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Science Tuesday - All Evolution, all the time!
From a Few Genes, Life’s Myriad Shapes
By CAROL KAESUK YOON, The New York Times, June 26, 2007
Since its humble beginnings as a single cell, life has evolved into a spectacular array of shapes and sizes, from tiny fleas to towering Tyrannosaurus rex, from slow-soaring vultures to fast-swimming swordfish, and from modest ferns to alluring orchids. But just how such diversity of form could arise out of evolution’s mess of random genetic mutations — how a functional wing could sprout where none had grown before, or how flowers could blossom in what had been a flowerless world — has remained one of the most fascinating and intractable questions in evolutionary biology.
Now finally, after more than a century of puzzling, scientists are finding answers coming fast and furious and from a surprising quarter, the field known as evo-devo. Just coming into its own as a science, evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.
For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison. “The first response is ‘Huh?’ and the second response is ‘Far out.’ ”
“This is the illumination of the utterly dark,” Dr. Carroll added.
The development of an organism — how one end gets designated as the head or the tail, how feet are enticed to grow at the end of a leg rather than at the wrist — is controlled by a hierarchy of genes, with master genes at the top controlling a next tier of genes, controlling a next and so on. But the real interest for evolutionary biologists is that these hierarchies not only favor the evolution of certain forms but also disallow the growth of others, determining what can and cannot arise not only in the course of the growth of an embryo, but also over the history of life itself.
“It’s been said that classical evolutionary theory looks at survival of the fittest,” said Dr. Scott F. Gilbert, a developmental biologist at Swarthmore College. By looking at what sorts of organisms are most likely or impossible to develop, he explained, “evo-devo looks at the arrival of the fittest.”
Charles Darwin saw it first. He pointed out well over a century ago that developing forms of life would be central to the study of evolution. Little came of it initially, for a variety of reasons. Not least of these was the discovery that perturbing the process of development often resulted in a freak show starring horrors like bipedal goats and insects with legs growing out of their mouths, monstrosities that seemed to shed little light on the wonders of evolution.
But the advent of molecular biology reinvigorated the study of development in the 1980s, and evo-devo quickly got scientists’ attention when early breakthroughs revealed that the same master genes were laying out fundamental body plans and parts across the animal kingdom. For example, researchers discovered that genes in the Pax6 family could switch on the development of eyes in animals as different as flies and people. More recent work has begun looking beyond the body’s basic building blocks to reveal how changes in development have resulted in some of the world’s most celebrated of evolutionary events.
In one of the most exciting of the new studies, a team of scientists led by Dr. Cliff Tabin, a developmental biologist at Harvard Medical School, investigated a classic example of evolution by natural selection, the evolution of Darwin’s finches on the Galápagos Islands.
Like the other organisms that made it to the remote archipelago off the coast of Ecuador, Darwin’s finches have flourished in their isolation, evolving into many and varied species. But, while the finches bear his name and while Darwin was indeed inspired to thoughts of evolution by animals on these islands, the finches left him flummoxed. Darwin did not realize for quite some time that these birds were all finches or even that they were related to one another.
He should be forgiven, however. For while the species are descendants of an original pioneering finch, they no longer bear its characteristic short, slender beak, which is excellent for hulling tiny seeds. In fact, the finches no longer look very finchlike at all. Adapting to the strange new foods of the islands, some have evolved taller, broader, more powerful nut-cracking beaks; the most impressive of the big-beaked finches is Geospiza magnirostris. Other finches have evolved longer bills that are ideal for drilling holes into cactus fruits to get at the seeds; Geospiza conirostris is one species with a particularly elongated beak.
But how could such bills evolve from a simple finch beak? Scientists had assumed that the dramatic alterations in beak shape, height, width and strength would require the accumulation of many chance mutations in many different genes. But evo-devo has revealed that getting a fancy new beak can be simpler than anyone had imagined.
Genes are stretches of DNA that can be switched on so that they will produce molecules known as proteins. Proteins can then do a number of jobs in the cell or outside it, working to make parts of organisms, switching other genes on and so on. When genes are switched on to produce proteins, they can do so at a low level in a limited area or they can crank out lots of protein in many cells.
What Dr. Tabin and colleagues found, when looking at the range of beak shapes and sizes across different finch species, was that the thicker and taller and more robust a beak, the more strongly it expressed a gene known as BMP4 early in development. The BMP4 gene (its abbreviation stands for bone morphogenetic protein, No. 4) produces the BMP4 protein, which can signal cells to begin producing bone. But BMP4 is multitalented and can also act to direct early development, laying out a variety of architectural plans including signaling which part of the embryo is to be the backside and which the belly side. To verify that the BMP4 gene itself could indeed trigger the growth of grander, bigger, nut-crushing beaks, researchers artificially cranked up the production of BMP4 in the developing beaks of chicken embryos. The chicks began growing wider, taller, more robust beaks similar to those of a nut-cracking finch.
In the finches with long, probing beaks, researchers found at work a different gene, known as calmodulin. As with BMP4, the more that calmodulin was expressed, the longer the beak became. When scientists artificially increased calmodulin in chicken embryos, the chicks began growing extended beaks, just like a cactus driller.
So, with just these two genes, not tens or hundreds, the scientists found the potential to recreate beaks, massive or stubby or elongated.
“So now one wants to go in a number of directions,” Dr. Tabin said. “What happens in a stork? What happens in a hummingbird? A parrot?” For the evolution of beaks, the main tool with which a bird handles its food and makes its living, is central not only to Darwin’s finches, but to birds as a whole.
BMP4’s reach does not stop at the birds, however.
In lakes in Africa, the fish known as cichlids have evolved so rapidly into such a huge diversity of species that they have become one of the best known evolutionary radiations. The cichlids have evolved in different shapes and sizes, and with a variety of jaw types specialized for eating certain kinds of food. Robust, thick jaws are excellent at crushing snails, while longer jaws work well for sucking up algae. As with the beaks of finches, a range of styles developed.
Now in a new study, Dr. R. Craig Albertson, an evolutionary biologist at Syracuse University, and Dr. Thomas D. Kocher, a geneticist at the University of New Hampshire, have shown that more robust-jawed cichlids express more BMP4 during development than those with more delicate jaws. To test whether BMP4 was indeed responsible for the difference, these scientists artificially increased the expression of BMP4 in the zebrafish, the lab rat of the fish world. And, reprising the beak experiments, researchers found that increased production of BMP4 in the jaws of embryonic zebrafish led to the development of more robust chewing and chomping parts.
And if being a major player in the evolution of African cichlids and Darwin’s finches — two of the most famous evolutionary radiations of species — were not enough for BMP4, Dr. Peter R. Grant, an evolutionary biologist at Princeton University, predicted that the gene would probably be found to play an important role in the evolution of still other animals. He noted that jaw changes were a crucial element in the evolution of lizards, rabbits and mice, among others, making them prime candidates for evolution via BMP4.
“This is just the beginning,” Dr. Grant said. “These are exciting times for us all.”
Used to lay out body plans, build beaks and alter fish jaws, BMP4 illustrates perfectly one of the major recurring themes of evo-devo. New forms can arise via new uses of existing genes, in particular the control genes or what are sometimes called toolkit genes that oversee development. It is a discovery that can explain much that has previously been mysterious, like the observation that without much obvious change to the genome over all, one can get fairly radical changes in form.
“There aren’t new genes arising every time a new species arises,” said Dr. Brian K. Hall, a developmental biologist at Dalhousie University in Nova Scotia. “Basically you take existing genes and processes and modify them, and that’s why humans and chimps can be 99 percent similar at the genome level.”
Evo-devo has also begun to shine a light on a phenomenon with which evolutionary biologists have long been familiar, the way in which different species will come up with sometimes jaw-droppingly similar solutions when confronted with the same challenges.
Among the placental mammals of the Americas and the marsupials of Australia, for example, have evolved the same sorts of animals independently: beasts that burrowed, loping critters that grazed, creatures that had long snouts for eating ants, and versions of wolf.
In the same way, the cichlids have evolved pairs of matching species, arising independently in separate lakes in Africa. In Lake Malawi, for example, there is a long and flat-headed species with a deep underbite that looks remarkably like an unrelated species that lives a similar lifestyle in Lake Tanganyika. There is another cichlid with a bulging brow and frowning lips in Lake Malawi with, again, an unrelated but otherwise extremely similar-looking cichlid in Lake Tanganyika. The same jaws, heads, and ways of living can be seen to evolve again and again.
The findings of evo-devo suggest that such parallels might in fact be expected. For cichlids are hardly coming up with new genetic solutions to eating tough snails as they each crank up the BMP4 or tinker with other toolkit genes. Instead, whether in Lake Malawi or Lake Tanganyika, they may be using the same genes to develop the same forms that provide the same solutions to the same ecological challenges. Why not, when even the beaked birds flying overhead are using the very same genes?
Evo-devo has even begun to give biologists new insight into one of the most beautiful examples of recurring forms: the evolution of mimicry.
It has long been a source of amazement how some species seem so able to evolve near-perfect mimicry of another. Poisonous species often evolve bright warning colors, which have been reproduced by nonpoisonous species or by other, similarly poisonous species, hoping to fend off curious predators.
Now in a new study of Heliconius butterflies, Dr. Mathieu Joron, an evolutionary biologist at the University of Edinburgh, and colleagues, found evidence that the mimics may be using some of the same genes to produce their copycat warning colors and patterns.
The researchers studied several species of tropical Heliconius butterflies, all of which are nasty-tasting to birds and which mimic one another’s color patterns. Dr. Joron and colleagues found that some of the main elements of the patterns — a yellow band in Heliconius melpomene and Heliconius erato and a complex tiger-stripe pattern in Heliconius numata — are controlled by a single region of DNA, a tightly linked set of genes known as a supergene.
Dr. Joron said he and colleagues were still mapping the details of color pattern control within the supergene. But if this turned out to function, as researchers suspected, like a toolkit gene turning the patterns on and off, it could explain both the prevalence of mimicry in Heliconius and the apparent ease with which these species have been shown to repeatedly evolve such superbly matching patterns.
One of evo-devo’s greatest strengths is its cross-disciplinary nature, bridging not only evolutionary and developmental studies but gaps as broad as those between fossil-hunting paleontologists and molecular biologists. One researcher whose approach epitomizes the power of such synthesis is Dr. Neil Shubin, an evolutionary biologist at the University of Chicago and the Field Museum.
Last year, Dr. Shubin and colleagues reported the discovery of a fossil fish on Ellesmere Island in northern Canada. They had found Tiktaalik, as they named the fish, after searching for six years. They persisted for so long because they were certain that they had found the right age and kind of rock where a fossil of a fish trying to make the transition to life on land was likely to be found. And Tiktaalik appeared to be just such a fish, but it also had a few surprises for the researchers.
“Tiktaalik is special,” Dr. Shubin said. “It has a flat head with eyes on top. It has gills and lungs. It’s an animal that’s exploring the interface between water and land.”
But Tiktaalik was a truly stunning discovery because this water-loving fish bore wrists, an attribute thought to have been an innovation confined strictly to animals that had already made the transition to land.
“This was telling us that a piece of the toolkit, to make arms, legs, hand and feet, could very well be present in fish limbs,” Dr. Shubin said. In other words, the genetic tools or toolkit genes for making limbs to walk on land might well have been present long before fish made that critical leap. But as fascinating as Tiktaalik was, it was also rock hard and provided no DNA that might shed light on the presence or absence of any particular gene.
So Dr. Shubin did what more and more evo-devo researchers are learning to do: take off one hat (paleontologist) and don another (molecular biologist). Dr. Shubin oversees one of what he says is a small but growing number of laboratories where old-fashioned rock-pounding takes place alongside high-tech molecular DNA studies.
He and colleagues began a study of the living but ancient fish known as the paddlefish. What they found, reported last month in the journal Nature, was that these thoroughly fishy fish were turning on control genes known as Hox genes, in a manner characteristic of the four-limbed, land-loving beasts known as tetrapods.
Tetrapods include cows, people, birds, rodents and so on. In other words, the potential for making fingers, hands and feet, crucial innovations used in emerging from the water to a life of walking and crawling on land, appears to have been present in fish, long before they began flip-flopping their way out of the muck. “The genetic tools to build fingers and toes were in place for a long time,” Dr. Shubin wrote in an e-mail message. “Lacking were the environmental conditions where these structures would be useful.” He added, “Fingers arose when the right environments arose.”
And here is another of the main themes to emerge from evo-devo. Major events in evolution like the transition from life in the water to life on land are not necessarily set off by the arising of the genetic mutations that will build the required body parts, or even the appearance of the body parts themselves, as had long been assumed. Instead, it is theorized that the right ecological situation, the right habitat in which such bold, new forms will prove to be particularly advantageous, may be what is required to set these major transitions in motion.
So far, most of the evo-devo work has been on animals, but researchers have begun to ask whether the same themes are being played out in plants.
Of particular interest to botanists is what Darwin described as an “abominable mystery”: the origin of flowering plants. A critical event in the evolution of plants, it happened, by paleontological standards, rather suddenly.
So what genes were involved in the origin of flowers? Botanists know that during development, the genes known as MADS box genes lay out the architecture of the blossom. They do so by turning on other genes, thereby determining what will develop where — petals here, reproductive parts there and so on, in much the same manner that Hox genes determine the general layout of parts in animals. Hox genes have had an important role in the evolution of animal form. But have MADS box genes had as central a role in the evolution of plants?
So far, said Dr. Vivian F. Irish, a developmental biologist at Yale University, the answer appears to be yes. There is a variety of circumstantial evidence, the most interesting of which is the fact that the MADS box genes exploded in number right around the time that flowering plants first appeared.
“It’s really analogous to what’s going on in Hox genes,” said Dr. Irish, though she noted that details of the role of the MADS box genes remained to be worked out. “It’s very cool that evolution has used a similar strategy in two very different kingdoms.”
Amid the enthusiast hubbub, cautionary notes have been sounded. Dr. Jerry Coyne, an evolutionary biologist at the University of Chicago, said that as dramatic as the changes in form caused by mutations in toolkit genes can be, it was premature to credit these genes with being the primary drivers of the evolution of novel forms and diversity. He said that too few studies had been done so far to support such broad claims, and that it could turn out that other, more mundane workaday genes, of the sort that were being studied long before evo-devo appeared on the scene, would play equally or even more important roles.
“I urge caution,” Dr. Coyne said. “We just don’t know.”
All of which goes to show that like all emerging fields, evo-devo’s significance and the uniqueness of its contributions will continue to be reassessed. It will remain to be seen just how separate or incorporated into the rest of evolutionary thinking its findings will end up being. Paradoxically, it was during just such a flurry of intellectual synthesis and research activity, the watershed known as the New or Modern Synthesis in which modern evolutionary biology was born in the last century, that developmental thinking was almost entirely ejected from the science of evolution.
But perhaps today synthesizers can do better, broadening their focus without constricting their view of evolution as they try to take in all of the great pageant that is the history of life.
“We’re still a very young field,” Dr. Gilbert said. “But I think this is a new evolutionary synthesis, an emerging evolutionary synthesis. I think we’re seeing it.”
Humans Have Spread Globally, and Evolved Locally
By NICHOLAS WADE, The New York Times, June 26, 2007
Historians often assume that they need pay no attention to human evolution because the process ground to a halt in the distant past. That assumption is looking less and less secure in light of new findings based on decoding human DNA.
People have continued to evolve since leaving the ancestral homeland in northeastern Africa some 50,000 years ago, both through the random process known as genetic drift and through natural selection. The genome bears many fingerprints in places where natural selection has recently remolded the human clay, researchers have found, as people in the various continents adapted to new diseases, climates, diets and, perhaps, behavioral demands.
A striking feature of many of these changes is that they are local. The genes under selective pressure found in one continent-based population or race are mostly different from those that occur in the others. These genes so far make up a small fraction of all human genes.
A notable instance of recent natural selection is the emergence of lactose tolerance — the ability to digest lactose in adulthood — among the cattle-herding people of northern Europe some 5,000 years ago. Lactase, the enzyme that digests the principal sugar of milk, is usually switched off after weaning. But because of the great nutritional benefit for cattle herders of being able to digest lactose in adulthood, a genetic change that keeps the lactase gene switched on spread through the population.
Lactose tolerance is not confined to Europeans. Last year, Sarah Tishkoff of the University of Maryland and colleagues tested 43 ethnic groups in East Africa and found three separate mutations, all different from the European one, that keep the lactase gene switched on in adulthood. One of the mutations, found in peoples of Kenya and Tanzania, may have arisen as recently as 3,000 years ago.
That lactose tolerance has evolved independently four times is an instance of convergent evolution. Natural selection has used the different mutations available in European and East African populations to make each develop lactose tolerance. In Africa, those who carried the mutation were able to leave 10 times more progeny, creating a strong selective advantage.
Researchers studying other single genes have found evidence for recent evolutionary change in the genes that mediate conditions like skin color, resistance to malaria and salt retention.
The most striking instances of recent human evolution have emerged from a new kind of study, one in which the genome is scanned for evidence of selective pressures by looking at a few hundred thousand specific sites where variation is common.
Last year Benjamin Voight, Jonathan Pritchard and colleagues at the University of Chicago searched for genes under natural selection in Africans, Europeans and East Asians. In each race, some 200 genes showed signals of selection, but without much overlap, suggesting that the populations on each continent were adapting to local challenges.
Another study, by Scott Williamson of Cornell University and colleagues, published in PLoS Genetics this month, found 100 genes under selection in Chinese, African-Americans and European-Americans.
In most cases, the source of selective pressure is unknown. But many genes associated with resistance to disease emerge from the scans, confirming that disease is a powerful selective force. Another category of genes under selective pressure covers those involved in metabolism, suggesting that people were responding to changes in diet, perhaps associated with the switch from hunting and gathering to agriculture.
Several genes involved in determining skin color have been under selective pressure in Europeans and East Asians. But Dr. Pritchard’s study detected skin color genes only in Europeans, and Dr. Williamson found mostly genes selected in Chinese.
The reason for the difference is that Dr. Pritchard’s statistical screen detects genetic variants that have become very common in a population but are not yet universal. Dr. Williamson’s picks up variants that have already swept through a population and are possessed by almost everyone.
The findings suggest that Europeans and East Asians acquired their pale skin through different genetic routes and, in the case of Europeans, perhaps as recently as around 7,000 years ago.
Another puzzle is presented by selected genes involved in brain function, which occur in different populations and could presumably be responses to behavioral challenges encountered since people left the ancestral homeland in Africa.
But some genes have more than one role, and some of these brain-related genes could have been selected for other properties.
Two years ago, Bruce Lahn, a geneticist at the University of Chicago, reported finding signatures of selection in two brain-related genes of a type known as microcephalins, because when mutated, people are born with very small brains. Two of the microcephalins had come under selection in Europeans and one in Chinese, Dr. Lahn reported.
He suggested that the selected forms of the gene had helped improved cognitive capacity and that many other genes, yet to be identified, would turn out to have done the same in these and other populations.
Neither microcephalin gene turned up in Dr. Pritchard’s or Dr. Williamson’s list of selected genes, and other researchers have disputed Dr. Lahn’s claims. Dr. Pritchard found that two other microcephalin genes were under selection, one in Africans and the other in Europeans and East Asians.
Even more strikingly, Dr. Williamson’s group reported that a version of a gene called DAB1 had become universal in Chinese but not in other populations. DAB1 is involved in organizing the layers of cells in the cerebral cortex, the site of higher cognitive functions.
Variants of two genes involved in hearing have become universal, one in Chinese, the other in Europeans.
The emerging lists of selected human genes may open new insights into the interactions between history and genetics. “If we ask what are the most important evolutionary events of the last 5,000 years, they are cultural, like the spread of agriculture, or extinctions of populations through war or disease,” said Marcus Feldman, a population geneticist at Stanford. These cultural events are likely to have left deep marks in the human genome.
A genomic survey of world populations by Dr. Feldman, Noah Rosenberg and colleagues in 2002 showed that people clustered genetically on the basis of small differences in DNA into five groups that correspond to the five continent-based populations: Africans, Australian aborigines, East Asians, American Indians and Caucasians, a group that includes Europeans, Middle Easterners and people of the Indian subcontinent. The clusterings reflect “serial founder effects,” Dr. Feldman said, meaning that as people migrated around the world, each new population carried away just part of the genetic variation in the one it was derived from.
The new scans for selection show so far that the populations on each continent have evolved independently in some ways as they responded to local climates, diseases and, perhaps, behavioral situations.
The concept of race as having a biological basis is controversial, and most geneticists are reluctant to describe it that way. But some say the genetic clustering into continent-based groups does correspond roughly to the popular conception of racial groups.
“There are difficulties in where you put boundaries on the globe, but we know now there are enough genetic differences between people from different parts of the world that you can classify people in groups that correspond to popular notions of race,” Dr. Pritchard said.
David Reich, a population geneticist at the Harvard Medical School, said that the term “race” was scientifically inexact and that he preferred “ancestry.” Genetic tests of ancestry are now so precise, he said, that they can identify not just Europeans but can distinguish between northern and southern Europeans. Ancestry tests are used in trying to identify genes for disease risk by comparing patients with healthy people. People of different races are excluded in such studies. Their genetic differences would obscure the genetic difference between patients and unaffected people.
No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.
This is the case with lactose tolerance in European and African peoples and with pale skin in East Asians and Europeans.
Fast-Reproducing Microbes Provide a Window on Natural Selection
By CARL ZIMMER, The New York Times, June 26, 2007
In the corner of a laboratory at Michigan State University, one of the longest-running experiments in evolution is quietly unfolding. A dozen flasks of sugary broth swirl on a gently rocking table. Each is home to hundreds of millions of Escherichia coli, the common gut microbe. These 12 lines of bacteria have been reproducing since 1989, when the biologist Richard E. Lenski bred them from a single E. coli. “I originally thought it might go a couple thousand generations, but it’s kept going and stayed interesting,” Dr. Lenski said. He is up to 40,000 generations now, and counting.
In that time, the bacteria have changed significantly. For one thing, they are bigger — twice as big on average as their common ancestor. They are also far better at reproducing in these flasks, dividing 70 percent faster than their ancestor. These changes have emerged through spontaneous mutations and natural selection, and Dr. Lenski and his colleagues have been able to watch them unfold.
When Dr. Lenski began his experiment 18 years ago, only a few scientists believed they could observe evolution so closely. Today evolutionary experiments on microbes are under way in many laboratories. And thanks to the falling price of genome-sequencing technology, scientists can now zero in on the precise genetic changes that unfold during evolution, a power previous generations of researchers only dreamed of.
“It’s fun for us, because we can watch the game of life at the molecular level,” said Bernhard Palsson of the University of California, San Diego. “Many features of evolutionary theory are showing up in these experiments, and that’s why people are so excited by them.”
In the past century scientists have gathered a wealth of evidence about the power of natural selection. But much of that evidence has been indirect. Natural selection is a process that takes place over many generations, that may affect thousands or millions of individuals, and that may be shaped by many different conditions. To document it scientists have searched for historical fingerprints. They study fossils, for example, or compare the DNA of related species.
In the late 1980s a few scientists began experimenting with microbes, hoping to observe natural selection in something closer to real time. Microbes can reproduce several times a day, and a billion of them can fit comfortably in a flask. Scientists can carefully control the conditions in which the microbes live, setting up different kinds of evolutionary pressures.
While working at the University of California, Irvine, Dr. Lenski decided to set up a straightforward experiment: he made life miserable for some bacteria. He created 12 identical lines of E. coli and then fed them a meager diet of glucose. The bacteria would run out of sugar by the afternoon, and the following morning Dr. Lenski would transfer a few of the survivors to a freshly supplied flask.
From time to time Dr. Lenski also froze some of the bacteria from each of the 12 lines. It became what he likes to call a “frozen fossil record.” By thawing them out later, Dr. Lenski could directly compare them with younger bacteria.
Within a few hundred generations, Dr. Lenski was seeing changes, and the bacteria have been changing ever since. The microbes have adapted to their environment, reproducing faster and faster over the years. One striking lesson of the experiment is that evolution often follows the same path. “We’ve found a lot of parallel changes,” Dr. Lenski said.
In all 12 lines the speed of adaptation was greatest in the first few months of the experiment and has since been tapering off. The bacteria have all become larger as well, although Dr. Lenski is not sure what kind of adaptation this represents. When other scientists saw these sorts of results begin to emerge, they set up their own experiments with microbes. Today they are observing bacteria, viruses and even yeast as they adapt to challenges as diverse as infections, antibiotics and cold and heat.
Albert F. Bennett, a physiologist at the University of California, Irvine, is an expert on temperature adaptation. He started out studying animals like reptiles and fish, but he seized on bacteria after hearing about Dr. Lenski’s experiments. “It was one of those ‘Star Trek’ moments,” he said. “I was looking out the window, and for about 10 minutes my mind was going into hyperdrive.”
Dr. Bennett was particularly curious about how organisms adapt to different temperatures. He wondered if adapting to low temperatures meant organisms would fare worse at higher ones, a long-standing question. Working with Dr. Lenski, Dr. Bennett allowed 24 lines of E. coli to adapt to a relatively chilly 68 degrees for 2,000 generations. They then measured how quickly these cold-adapted microbes reproduced at a simmering 104 degrees.
Two-thirds of the lines did worse at high temperatures than their ancestors, experiencing the expected trade-off. “If you’re a betting person, that’s the way you’d better bet,” Dr. Bennett said. But the pattern was not universal. The bacteria that reproduced fastest in the cold did not do the worst job of breeding in the heat. A third of the cold-adapted lines did as well or better in the heat than the ancestor. Dr. Bennett and Dr. Lenski published their latest findings last month in The Proceedings of the National Academy of Sciences.
Other scientists are watching individual microbes evolve into entire ecosystems. Paul Rainey, a biologist at the New Zealand Institute for Advanced Study at Massey University, has observed this evolution in bacteria, called Pseudomonas fluorescens, that live on plants. When he put a single Pseudomonas in a flask, it produced descendants that floated in the broth, feeding on nutrients. But within a few hundred generations, some of its descendants mutated and took up new ways of life. One strain began to form fuzzy carpets on the bottom of the flask. Another formed a mat of cellulose, where it could take in oxygen from above and food from below.
But Dr. Rainey is only beginning to decipher the complexity that evolves in his flasks. The different types of Pseudomonas interact with one another in intricate ways. The bottom-growers somehow kill off most of the ancestral free-floating microbes. But they in turn are wiped out by the mat-builders, which cut off oxygen to the rest of the flask. In time, however, cheaters appear in the mat. They do not produce their own cellulose, instead depending on other bacteria to hold them up. Eventually the mat collapses. The other types of Pseudomonas recover, and the cycle begins again, with hundreds of other forms appearing over time. “The interactions are everything you’d expect in a rain forest,” Dr. Rainey said.
Scientists have long known that underlying these visible changes were genetic ones. But only now are they documenting the mutations that allow this evolution to happen in the first place.
Dr. Palsson has been running experiments in which E. coli must adapt to a diet of glycerol, an ingredient in soap. He found that within a few hundred generations, the bacteria could grow two to three times as fast as their ancestor. He then selected some of the evolved microbes and sequenced their genome. He compared their DNA with that of their common ancestor and pinpointed a few mutations that each line had acquired.
Dr. Palsson then inserted copies of these mutated genes into the ancestor and found that it now could thrive on glycerol as well. But the order in which he inserted the genes made a big difference to the bacteria.
Some mutations were beneficial only if the bacteria already carried other mutations. On their own, the mutations could even be harmful. Dr. Palsson’s results offer a detailed picture of what biologists call epistasis — the intimate ways in which mutations can influence the effects of other mutations during evolution.
As Dr. Palsson and other scientists have pinpointed mutations in microbes, they have been surprised by how mysterious the mutations are. They are struggling to find out how the mutations benefit the organisms. And in some cases, they do not even know what the mutated genes did before they mutated.
“It just makes you ask, ‘What on earth is that doing?’ ” said Gregory J. Velicer, a former student of Dr. Lenski’s who is now an associate professor at Indiana University. Dr. Velicer experienced this bafflement firsthand while watching the evolution of a predatory microbe called Myxococcus xanthus. Myxococcus swarms lash their tails together and hunt in a pack, releasing enzymes to kill their prey and feasting on the remains. If the bacteria starve, they come together to form a mound of spores. It is a cooperative effort. Only a few percent of the bacteria end up forming spores, while the rest face almost certain death.
This social behavior costs Myxococcus energy that it could otherwise use to grow, Dr. Velicer discovered. He and his colleagues allowed the bacteria to evolve for 1,000 generations in a rich broth. Most of the lines of bacteria lost the ability to swarm or form spores, or both.
Dr. Velicer discovered that some of the newly evolved bacteria were not just asocial — they were positively antisocial. These mutant cheaters could no longer make mounds of spores on their own. But if they were mixed with ordinary Myxococcus, they could make spores. In fact, they were 10 times as likely to form a spore as normal microbes.
Dr. Velicer set up a new experiment in which the bacteria alternated between a rich broth and a dish with no food. Over the generations, the cheaters became more common because of their advantage at making spores. But if the cheaters became too common, the entire population died out, because there were not enough ordinary Myxococcus left to make the spore mounds in the times of famine.
During this experiment, one of Dr. Velicer’s colleagues, Francesca Fiegna of the Max Planck Institute for Developmental Biology, discovered something strange. She had just transferred a population of cheaters to a dish, expecting them to die out. But the cheaters were making seven times as many spores as their normal ancestors. “It just made no sense,” Dr. Velicer said. “I asked her I don’t know how many times, ‘Are you sure you marked the plates correctly?’ ”
She had. It turned out that a single Myxococcus cheater had mutated into a cooperator. In fact, it had evolved into a cooperator far superior to its cooperative ancestors. Dr. Velicer and his colleagues sequenced the genome of the new cooperator and discovered a single mutation. The new mutation did not simply reverse the mutation that had originally turned the microbe’s ancestors into cheaters. Instead, it struck a new part of the genome.
But Dr. Velicer has no idea at the moment how the mutation brought about the remarkable transformation in behavior. The mutated segment of DNA actually lies near, but not inside, a gene. It is possible that proteins latch on to this region and switch the nearby gene on or off. But no one actually knows what the gene normally does.
Mutations like this one, Dr. Velicer said, “make for a much more complicated story.” It is a story he and other scientists are looking forward to revealing.
The Human Family Tree Has Become a Bush With Many Branches
By JOHN NOBLE WILFORD, The New York Times, June 26, 2007
Time was, fossils and a few stone artifacts were about the only means scientists had of tracing the lines of early human evolution. And gaps in such material evidence were frustratingly wide.
When molecular biologists joined the investigation some 30 years ago, their techniques of genetic analysis yielded striking insights. DNA studies pointed to a common maternal ancestor of all anatomically modern humans in Africa by at least 130,000 years. She inevitably became known as the African Eve.
Other genetic research plotted ancestral migration patterns and the extremely close DNA relationship between humans and chimpanzees, our nearest living relatives. Genetic clues also set the approximate time of the divergence of the human lineage from a common ancestor with apes: between six million and eight million years ago.
Fossil researchers were skeptical at first, a reaction colored perhaps by their dismay at finding scientific poachers on their turf. These paleoanthropologists contended that the biologists’ “molecular clocks” were unreliable, and in some cases they were, though apparently not to a significant degree.
Now paleoanthropologists say they accept the biologists as allies triangulating the search for human origins from different angles. As much as anything, a rapid succession of fossil discoveries since the early 1990s has restored the confidence of paleoanthropologists in the relevance of their approach to the study of early hominids, those fossil ancestors and related species in human evolution.
The new finds have filled in some of the yawning gaps in the fossil record. They have doubled the record’s time span from 3.5 million back almost to 7 million years ago and more than doubled the number of earliest known hominid species. The teeth and bone fragments suggest the form — the morphology — of these ancestors that lived presumably just this side of the human-ape split.
“The amount of discord between morphology and molecules is actually not that great anymore,” said Frederick E. Grine, a paleoanthropologist at the State University of New York at Stony Brook.
With more abundant data, Dr. Grine said, scientists are, in a sense, fleshing out the genetic insights with increasingly earlier fossils. It takes the right bones to establish that a species walked upright, which is thought to be a defining trait of hominids after the split with the ape lineage.
“All biology can tell you is that my nearest relative is a chimpanzee and about when we had a common ancestor,” he said. “But biology can’t tell us what the common ancestor looked like, what shaped that evolutionary change or at what rate that change took place.”
Although hominid species were much more apelike in their earliest forms, Tim D. White of the University of California, Berkeley, said: “We’ve come to appreciate that you cannot simply extrapolate from the modern chimp to get a picture of the last common ancestor. Humans and chimps have been changing down through time.”
But Dr. White, one of the most experienced hominid hunters, credits the genetic data with giving paleoanthropologists a temporal framework for their research. Their eyes are always fixed on a time horizon for hominid origins, which now appears to be at least seven million years ago.
Ever since its discovery in 1973, the species Australopithecus afarensis, personified by the famous Lucy skeleton, has been the continental divide in the exploration of hominid evolution. Donald Johanson, the Lucy discoverer, and Dr. White determined that the apelike individual lived 3.2 million years ago, walked upright and was probably a direct human ancestor. Other afarensis specimens and some evocative footprints showed the species existed for almost a million years, down to three million years ago.
In the 1990s, scientists finally crossed the Lucy divide. In Kenya, Meave G. Leakey of the celebrated fossil-hunting family came up with Australopithecus anamensis, which lived about four million years ago and appeared to be an afarensis precursor. Another discovery by Dr. Leakey challenged the prevailing view that the family tree had a more or less single trunk rising from ape roots to a pinnacle occupied by Homo sapiens. Yet here was evidence that the new species Kenyanthropus platyops co-existed with Lucy’s afarensis kin.
The family tree now looks more like a bush with many branches. “Just because there’s only one human species around now doesn’t mean it was always that way,” Dr. Grine said.
Few hominid fossils have turned up from the three-million- to two-million-year period, during which hominids began making stone tools. The first Homo species enter the fossil record sometime before two million years ago, and the transition to much larger brains began with Homo erectus, about 1.7 million years ago.
Other recent discoveries have pushed deeper in time, closer to the hominid origins predicted by molecular biologists.
Dr. White was involved in excavations in Ethiopia of many specimens that lived 4.4 million years ago and were more primitive and apelike than Lucy. The species was named Ardipithecus ramidus. Later, a related species from 5.2 million to 5.8 million years ago was classified Ardipithecus kadabba.
At that time, six years ago, C. Owen Lovejoy of Kent State University said, “We are indeed coming very close to that point in the fossil record where we simply will not be able to distinguish ancestral hominid from ancestral” chimpanzees, because, he said, “They were so anatomically similar.”
Two even earlier specimens are even harder to interpret. One found in Kenya by a French team has been dated to six million years and named Orrorin tugenensis. The teeth and bone pieces are few, though the discoverers think a thigh fragment suggests that the individual was a biped — a walker on two legs.
Another French group then uncovered 6.7-million-year-old fossils in Chad. Named Sahelanthropus tchadensis, the sole specimen includes only a few teeth, a jawbone and a crushed cranium. Scientists said the head appeared to have perched atop a biped.
“These are clearly the earliest hominids we have,” said Eric Delson, a human-origins scientist at the American Museum of Natural History. “But we still know rather little about any of these specimens. The farther back we go toward the divergence point, the more similar specimens will look on both sides of the split.”
Other challenges arise from human evolution in more recent epochs. Just who were the “little people” found a few years ago in a cave on the island of Flores in Indonesia? The Australian and Indonesian discoverers concluded that one partial skeleton and other bones belonged to a now-extinct separate human species, Homo floresiensis, which lived as recently as 18,000 years ago.
The apparent diminutive stature and braincase of the species prompted howls of dispute. Critics contended that this was not a distinct species, but just another dwarf-size Homo sapiens, possibly with a brain disorder. Several prominent scientists, however, support the new-species designation.
The tempest over the Indonesian find is nothing new in a field known for controversy. Some scholars counsel patience, recalling that it was years after the discovery of the first Neanderthal skull, in 1856, before it was accepted as an ancient branch of the human family. Critics had at first dismissed the find as only the skull of a degenerate modern human or a Cossack who died in the Napoleonic wars.
Perhaps the analogy is not as encouraging as intended. Scientists to this day are arguing about Neanderthals, their exact relationship to us and the cause of their extinction 30,000 years ago, not long after the arrival in Europe of the sole surviving hominid that is so curious about its origins.
By CAROL KAESUK YOON, The New York Times, June 26, 2007
Since its humble beginnings as a single cell, life has evolved into a spectacular array of shapes and sizes, from tiny fleas to towering Tyrannosaurus rex, from slow-soaring vultures to fast-swimming swordfish, and from modest ferns to alluring orchids. But just how such diversity of form could arise out of evolution’s mess of random genetic mutations — how a functional wing could sprout where none had grown before, or how flowers could blossom in what had been a flowerless world — has remained one of the most fascinating and intractable questions in evolutionary biology.
Now finally, after more than a century of puzzling, scientists are finding answers coming fast and furious and from a surprising quarter, the field known as evo-devo. Just coming into its own as a science, evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.
For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison. “The first response is ‘Huh?’ and the second response is ‘Far out.’ ”
“This is the illumination of the utterly dark,” Dr. Carroll added.
The development of an organism — how one end gets designated as the head or the tail, how feet are enticed to grow at the end of a leg rather than at the wrist — is controlled by a hierarchy of genes, with master genes at the top controlling a next tier of genes, controlling a next and so on. But the real interest for evolutionary biologists is that these hierarchies not only favor the evolution of certain forms but also disallow the growth of others, determining what can and cannot arise not only in the course of the growth of an embryo, but also over the history of life itself.
“It’s been said that classical evolutionary theory looks at survival of the fittest,” said Dr. Scott F. Gilbert, a developmental biologist at Swarthmore College. By looking at what sorts of organisms are most likely or impossible to develop, he explained, “evo-devo looks at the arrival of the fittest.”
Charles Darwin saw it first. He pointed out well over a century ago that developing forms of life would be central to the study of evolution. Little came of it initially, for a variety of reasons. Not least of these was the discovery that perturbing the process of development often resulted in a freak show starring horrors like bipedal goats and insects with legs growing out of their mouths, monstrosities that seemed to shed little light on the wonders of evolution.
But the advent of molecular biology reinvigorated the study of development in the 1980s, and evo-devo quickly got scientists’ attention when early breakthroughs revealed that the same master genes were laying out fundamental body plans and parts across the animal kingdom. For example, researchers discovered that genes in the Pax6 family could switch on the development of eyes in animals as different as flies and people. More recent work has begun looking beyond the body’s basic building blocks to reveal how changes in development have resulted in some of the world’s most celebrated of evolutionary events.
In one of the most exciting of the new studies, a team of scientists led by Dr. Cliff Tabin, a developmental biologist at Harvard Medical School, investigated a classic example of evolution by natural selection, the evolution of Darwin’s finches on the Galápagos Islands.
Like the other organisms that made it to the remote archipelago off the coast of Ecuador, Darwin’s finches have flourished in their isolation, evolving into many and varied species. But, while the finches bear his name and while Darwin was indeed inspired to thoughts of evolution by animals on these islands, the finches left him flummoxed. Darwin did not realize for quite some time that these birds were all finches or even that they were related to one another.
He should be forgiven, however. For while the species are descendants of an original pioneering finch, they no longer bear its characteristic short, slender beak, which is excellent for hulling tiny seeds. In fact, the finches no longer look very finchlike at all. Adapting to the strange new foods of the islands, some have evolved taller, broader, more powerful nut-cracking beaks; the most impressive of the big-beaked finches is Geospiza magnirostris. Other finches have evolved longer bills that are ideal for drilling holes into cactus fruits to get at the seeds; Geospiza conirostris is one species with a particularly elongated beak.
But how could such bills evolve from a simple finch beak? Scientists had assumed that the dramatic alterations in beak shape, height, width and strength would require the accumulation of many chance mutations in many different genes. But evo-devo has revealed that getting a fancy new beak can be simpler than anyone had imagined.
Genes are stretches of DNA that can be switched on so that they will produce molecules known as proteins. Proteins can then do a number of jobs in the cell or outside it, working to make parts of organisms, switching other genes on and so on. When genes are switched on to produce proteins, they can do so at a low level in a limited area or they can crank out lots of protein in many cells.
What Dr. Tabin and colleagues found, when looking at the range of beak shapes and sizes across different finch species, was that the thicker and taller and more robust a beak, the more strongly it expressed a gene known as BMP4 early in development. The BMP4 gene (its abbreviation stands for bone morphogenetic protein, No. 4) produces the BMP4 protein, which can signal cells to begin producing bone. But BMP4 is multitalented and can also act to direct early development, laying out a variety of architectural plans including signaling which part of the embryo is to be the backside and which the belly side. To verify that the BMP4 gene itself could indeed trigger the growth of grander, bigger, nut-crushing beaks, researchers artificially cranked up the production of BMP4 in the developing beaks of chicken embryos. The chicks began growing wider, taller, more robust beaks similar to those of a nut-cracking finch.
In the finches with long, probing beaks, researchers found at work a different gene, known as calmodulin. As with BMP4, the more that calmodulin was expressed, the longer the beak became. When scientists artificially increased calmodulin in chicken embryos, the chicks began growing extended beaks, just like a cactus driller.
So, with just these two genes, not tens or hundreds, the scientists found the potential to recreate beaks, massive or stubby or elongated.
“So now one wants to go in a number of directions,” Dr. Tabin said. “What happens in a stork? What happens in a hummingbird? A parrot?” For the evolution of beaks, the main tool with which a bird handles its food and makes its living, is central not only to Darwin’s finches, but to birds as a whole.
BMP4’s reach does not stop at the birds, however.
In lakes in Africa, the fish known as cichlids have evolved so rapidly into such a huge diversity of species that they have become one of the best known evolutionary radiations. The cichlids have evolved in different shapes and sizes, and with a variety of jaw types specialized for eating certain kinds of food. Robust, thick jaws are excellent at crushing snails, while longer jaws work well for sucking up algae. As with the beaks of finches, a range of styles developed.
Now in a new study, Dr. R. Craig Albertson, an evolutionary biologist at Syracuse University, and Dr. Thomas D. Kocher, a geneticist at the University of New Hampshire, have shown that more robust-jawed cichlids express more BMP4 during development than those with more delicate jaws. To test whether BMP4 was indeed responsible for the difference, these scientists artificially increased the expression of BMP4 in the zebrafish, the lab rat of the fish world. And, reprising the beak experiments, researchers found that increased production of BMP4 in the jaws of embryonic zebrafish led to the development of more robust chewing and chomping parts.
And if being a major player in the evolution of African cichlids and Darwin’s finches — two of the most famous evolutionary radiations of species — were not enough for BMP4, Dr. Peter R. Grant, an evolutionary biologist at Princeton University, predicted that the gene would probably be found to play an important role in the evolution of still other animals. He noted that jaw changes were a crucial element in the evolution of lizards, rabbits and mice, among others, making them prime candidates for evolution via BMP4.
“This is just the beginning,” Dr. Grant said. “These are exciting times for us all.”
Used to lay out body plans, build beaks and alter fish jaws, BMP4 illustrates perfectly one of the major recurring themes of evo-devo. New forms can arise via new uses of existing genes, in particular the control genes or what are sometimes called toolkit genes that oversee development. It is a discovery that can explain much that has previously been mysterious, like the observation that without much obvious change to the genome over all, one can get fairly radical changes in form.
“There aren’t new genes arising every time a new species arises,” said Dr. Brian K. Hall, a developmental biologist at Dalhousie University in Nova Scotia. “Basically you take existing genes and processes and modify them, and that’s why humans and chimps can be 99 percent similar at the genome level.”
Evo-devo has also begun to shine a light on a phenomenon with which evolutionary biologists have long been familiar, the way in which different species will come up with sometimes jaw-droppingly similar solutions when confronted with the same challenges.
Among the placental mammals of the Americas and the marsupials of Australia, for example, have evolved the same sorts of animals independently: beasts that burrowed, loping critters that grazed, creatures that had long snouts for eating ants, and versions of wolf.
In the same way, the cichlids have evolved pairs of matching species, arising independently in separate lakes in Africa. In Lake Malawi, for example, there is a long and flat-headed species with a deep underbite that looks remarkably like an unrelated species that lives a similar lifestyle in Lake Tanganyika. There is another cichlid with a bulging brow and frowning lips in Lake Malawi with, again, an unrelated but otherwise extremely similar-looking cichlid in Lake Tanganyika. The same jaws, heads, and ways of living can be seen to evolve again and again.
The findings of evo-devo suggest that such parallels might in fact be expected. For cichlids are hardly coming up with new genetic solutions to eating tough snails as they each crank up the BMP4 or tinker with other toolkit genes. Instead, whether in Lake Malawi or Lake Tanganyika, they may be using the same genes to develop the same forms that provide the same solutions to the same ecological challenges. Why not, when even the beaked birds flying overhead are using the very same genes?
Evo-devo has even begun to give biologists new insight into one of the most beautiful examples of recurring forms: the evolution of mimicry.
It has long been a source of amazement how some species seem so able to evolve near-perfect mimicry of another. Poisonous species often evolve bright warning colors, which have been reproduced by nonpoisonous species or by other, similarly poisonous species, hoping to fend off curious predators.
Now in a new study of Heliconius butterflies, Dr. Mathieu Joron, an evolutionary biologist at the University of Edinburgh, and colleagues, found evidence that the mimics may be using some of the same genes to produce their copycat warning colors and patterns.
The researchers studied several species of tropical Heliconius butterflies, all of which are nasty-tasting to birds and which mimic one another’s color patterns. Dr. Joron and colleagues found that some of the main elements of the patterns — a yellow band in Heliconius melpomene and Heliconius erato and a complex tiger-stripe pattern in Heliconius numata — are controlled by a single region of DNA, a tightly linked set of genes known as a supergene.
Dr. Joron said he and colleagues were still mapping the details of color pattern control within the supergene. But if this turned out to function, as researchers suspected, like a toolkit gene turning the patterns on and off, it could explain both the prevalence of mimicry in Heliconius and the apparent ease with which these species have been shown to repeatedly evolve such superbly matching patterns.
One of evo-devo’s greatest strengths is its cross-disciplinary nature, bridging not only evolutionary and developmental studies but gaps as broad as those between fossil-hunting paleontologists and molecular biologists. One researcher whose approach epitomizes the power of such synthesis is Dr. Neil Shubin, an evolutionary biologist at the University of Chicago and the Field Museum.
Last year, Dr. Shubin and colleagues reported the discovery of a fossil fish on Ellesmere Island in northern Canada. They had found Tiktaalik, as they named the fish, after searching for six years. They persisted for so long because they were certain that they had found the right age and kind of rock where a fossil of a fish trying to make the transition to life on land was likely to be found. And Tiktaalik appeared to be just such a fish, but it also had a few surprises for the researchers.
“Tiktaalik is special,” Dr. Shubin said. “It has a flat head with eyes on top. It has gills and lungs. It’s an animal that’s exploring the interface between water and land.”
But Tiktaalik was a truly stunning discovery because this water-loving fish bore wrists, an attribute thought to have been an innovation confined strictly to animals that had already made the transition to land.
“This was telling us that a piece of the toolkit, to make arms, legs, hand and feet, could very well be present in fish limbs,” Dr. Shubin said. In other words, the genetic tools or toolkit genes for making limbs to walk on land might well have been present long before fish made that critical leap. But as fascinating as Tiktaalik was, it was also rock hard and provided no DNA that might shed light on the presence or absence of any particular gene.
So Dr. Shubin did what more and more evo-devo researchers are learning to do: take off one hat (paleontologist) and don another (molecular biologist). Dr. Shubin oversees one of what he says is a small but growing number of laboratories where old-fashioned rock-pounding takes place alongside high-tech molecular DNA studies.
He and colleagues began a study of the living but ancient fish known as the paddlefish. What they found, reported last month in the journal Nature, was that these thoroughly fishy fish were turning on control genes known as Hox genes, in a manner characteristic of the four-limbed, land-loving beasts known as tetrapods.
Tetrapods include cows, people, birds, rodents and so on. In other words, the potential for making fingers, hands and feet, crucial innovations used in emerging from the water to a life of walking and crawling on land, appears to have been present in fish, long before they began flip-flopping their way out of the muck. “The genetic tools to build fingers and toes were in place for a long time,” Dr. Shubin wrote in an e-mail message. “Lacking were the environmental conditions where these structures would be useful.” He added, “Fingers arose when the right environments arose.”
And here is another of the main themes to emerge from evo-devo. Major events in evolution like the transition from life in the water to life on land are not necessarily set off by the arising of the genetic mutations that will build the required body parts, or even the appearance of the body parts themselves, as had long been assumed. Instead, it is theorized that the right ecological situation, the right habitat in which such bold, new forms will prove to be particularly advantageous, may be what is required to set these major transitions in motion.
So far, most of the evo-devo work has been on animals, but researchers have begun to ask whether the same themes are being played out in plants.
Of particular interest to botanists is what Darwin described as an “abominable mystery”: the origin of flowering plants. A critical event in the evolution of plants, it happened, by paleontological standards, rather suddenly.
So what genes were involved in the origin of flowers? Botanists know that during development, the genes known as MADS box genes lay out the architecture of the blossom. They do so by turning on other genes, thereby determining what will develop where — petals here, reproductive parts there and so on, in much the same manner that Hox genes determine the general layout of parts in animals. Hox genes have had an important role in the evolution of animal form. But have MADS box genes had as central a role in the evolution of plants?
So far, said Dr. Vivian F. Irish, a developmental biologist at Yale University, the answer appears to be yes. There is a variety of circumstantial evidence, the most interesting of which is the fact that the MADS box genes exploded in number right around the time that flowering plants first appeared.
“It’s really analogous to what’s going on in Hox genes,” said Dr. Irish, though she noted that details of the role of the MADS box genes remained to be worked out. “It’s very cool that evolution has used a similar strategy in two very different kingdoms.”
Amid the enthusiast hubbub, cautionary notes have been sounded. Dr. Jerry Coyne, an evolutionary biologist at the University of Chicago, said that as dramatic as the changes in form caused by mutations in toolkit genes can be, it was premature to credit these genes with being the primary drivers of the evolution of novel forms and diversity. He said that too few studies had been done so far to support such broad claims, and that it could turn out that other, more mundane workaday genes, of the sort that were being studied long before evo-devo appeared on the scene, would play equally or even more important roles.
“I urge caution,” Dr. Coyne said. “We just don’t know.”
All of which goes to show that like all emerging fields, evo-devo’s significance and the uniqueness of its contributions will continue to be reassessed. It will remain to be seen just how separate or incorporated into the rest of evolutionary thinking its findings will end up being. Paradoxically, it was during just such a flurry of intellectual synthesis and research activity, the watershed known as the New or Modern Synthesis in which modern evolutionary biology was born in the last century, that developmental thinking was almost entirely ejected from the science of evolution.
But perhaps today synthesizers can do better, broadening their focus without constricting their view of evolution as they try to take in all of the great pageant that is the history of life.
“We’re still a very young field,” Dr. Gilbert said. “But I think this is a new evolutionary synthesis, an emerging evolutionary synthesis. I think we’re seeing it.”
Humans Have Spread Globally, and Evolved Locally
By NICHOLAS WADE, The New York Times, June 26, 2007
Historians often assume that they need pay no attention to human evolution because the process ground to a halt in the distant past. That assumption is looking less and less secure in light of new findings based on decoding human DNA.
People have continued to evolve since leaving the ancestral homeland in northeastern Africa some 50,000 years ago, both through the random process known as genetic drift and through natural selection. The genome bears many fingerprints in places where natural selection has recently remolded the human clay, researchers have found, as people in the various continents adapted to new diseases, climates, diets and, perhaps, behavioral demands.
A striking feature of many of these changes is that they are local. The genes under selective pressure found in one continent-based population or race are mostly different from those that occur in the others. These genes so far make up a small fraction of all human genes.
A notable instance of recent natural selection is the emergence of lactose tolerance — the ability to digest lactose in adulthood — among the cattle-herding people of northern Europe some 5,000 years ago. Lactase, the enzyme that digests the principal sugar of milk, is usually switched off after weaning. But because of the great nutritional benefit for cattle herders of being able to digest lactose in adulthood, a genetic change that keeps the lactase gene switched on spread through the population.
Lactose tolerance is not confined to Europeans. Last year, Sarah Tishkoff of the University of Maryland and colleagues tested 43 ethnic groups in East Africa and found three separate mutations, all different from the European one, that keep the lactase gene switched on in adulthood. One of the mutations, found in peoples of Kenya and Tanzania, may have arisen as recently as 3,000 years ago.
That lactose tolerance has evolved independently four times is an instance of convergent evolution. Natural selection has used the different mutations available in European and East African populations to make each develop lactose tolerance. In Africa, those who carried the mutation were able to leave 10 times more progeny, creating a strong selective advantage.
Researchers studying other single genes have found evidence for recent evolutionary change in the genes that mediate conditions like skin color, resistance to malaria and salt retention.
The most striking instances of recent human evolution have emerged from a new kind of study, one in which the genome is scanned for evidence of selective pressures by looking at a few hundred thousand specific sites where variation is common.
Last year Benjamin Voight, Jonathan Pritchard and colleagues at the University of Chicago searched for genes under natural selection in Africans, Europeans and East Asians. In each race, some 200 genes showed signals of selection, but without much overlap, suggesting that the populations on each continent were adapting to local challenges.
Another study, by Scott Williamson of Cornell University and colleagues, published in PLoS Genetics this month, found 100 genes under selection in Chinese, African-Americans and European-Americans.
In most cases, the source of selective pressure is unknown. But many genes associated with resistance to disease emerge from the scans, confirming that disease is a powerful selective force. Another category of genes under selective pressure covers those involved in metabolism, suggesting that people were responding to changes in diet, perhaps associated with the switch from hunting and gathering to agriculture.
Several genes involved in determining skin color have been under selective pressure in Europeans and East Asians. But Dr. Pritchard’s study detected skin color genes only in Europeans, and Dr. Williamson found mostly genes selected in Chinese.
The reason for the difference is that Dr. Pritchard’s statistical screen detects genetic variants that have become very common in a population but are not yet universal. Dr. Williamson’s picks up variants that have already swept through a population and are possessed by almost everyone.
The findings suggest that Europeans and East Asians acquired their pale skin through different genetic routes and, in the case of Europeans, perhaps as recently as around 7,000 years ago.
Another puzzle is presented by selected genes involved in brain function, which occur in different populations and could presumably be responses to behavioral challenges encountered since people left the ancestral homeland in Africa.
But some genes have more than one role, and some of these brain-related genes could have been selected for other properties.
Two years ago, Bruce Lahn, a geneticist at the University of Chicago, reported finding signatures of selection in two brain-related genes of a type known as microcephalins, because when mutated, people are born with very small brains. Two of the microcephalins had come under selection in Europeans and one in Chinese, Dr. Lahn reported.
He suggested that the selected forms of the gene had helped improved cognitive capacity and that many other genes, yet to be identified, would turn out to have done the same in these and other populations.
Neither microcephalin gene turned up in Dr. Pritchard’s or Dr. Williamson’s list of selected genes, and other researchers have disputed Dr. Lahn’s claims. Dr. Pritchard found that two other microcephalin genes were under selection, one in Africans and the other in Europeans and East Asians.
Even more strikingly, Dr. Williamson’s group reported that a version of a gene called DAB1 had become universal in Chinese but not in other populations. DAB1 is involved in organizing the layers of cells in the cerebral cortex, the site of higher cognitive functions.
Variants of two genes involved in hearing have become universal, one in Chinese, the other in Europeans.
The emerging lists of selected human genes may open new insights into the interactions between history and genetics. “If we ask what are the most important evolutionary events of the last 5,000 years, they are cultural, like the spread of agriculture, or extinctions of populations through war or disease,” said Marcus Feldman, a population geneticist at Stanford. These cultural events are likely to have left deep marks in the human genome.
A genomic survey of world populations by Dr. Feldman, Noah Rosenberg and colleagues in 2002 showed that people clustered genetically on the basis of small differences in DNA into five groups that correspond to the five continent-based populations: Africans, Australian aborigines, East Asians, American Indians and Caucasians, a group that includes Europeans, Middle Easterners and people of the Indian subcontinent. The clusterings reflect “serial founder effects,” Dr. Feldman said, meaning that as people migrated around the world, each new population carried away just part of the genetic variation in the one it was derived from.
The new scans for selection show so far that the populations on each continent have evolved independently in some ways as they responded to local climates, diseases and, perhaps, behavioral situations.
The concept of race as having a biological basis is controversial, and most geneticists are reluctant to describe it that way. But some say the genetic clustering into continent-based groups does correspond roughly to the popular conception of racial groups.
“There are difficulties in where you put boundaries on the globe, but we know now there are enough genetic differences between people from different parts of the world that you can classify people in groups that correspond to popular notions of race,” Dr. Pritchard said.
David Reich, a population geneticist at the Harvard Medical School, said that the term “race” was scientifically inexact and that he preferred “ancestry.” Genetic tests of ancestry are now so precise, he said, that they can identify not just Europeans but can distinguish between northern and southern Europeans. Ancestry tests are used in trying to identify genes for disease risk by comparing patients with healthy people. People of different races are excluded in such studies. Their genetic differences would obscure the genetic difference between patients and unaffected people.
No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.
This is the case with lactose tolerance in European and African peoples and with pale skin in East Asians and Europeans.
Fast-Reproducing Microbes Provide a Window on Natural Selection
By CARL ZIMMER, The New York Times, June 26, 2007
In the corner of a laboratory at Michigan State University, one of the longest-running experiments in evolution is quietly unfolding. A dozen flasks of sugary broth swirl on a gently rocking table. Each is home to hundreds of millions of Escherichia coli, the common gut microbe. These 12 lines of bacteria have been reproducing since 1989, when the biologist Richard E. Lenski bred them from a single E. coli. “I originally thought it might go a couple thousand generations, but it’s kept going and stayed interesting,” Dr. Lenski said. He is up to 40,000 generations now, and counting.
In that time, the bacteria have changed significantly. For one thing, they are bigger — twice as big on average as their common ancestor. They are also far better at reproducing in these flasks, dividing 70 percent faster than their ancestor. These changes have emerged through spontaneous mutations and natural selection, and Dr. Lenski and his colleagues have been able to watch them unfold.
When Dr. Lenski began his experiment 18 years ago, only a few scientists believed they could observe evolution so closely. Today evolutionary experiments on microbes are under way in many laboratories. And thanks to the falling price of genome-sequencing technology, scientists can now zero in on the precise genetic changes that unfold during evolution, a power previous generations of researchers only dreamed of.
“It’s fun for us, because we can watch the game of life at the molecular level,” said Bernhard Palsson of the University of California, San Diego. “Many features of evolutionary theory are showing up in these experiments, and that’s why people are so excited by them.”
In the past century scientists have gathered a wealth of evidence about the power of natural selection. But much of that evidence has been indirect. Natural selection is a process that takes place over many generations, that may affect thousands or millions of individuals, and that may be shaped by many different conditions. To document it scientists have searched for historical fingerprints. They study fossils, for example, or compare the DNA of related species.
In the late 1980s a few scientists began experimenting with microbes, hoping to observe natural selection in something closer to real time. Microbes can reproduce several times a day, and a billion of them can fit comfortably in a flask. Scientists can carefully control the conditions in which the microbes live, setting up different kinds of evolutionary pressures.
While working at the University of California, Irvine, Dr. Lenski decided to set up a straightforward experiment: he made life miserable for some bacteria. He created 12 identical lines of E. coli and then fed them a meager diet of glucose. The bacteria would run out of sugar by the afternoon, and the following morning Dr. Lenski would transfer a few of the survivors to a freshly supplied flask.
From time to time Dr. Lenski also froze some of the bacteria from each of the 12 lines. It became what he likes to call a “frozen fossil record.” By thawing them out later, Dr. Lenski could directly compare them with younger bacteria.
Within a few hundred generations, Dr. Lenski was seeing changes, and the bacteria have been changing ever since. The microbes have adapted to their environment, reproducing faster and faster over the years. One striking lesson of the experiment is that evolution often follows the same path. “We’ve found a lot of parallel changes,” Dr. Lenski said.
In all 12 lines the speed of adaptation was greatest in the first few months of the experiment and has since been tapering off. The bacteria have all become larger as well, although Dr. Lenski is not sure what kind of adaptation this represents. When other scientists saw these sorts of results begin to emerge, they set up their own experiments with microbes. Today they are observing bacteria, viruses and even yeast as they adapt to challenges as diverse as infections, antibiotics and cold and heat.
Albert F. Bennett, a physiologist at the University of California, Irvine, is an expert on temperature adaptation. He started out studying animals like reptiles and fish, but he seized on bacteria after hearing about Dr. Lenski’s experiments. “It was one of those ‘Star Trek’ moments,” he said. “I was looking out the window, and for about 10 minutes my mind was going into hyperdrive.”
Dr. Bennett was particularly curious about how organisms adapt to different temperatures. He wondered if adapting to low temperatures meant organisms would fare worse at higher ones, a long-standing question. Working with Dr. Lenski, Dr. Bennett allowed 24 lines of E. coli to adapt to a relatively chilly 68 degrees for 2,000 generations. They then measured how quickly these cold-adapted microbes reproduced at a simmering 104 degrees.
Two-thirds of the lines did worse at high temperatures than their ancestors, experiencing the expected trade-off. “If you’re a betting person, that’s the way you’d better bet,” Dr. Bennett said. But the pattern was not universal. The bacteria that reproduced fastest in the cold did not do the worst job of breeding in the heat. A third of the cold-adapted lines did as well or better in the heat than the ancestor. Dr. Bennett and Dr. Lenski published their latest findings last month in The Proceedings of the National Academy of Sciences.
Other scientists are watching individual microbes evolve into entire ecosystems. Paul Rainey, a biologist at the New Zealand Institute for Advanced Study at Massey University, has observed this evolution in bacteria, called Pseudomonas fluorescens, that live on plants. When he put a single Pseudomonas in a flask, it produced descendants that floated in the broth, feeding on nutrients. But within a few hundred generations, some of its descendants mutated and took up new ways of life. One strain began to form fuzzy carpets on the bottom of the flask. Another formed a mat of cellulose, where it could take in oxygen from above and food from below.
But Dr. Rainey is only beginning to decipher the complexity that evolves in his flasks. The different types of Pseudomonas interact with one another in intricate ways. The bottom-growers somehow kill off most of the ancestral free-floating microbes. But they in turn are wiped out by the mat-builders, which cut off oxygen to the rest of the flask. In time, however, cheaters appear in the mat. They do not produce their own cellulose, instead depending on other bacteria to hold them up. Eventually the mat collapses. The other types of Pseudomonas recover, and the cycle begins again, with hundreds of other forms appearing over time. “The interactions are everything you’d expect in a rain forest,” Dr. Rainey said.
Scientists have long known that underlying these visible changes were genetic ones. But only now are they documenting the mutations that allow this evolution to happen in the first place.
Dr. Palsson has been running experiments in which E. coli must adapt to a diet of glycerol, an ingredient in soap. He found that within a few hundred generations, the bacteria could grow two to three times as fast as their ancestor. He then selected some of the evolved microbes and sequenced their genome. He compared their DNA with that of their common ancestor and pinpointed a few mutations that each line had acquired.
Dr. Palsson then inserted copies of these mutated genes into the ancestor and found that it now could thrive on glycerol as well. But the order in which he inserted the genes made a big difference to the bacteria.
Some mutations were beneficial only if the bacteria already carried other mutations. On their own, the mutations could even be harmful. Dr. Palsson’s results offer a detailed picture of what biologists call epistasis — the intimate ways in which mutations can influence the effects of other mutations during evolution.
As Dr. Palsson and other scientists have pinpointed mutations in microbes, they have been surprised by how mysterious the mutations are. They are struggling to find out how the mutations benefit the organisms. And in some cases, they do not even know what the mutated genes did before they mutated.
“It just makes you ask, ‘What on earth is that doing?’ ” said Gregory J. Velicer, a former student of Dr. Lenski’s who is now an associate professor at Indiana University. Dr. Velicer experienced this bafflement firsthand while watching the evolution of a predatory microbe called Myxococcus xanthus. Myxococcus swarms lash their tails together and hunt in a pack, releasing enzymes to kill their prey and feasting on the remains. If the bacteria starve, they come together to form a mound of spores. It is a cooperative effort. Only a few percent of the bacteria end up forming spores, while the rest face almost certain death.
This social behavior costs Myxococcus energy that it could otherwise use to grow, Dr. Velicer discovered. He and his colleagues allowed the bacteria to evolve for 1,000 generations in a rich broth. Most of the lines of bacteria lost the ability to swarm or form spores, or both.
Dr. Velicer discovered that some of the newly evolved bacteria were not just asocial — they were positively antisocial. These mutant cheaters could no longer make mounds of spores on their own. But if they were mixed with ordinary Myxococcus, they could make spores. In fact, they were 10 times as likely to form a spore as normal microbes.
Dr. Velicer set up a new experiment in which the bacteria alternated between a rich broth and a dish with no food. Over the generations, the cheaters became more common because of their advantage at making spores. But if the cheaters became too common, the entire population died out, because there were not enough ordinary Myxococcus left to make the spore mounds in the times of famine.
During this experiment, one of Dr. Velicer’s colleagues, Francesca Fiegna of the Max Planck Institute for Developmental Biology, discovered something strange. She had just transferred a population of cheaters to a dish, expecting them to die out. But the cheaters were making seven times as many spores as their normal ancestors. “It just made no sense,” Dr. Velicer said. “I asked her I don’t know how many times, ‘Are you sure you marked the plates correctly?’ ”
She had. It turned out that a single Myxococcus cheater had mutated into a cooperator. In fact, it had evolved into a cooperator far superior to its cooperative ancestors. Dr. Velicer and his colleagues sequenced the genome of the new cooperator and discovered a single mutation. The new mutation did not simply reverse the mutation that had originally turned the microbe’s ancestors into cheaters. Instead, it struck a new part of the genome.
But Dr. Velicer has no idea at the moment how the mutation brought about the remarkable transformation in behavior. The mutated segment of DNA actually lies near, but not inside, a gene. It is possible that proteins latch on to this region and switch the nearby gene on or off. But no one actually knows what the gene normally does.
Mutations like this one, Dr. Velicer said, “make for a much more complicated story.” It is a story he and other scientists are looking forward to revealing.
The Human Family Tree Has Become a Bush With Many Branches
By JOHN NOBLE WILFORD, The New York Times, June 26, 2007
Time was, fossils and a few stone artifacts were about the only means scientists had of tracing the lines of early human evolution. And gaps in such material evidence were frustratingly wide.
When molecular biologists joined the investigation some 30 years ago, their techniques of genetic analysis yielded striking insights. DNA studies pointed to a common maternal ancestor of all anatomically modern humans in Africa by at least 130,000 years. She inevitably became known as the African Eve.
Other genetic research plotted ancestral migration patterns and the extremely close DNA relationship between humans and chimpanzees, our nearest living relatives. Genetic clues also set the approximate time of the divergence of the human lineage from a common ancestor with apes: between six million and eight million years ago.
Fossil researchers were skeptical at first, a reaction colored perhaps by their dismay at finding scientific poachers on their turf. These paleoanthropologists contended that the biologists’ “molecular clocks” were unreliable, and in some cases they were, though apparently not to a significant degree.
Now paleoanthropologists say they accept the biologists as allies triangulating the search for human origins from different angles. As much as anything, a rapid succession of fossil discoveries since the early 1990s has restored the confidence of paleoanthropologists in the relevance of their approach to the study of early hominids, those fossil ancestors and related species in human evolution.
The new finds have filled in some of the yawning gaps in the fossil record. They have doubled the record’s time span from 3.5 million back almost to 7 million years ago and more than doubled the number of earliest known hominid species. The teeth and bone fragments suggest the form — the morphology — of these ancestors that lived presumably just this side of the human-ape split.
“The amount of discord between morphology and molecules is actually not that great anymore,” said Frederick E. Grine, a paleoanthropologist at the State University of New York at Stony Brook.
With more abundant data, Dr. Grine said, scientists are, in a sense, fleshing out the genetic insights with increasingly earlier fossils. It takes the right bones to establish that a species walked upright, which is thought to be a defining trait of hominids after the split with the ape lineage.
“All biology can tell you is that my nearest relative is a chimpanzee and about when we had a common ancestor,” he said. “But biology can’t tell us what the common ancestor looked like, what shaped that evolutionary change or at what rate that change took place.”
Although hominid species were much more apelike in their earliest forms, Tim D. White of the University of California, Berkeley, said: “We’ve come to appreciate that you cannot simply extrapolate from the modern chimp to get a picture of the last common ancestor. Humans and chimps have been changing down through time.”
But Dr. White, one of the most experienced hominid hunters, credits the genetic data with giving paleoanthropologists a temporal framework for their research. Their eyes are always fixed on a time horizon for hominid origins, which now appears to be at least seven million years ago.
Ever since its discovery in 1973, the species Australopithecus afarensis, personified by the famous Lucy skeleton, has been the continental divide in the exploration of hominid evolution. Donald Johanson, the Lucy discoverer, and Dr. White determined that the apelike individual lived 3.2 million years ago, walked upright and was probably a direct human ancestor. Other afarensis specimens and some evocative footprints showed the species existed for almost a million years, down to three million years ago.
In the 1990s, scientists finally crossed the Lucy divide. In Kenya, Meave G. Leakey of the celebrated fossil-hunting family came up with Australopithecus anamensis, which lived about four million years ago and appeared to be an afarensis precursor. Another discovery by Dr. Leakey challenged the prevailing view that the family tree had a more or less single trunk rising from ape roots to a pinnacle occupied by Homo sapiens. Yet here was evidence that the new species Kenyanthropus platyops co-existed with Lucy’s afarensis kin.
The family tree now looks more like a bush with many branches. “Just because there’s only one human species around now doesn’t mean it was always that way,” Dr. Grine said.
Few hominid fossils have turned up from the three-million- to two-million-year period, during which hominids began making stone tools. The first Homo species enter the fossil record sometime before two million years ago, and the transition to much larger brains began with Homo erectus, about 1.7 million years ago.
Other recent discoveries have pushed deeper in time, closer to the hominid origins predicted by molecular biologists.
Dr. White was involved in excavations in Ethiopia of many specimens that lived 4.4 million years ago and were more primitive and apelike than Lucy. The species was named Ardipithecus ramidus. Later, a related species from 5.2 million to 5.8 million years ago was classified Ardipithecus kadabba.
At that time, six years ago, C. Owen Lovejoy of Kent State University said, “We are indeed coming very close to that point in the fossil record where we simply will not be able to distinguish ancestral hominid from ancestral” chimpanzees, because, he said, “They were so anatomically similar.”
Two even earlier specimens are even harder to interpret. One found in Kenya by a French team has been dated to six million years and named Orrorin tugenensis. The teeth and bone pieces are few, though the discoverers think a thigh fragment suggests that the individual was a biped — a walker on two legs.
Another French group then uncovered 6.7-million-year-old fossils in Chad. Named Sahelanthropus tchadensis, the sole specimen includes only a few teeth, a jawbone and a crushed cranium. Scientists said the head appeared to have perched atop a biped.
“These are clearly the earliest hominids we have,” said Eric Delson, a human-origins scientist at the American Museum of Natural History. “But we still know rather little about any of these specimens. The farther back we go toward the divergence point, the more similar specimens will look on both sides of the split.”
Other challenges arise from human evolution in more recent epochs. Just who were the “little people” found a few years ago in a cave on the island of Flores in Indonesia? The Australian and Indonesian discoverers concluded that one partial skeleton and other bones belonged to a now-extinct separate human species, Homo floresiensis, which lived as recently as 18,000 years ago.
The apparent diminutive stature and braincase of the species prompted howls of dispute. Critics contended that this was not a distinct species, but just another dwarf-size Homo sapiens, possibly with a brain disorder. Several prominent scientists, however, support the new-species designation.
The tempest over the Indonesian find is nothing new in a field known for controversy. Some scholars counsel patience, recalling that it was years after the discovery of the first Neanderthal skull, in 1856, before it was accepted as an ancient branch of the human family. Critics had at first dismissed the find as only the skull of a degenerate modern human or a Cossack who died in the Napoleonic wars.
Perhaps the analogy is not as encouraging as intended. Scientists to this day are arguing about Neanderthals, their exact relationship to us and the cause of their extinction 30,000 years ago, not long after the arrival in Europe of the sole surviving hominid that is so curious about its origins.
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The concept of race as having a biological basis is controversial, and most geneticists are reluctant to describe it that way. But some say the genetic clustering into continent-based groups does correspond roughly to the popular conception of racial groups.
What?! No! This goes against every bio-anthro class I've ever taken, which says there is no significant biological differences among "races," because races don't exist! And since when do continents uniformly describe races? Look at Asia, you've got the Middle East, Siberia, and Polynesia. Can you actually say that they all fit the standard conception of Asian? Or that you'd put them all in the same "race"
Genetic tests of ancestry are now so precise, he said, that they can identify not just Europeans but can distinguish between northern and southern Europeans.
What? How? Again, that shouldn't be possible. There is no major biological difference between "races," so how are they determining such precise differentiation between people? What genes are they looking at?
Hmmm, I dont know... But I really hope someone with a better understanding of human biology doesnt come here and beat me down.
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