed two lines of cress, and then allowed the hybrids to self-fertilize for two more generations. Some of the versions of the genes disappeared over the generations from the genomes of the plants, as you’d expect. But then something weird happened: in a new generation of plants, some of the vanished genes reappeared. The authors think that the vanished genes must have been hiding somewhere–perhaps encoded as RNA–and were then tranformed back into DNA.

Is cress the tip of a genetic iceberg (to mix my metaphors hideously)? Only more experiments will tell. If it is more than just a fluke, it may turn out to play an important part in evolution, joining some other weird mechanisms, such as "adaptive mutation," in which bacteria crank up their mutation rate when they undergo stress. But hold onto those Mendelian charts. These cress plants are wonderfully weird–but no more wonderfully weird than hawkweed.

Panda’s Thumb has an update on the ongoing drama over teaching creationism in public schools taking place in York, Pennsylvania. Last year a group of residents donated 58 copies of a creationst book called Of Pandas and People to the local school. The board of education reviewed them and gave them the green light. The books are now available in the school library.

Now someone has donated 23 science books, many of which deal with evolutionary biology, to see how the board deals with them. So far, the board has said it will review them as to their "educational appropriateness," and has left it at that.

It’s an honor for my book Evolution: The Triumph of an Idea to be on a list that includes work by luminaries such as Stephen Hawking and Ernst Mayr. But if the donor wants to make his point–that evolution is well-established science–even more clearly, I’d suggest adding a few extra items: some of the leading college textbooks in biology, botany, microbiology, genetics, zoology, and developmental biology. Open any of them up and you’re likely to find evolution acting as the backbone for all of the knowledge they have to offer. Would the board balk at them? If they did, you’d have to wonder whether they actually want their students to succeed in college.

Readers were busy this weekend, posting over fifty comments to my last post about HIV. Much of the discussion was sparked by the comments of a young-Earth creationist who claims that the evolutionary tree I presented was merely an example of microevolution, which–apparently–creationists have no trouble with. This claim, which has been around for a long time, holds that God created different "kinds" of plants and animals (and viruses, I guess), and since then these kinds have undergone minor changes, but have never become another "kind."

Some readers expressed frustration that the comments were getting side-tracked into arguments about creationism. I take a pretty relaxed attitutde to what goes on in the comment threads, though. Part of that attitude, I’ll admit, comes from the fact that I don’t have the time to hover over the comments all day. But I also don’t relish the thought of shutting down discussion, except of course when comments come from pornography-peddling bots.

I myself find that objections to evolution frequently turn into good opportunities to discuss interesting scientific research. For example, let’s take the claim that an evolutionary tree of HIV merely documents microevolution.

Here’s the tree from my last post, published in The Lancet. It compares a new aggressive, resistant strain of HIV to strains taken from other patients. These viruses all descend from a common ancestor. The descendants mutated, many mutants died, and some mutants thrived, thanks to their ability to evade the immune systems of their hosts. Strains that share a closer common ancestor fall on closer branches.

This new strain belongs to a group of strains known collectively as HIV-1. What happens if you compare HIV-1 to viruses found in animals? Is it impossible to link these viruses together on a single tree? Were they all created separately, each to plague its own host? That’s what one might expect if indeed the "microevolution-yes, macro-evolution no" idea was true. After all, viruses that infect different animals are generally different from one another. They can only survive if they have biological equipment suited to their host species, and different species offer different challenges to a virus.

It turns out that the same approach used to compare HIV strains found in individual people works on this larger scale. Scientists can draw a tree.

Here is the most up-to-date version of the tree, which appears in the latest issue of the Journal of Virology. The different branches of HIV-1 are marked in black. The red branches are viruses known as Simian Immunodeficiency Virus (SIV) found in certain populations of chimpanzees. The blue branches also represent chimp SIV’s, but these are more distantly related to HIV-1. (A side note: the Lancet paper doesn’t specify exactly which HIV-1 group the nasty new strain belongs to. That’s a matter of ongoing research.)

It appears, then, that HIV-1 evolved into a human scourge not once but several times from chimp SIV ancestors. One likely route is the increasing trade in chimpanzee meat in western Africa. Hunters who get chimpanzee blood in their own wounds can become infected, and certain strains that manage to survive in our species can then evolve into better-adapted forms.

Of course, tracing back HIV-1 evolution this far leads to the question, where did the ancestors of HIV-1 come from? The authors of the review in Journal of Virology takes another step back, comparing chimpanzee SIV to SIVs from other monkeys. Does this enterprise now finally collapse? Does "microevolution" finally hit the wall, unable to explain "macroevolution"?

Nope. Here’s what they find. The tree on the left is based on studies of one HIV/SIV gene called Pol, and the one on the right is based on another called Env. SIVcpz refers to chimp SIV, and the other abbreviations refer to SIV’s found in various monkeys.

It turns out that different genes in chimp SIV have different evolutionary histories. This is no big surprise. Virologists have known for a long time that a single animal can get infected by two different viruses, which–on rare occassion–may combine their genetic material into a single package. The scientists hypothesize that chimp SIV evolved from SIV found in red-capped sooty mangabeys as well as SIV that infects greater spot-nosed, mustached, and mona monkeys. Just as humans hunt chimpanzees, chimpanzees hunt and eat monkeys. So they may have been infected in this manner.

You can take the same walk back in time with any virus that’s been studied carefully–or any species of animal or plant. Take us. Scientists publish evolutionary trees all the time in which they compare the DNA of individual people. They also use the same methods to demonstrate that chimpanzees are our closest living relatives, that primates descend from small shrew-like mammal ancestors, that mammals and other land vertebrates descend from fish, and so on. (I don’t have time this morning to grab examples of these trees, but if I have time tonight I will.) Certainly there are parts of these trees that are still difficult to make out. DNA sometimes evolves so much that a gene can wind up obscuring its own history, for example. But scientists have never hit the wall that creationists claim exists.