LB3C. Stay Current—The Origins of Species

2024-05-24. Stripey stick insects show evolution can repeat itself—predictably. By CATHERINE OFFORD, Science. Excerpt: Does evolution repeat itself? The answer to this long-standing question may be one step closer thanks to research on the crawly living twigs known as stick insects. Based on an analysis of decades of data from tens of thousands of walking sprigs in California, researchers report today in Science Advances that the prevalence of certain camouflage patterns rises and falls in predictable cycles across different populations. Some research has indeed found organisms evolving the same traits over and over. Studies of sticklebacks, for example, have shown that different populations that moved from salt to freshwater consistently underwent the same morphological and physiological changes to organs such as their kidneys, with genetic changes to match. Lab experiments in bacteria have found that microbes exposed to certain antibiotics hit on the same genetic changes to help them survive. …“It’s really observing evolution before our very eyes.” Full article at

2024-03-11. Amazing diversity of today’s ants tied to rise of flowering plants. [] By ELIZABETH PENNISI, Science. Excerpt: As spring’s first buds emerge in the Northern Hemisphere, there’s fresh evidence of the evolutionary importance of angiosperms, better known as flowering plants. Their rise some 150 million years ago, a study concludes, powered the amazing diversification and spread of ants, helping more recent ant species survive, while changing conditions drove earlier forms to extinction. The research, reported today in the Proceedings of the National Academy of Sciences, combines extensive ant fossil and DNA data to validate a nearly 2-decade-old idea that flowering plants had been central to the insects’ success. …As the climate changed and ferns and conifers declined the specialist stem ants began to go extinct, but the models suggest the generalists could tap new food sources provided by flowering plants. “The rise of angiosperms shaped ant diversity in two ways, by favoring diversification and buffering against extinction,” says Rachelle Adams, an evolutionary biologist at Ohio State University….

2023-11-24. Brought up in a creationist home, a scientist fights for evolution. [] By JEFFREY MERVIS, Science. Excerpt: The National Center for Science Education (NCSE), known for fighting to defend evolution’s place in school curricula, has a new leader who knows how hard that work can be. Amanda (Glaze) Townley, who next month becomes executive director of the Oakland, California–based nonprofit, grew up in rural northeastern Alabama, where she learned firsthand how religion and culture can collide with one of the central tenets in biology. “I grew up in a young Earth creationism home, with a worldview that was based in evangelical Christianity and a literal translation of the Bible,” recalls the 42-year-old Townley. “And when I took honors biology in high school, my teacher said she’s not going to teach evolution because she doesn’t believe in it.” …NCSE is best known for monitoring state and local legislative and ballot initiatives affecting the teaching of evolution. It played a key role in a landmark 2005 case in which a federal judge ruled that intelligent design is not science and doesn’t belong in the classroom. In 2012 it added climate change to its portfolio. Threats to both subjects have increased in recent years as part of a broader campaign by conservatives to ban certain topics from classrooms….

2023-10-04. Study of 17,000 years of fish fossils reveals rapid evolution. [] By ELIZABETH PENNISI, Science. Excerpt: When a new island or lake appears, the plants and animals that get there first have a leg up on later arrivals and are more likely to diversify into new species—or so evolutionary biologists have long assumed. But a study of fossils from East Africa’s Lake Victoria shows that it takes more than arriving early to win the speciation race. Although several kinds of fish colonized this lake around the same time, only cichlids took off, forming 500 species in less than 17,000 years, the team reports today in Nature. …The findings suggest opportunity and versatility matter more than primacy, adds George Turner, an evolutionary biologist and cichlid fish expert at Bangor University who was also not involved. Most cases of adaptive radiation, wherein one species gives rise to many more, took place over millions of years, making it nearly impossible for scientists to figure out why that one colonizing species became so successful. But the extreme diversity within a group of fish called cichlids began to arise a mere 17,000 years ago, when the modern version of Lake Victoria began to fill where today the borders of Uganda, Kenya, and Tanzania meet. Now 500 species strong—each inhabiting a particular niche within the lake—this group’s evolution represents “the most rapid radiation event known among vertebrates,” says Nare Ngoepe, an evolutionary biologist at the University of Bern….

\2023-08-04. Maverick in the genome. [] By Sonya A. Widen, Israel Campo Bes, Alevtina Koreshova, Pinelopi Pliota, Daniel Krogull, Alejandro Burga, Science. Excerpt: It was long thought that the barriers to gene flow between animal species were impenetrable. Without reproduction, there was simply no way that DNA could move from one animal to another. Indeed, even after the discovery that bacteria can give and receive genes with reckless abandon, the notion that something similar could happen in insects or fish—let alone reptiles or mammals—seemed ridiculous on its face. …But, against all odds, cases of horizontal gene transfer kept cropping up. Now, it’s clear DNA can and has jumped between animals—the big question that remains is how. Lots of ideas have been proposed, but the evidence has been handwavy. That is, until a largely overlooked paper published in Science last month reported that virus-like segments of mobile DNA called Mavericks have been shuttling genes between different species of roundworms (nematodes) for millennia….

2022-10-20. For some wolves, a black coat isn’t just fashionable—it’s a lifesaver. [] By Elizabeth Pennisi, Science Magazine, . Excerpt: Thousands of years ago, wolves bred with black dogs. The tryst didn’t just give some of today’s wolves a black coat—it has also helped them survive in parts of North America where a measleslike virus can run rampant, according to a new study. That’s because gray wolves are more likely to mate with black wolves when this virus is present—a rare demonstration in the wild of how pathogens can drive evolution. “This paper takes a very elegant approach to understanding a fundamental question in biology: how animals choose mates,” says Rena Schweizer, an evolutionary biologist at the University of Montana, Missoula, who was not involved with the work. Humans aren’t the only animals that show off their bodies to lure mates. Brighter bills in blackbirds and zebra finches do the same thing. One key signal in these species is color: The pigment that gives them their brilliant hues also improves their immune system, flagging to mates they’re a good catch.…

2022-08-25. How the sea fireflies of the Caribbean are shining new light on evolution. [] By Elizabeth Pennisi, Science Magazine. Excerpt: In the 18th century, the French naturalist Godeheu de Riville was sailing across the Indian Ocean when he came upon a remarkable sight. The sea “was covered over with small stars; every wave which broke about us dispersed a most vivid light, in complexion like that of a silver tissue electrified in the dark,” he recounted in his journal. When de Riville examined the sparkling water with his microscope, he discovered that the “small stars” were tiny crustaceans now known as ostracods. …in the Caribbean, and only in the Caribbean, as Morin and colleagues discovered, those bright blue dots can double as mating calls. Today, thousands of dives later, they believe those signals have driven Caribbean ostracods to diversify into more than 100 species. …With modern genetic tools, they’ve been using these creatures to investigate the factors that wedge species apart, including sexual selection, driven by female preferences; geographic isolation; and genetic drift—the accumulation of random genetic changes. In just the past 2 years, researchers have figured out how to grow ostracods in the lab, a development that will allow them to dissect the molecular mechanisms of evolution in a way once possible only in more conventional lab animals such as nematodes and fruit flies.…

2022-06-06. How the wild jungle fowl became the chicken. [] By Ann Gibbons, Science Magazine. Excerpt: …A pair of new archaeological studies suggest that without rice, chickens may have never existed. The work reveals that chickens may have been domesticated thousands of years later than scientists thought, and only after humans began cultivating rice within range of the wild red jungle fowl, in Thailand or nearby in peninsular Southeast Asia, says Dale Serjeantson, an archaeologist at the University of Southampton who was not involved with the research. …Charles Darwin proposed that chickens descended from the red jungle fowl—a colorful tropical bird in the pheasant family–because the two look so much alike. …In 2020, a study of 863 living chickens’ genomes confirmed that the jungle fowl Gallus gallus spaedicus subspecies was the ancestor of living chickens; chickens share more of their DNA with that subspecies than other types of jungle fowl. …the oldest bones of likely chickens came from a site called Ban Non Wat in central Thailand, where farmers grew rice 3250 to 3650 years ago, the team reports today in the Proceedings of the National Academy of Sciences.…

2021-10-21. Civil war drove these elephants to lose their tusks—through evolution. By Erik Stokstad, Science Magazine. Excerpt: As ivory poachers wiped out herds, tuskless elephants became more common. …When humans hunt, they can cause their quarry to evolve by targeting individuals with particular traits, like big fish or sheep with hefty horns. But it’s rare to figure out the genetics behind this human-caused evolution, experts say. Shane Campbell-Staton, an evolutionary biologist now at Princeton University, was curious about the elephants of Gorongosa National Park in Mozambique, where tuskless elephants—which are all female—are unusually common.… []

2021-06-25. [] – Stunning ‘Dragon Man’ skull may be an elusive Denisovan—or a new species of human. By Ann Gibbons, Science Magazine. Excerpt: Almost 90 years ago, Japanese soldiers occupying northern China forced a Chinese man to help build a bridge across the Songhua River in Harbin. While his supervisors weren’t looking, he found a treasure: a remarkably complete human skull buried in the riverbank. He wrapped up the heavy cranium and hid it in a well to prevent his Japanese supervisors from finding it. Today, the skull is finally coming out of hiding, and it has a new name: Dragon Man, the newest member of the human family, who lived more than 146,000 years ago. In three papers in the year-old journal The Innovation, paleontologist Qiang Ji of Hebei GEO University and his team call the new species Homo longi. (Long means dragon in Mandarin.) They also claim the new species belongs to the sister group of H. sapiens, and thus, an even closer relative of humans than Neanderthals. Other researchers …think it may be the long-sought skull of a Denisovan, an elusive human ancestor from Asia known chiefly from DNA….

2021-02-10. Fish had the genes to adapt to life on land—while they were still swimming the seas. By Elizabeth Pennisi, Science Magazine. Excerpt: Almost 700 years ago, Jacob van Maerlant, a Dutch poet, envisioned a fish all set for life on land: It had sprouted arms to hoist itself ashore. Now, three genetic studies make his fantasy look remarkably prescient. Together, the studies suggest that in terms of genes, the aquatic precursors of four-limbed land animals, or tetrapods, were as well-prepared as the Dutch fantasy fish. They were pre-equipped with genes that could be turned to making limbs, efficient air-breathing lungs, and nervous systems tuned to the challenges of life on land. …In the trio of studies published last week in Cell, genes in living fish took the place of fossils as a way to peer back in time. One set of clues came from studies of mutagenized zebrafish, a favorite model for studying development. M. Brent Hawkins, then a Harvard University graduate student and now a postdoc, was shocked to discover zebrafish mutants with two bones resembling the forelimb bones of land animals in their front fins, complete with muscles, joints, and blood vessels…. []

2021-01-28.  Your amazing thumb is about 2 million years old. By Michael Price, Science Magazine. Excerpt: The human thumb is a nimble wonder, allowing us to make tools, sew clothing, and open pickle jars. But just how and when this unique digit evolved has long been a mystery. Now, a new study modeling muscle in fossilized thumbs suggests about 2 million years ago, our ancient ancestors evolved a uniquely dexterous appendage while our other close relatives remained … all thumbs…. [

2020-06-02. Urban foxes may be self-domesticating in our midst. By Virginia Morel, Science Magazine. Excerpt: In a famous ongoing experiment started in 1960, scientists turned foxes into tame, doglike canines by breeding only the least aggressive ones generation after generation. The creatures developed stubby snouts, floppy ears, and even began to bark. Now, it appears that some rural red foxes in the United Kingdom are doing this on their own. When the animals moved from the forest to city habitats, they began to evolve doglike traits, new research reveals, potentially setting themselves on the path to domestication. …The renowned Siberian study immediately came to mind when Kevin Parsons heard about a large collection of red fox skulls at National Museums Scotland. …Most significantly, the urban foxes, like those in the Russian experiment, had noticeably shorter and wider muzzles, and smaller brains, than their rural fellows. …All of these changes are typical of what Charles Darwin labeled domestication syndrome []. Overall, urban foxes’ skulls seemed to be designed for a stronger bite than were those of rural foxes, which are shaped for speed. Perhaps that’s because in the city, a fox can simply stand at a human trash pile and feed on the food we’ve tossed out, where they may encounter more bones that can only be crushed with stronger jaws, Parsons speculates. Still, he emphasizes that the urban red foxes are not domesticated. But the study does show how exposure to human activity can set an animal down this path,…. [

2020-05-14. How Venus flytraps evolved their taste for meat. By Elizabeth Pennisi, Science Magazine. Excerpt: How does a plant develop a taste for flesh? In the play Little Shop of Horrors, all it takes is a drop of human blood. But in real life, it takes much more. Now, a study of three closely related carnivorous plants suggests dextrous genetic shuffling helped them evolve the ability to catch and digest protein-rich meals. Carnivorous plants have developed many devious ways to snare prey. Pitcher plants, for example, use “pitfall traps” that contain enzymes for digesting stray insects. Others—including the closely related Venus flytrap (Dionaea muscipula), the aquatic waterwheel plant (Aldrovanda vesiculosa), and the sundew (Drosera spatulata)—use moving traps. The sundew rolls up its sticky landing pad when mosquitoes get caught. And the Venus flytrap uses modified leaves, or pads, that snap shut when an insect lands—but only after the pads sense multiple touches on their trigger hairs. To find out how these traps evolved, researchers led by computational evolutionary biologist Jörg Schultz and plant biologist Rainer Hedrich, both of the University of Würzburg, sequenced the genomes of the sundew, the aquatic waterwheel, and the Venus flytrap, which are all closely related. They then compared their genomes with those of nine other plants, including a carnivorous pitcher plant and noncarnivorous beetroot and papaya plants. They found that the key to the evolution of meat eating in this part of the plant kingdom was the duplication of the entire genome in a common ancestor that lived about 60 million years ago, the team reports today in Current Biology []. That duplication freed up copies of genes once used in roots, leaves, and sensory systems to detect and digest prey. For example, carnivorous plants repurposed copies of genes that help roots absorb nutrients, to absorb the nutrients in digested prey. “That root genes are being expressed in the leaves of carnivores is absolutely fascinating,” says Kenneth Cameron, a botanist at the University of Wisconsin, Madison…. []  

2020-05-13. Lab-evolved algae could protect coral reefs. By Warren Cornwall, Science Magazine. Excerpt: For the third time in 5 years, an underwater heat wave has turned vast stretches of coral on Australia’s Great Barrier Reef ghostly white, a desperate survival strategy that is often a prelude to coral death. Now, scientists there have taken a small step toward helping coral survive in a warmer world. For the first time, researchers have grown algae in a lab that can reduce coral bleaching, as it’s known. The results are a notable advance in the growing field of “assisted evolution,” in which scientists are working to alter coral genetics to help them endure hotter water.  …Coral and their algae are deeply intertwined. The tiny, plantlike organisms live inside the cells of coral polyps, the small, anemonelike single animals that form colonies to create the fantastically shaped skeletons typically called coral. The algae, called zooxanthellae, use coral waste products to help photosynthesize food, while in turn nourishing the coral host. But that relationship sours during heat waves. Coral polyps eject the algae from their bodies, a phenomenon scientists suspect is a reaction to a flood of tissue-damaging molecules released by the overheated algae. Without their algae, the corals turn white, and, if the bleaching is severe enough, they can starve to death. Coral geneticist Madeleine van Oppen hoped the algae could be coaxed to evolve into strains that reduced the bleaching response…. []
2019-02-14. Seventy years ago, humans unleashed a killer virus on rabbits. Here’s how they beat it. By Elizabeth Pennisi, Science Magazine.

2018-08-13. The Scientist Who Scrambled Darwin’s Tree of Life. By David Quammen, The New York Times. [] Excerpt: On Nov. 3, 1977, a new scientific revolution was heralded to the world — but it came cryptically, in slightly confused form. …a man named Carl R. Woese, a microbiologist at the University of Illinois in Urbana, …. The article, by a veteran Times reporter named Richard D. Lyons, began: Scientists studying the evolution of primitive organisms reported today the existence of a separate form of life that is hard to find in nature. They described it as a “third kingdom” of living material, composed of ancestral cells that abhor oxygen, digest carbon dioxide and produce methane. This “separate form of life” would become known as the archaea, reflecting the impression that these organisms were primitive, primordial, especially old. They were single-celled creatures, simple in structure, with no cell nucleus. Through a microscope, they looked like bacteria, and they had been mistaken for bacteria by all earlier microbiologists. They lived in extreme environments, at least some of them — hot springs, salty lakes, sewage — and some had unusual metabolic habits, such as metabolizing without oxygen and, as the Times account said, producing methane. But these archaea, these whatevers, were drastically unlike bacteria if you looked at their DNA, which is what …that the history of life could be drawn as a tree…. …the prevailing tree of 1977, the orthodox image of life’s history, was wrong. It showed two major limbs arising from the trunk. According to what Woese had just announced to the world, it ought to show three…. [See also Science Friday “How A Humble Microbe Shook The Evolutionary Tree”]

2018-07-20. White Clover Can Be an Annoying Weed. It May Also Hold Secrets to Urban Evolution. By Karen Weintraub, The New York Times. Excerpt: It’s considered a nuisance or a weed when it pops up in luscious suburban lawns, long the bane of gardeners and homeowners…. But …white clover …is one of the most rapidly evolving species of flora, learning quickly how to survive in the toughest of urban environments. Some green thumbs would not be surprised at its stubborn spread, while others might welcome a haven for bee recovery…. According to a study published Tuesday in the Proceedings of the Royal Society B, white clover (Trifolium repens) adapts equally well to cities of all sizes — with 20 studied in Ontario, Canada, from London, with a population near 400,000 to tiny Everett, population 1,670. …Cities work as great natural test cases for evolution, said Marc Johnson, the director of the Centre for Urban Environments at the University of Toronto, Mississauga, who led the research. …With climate change advancing and more than half the world’s population living in cities — a figure expected to jump to 70 percent by 2050 — Dr. Johnson said it would be crucial for scientists to figure out how human encroachment and activity affect the plants and animals that surround us….

2018-06-01. This saltwater trout evolved to live in freshwater—in just 100 years. By Elizabeth Pennisi, Science Magazine. Excerpt: Although we tend to think of evolution as happening over thousands, if not millions, of years, critical changes can take little more than a century. That’s what happened with a group of steelhead trout transplanted from the salty seas of California to the fresh waters of Lake Michigan for game fishermen in the 1890s. A new study shows that the fish, which typically live part of their lives in the ocean like salmon, developed key genetic differences that allowed it to live wholly in freshwater—in little more than 100 years. The discovery shows how quickly organisms can adapt to a new lifestyle—if they have some of the right genes to start with, says Michael Blouin, a geneticist at Oregon State University in Corvallis. “The work is a nice example” of how evolution can happen “over very short time periods.” …So how did the genes change so quickly from one version to another? Intriguingly, there was no sign that steelhead had interbred with rainbow trout to get the genes they needed to thrive. They also didn’t have to mutate, Christie explains. Instead, there were likely a few steelhead among the first batch of transplants that already had the right versions of these genes—they simply survived and reproduced much more successfully than their peers. Eventually, the less well-adapted steelhead disappeared….

2018-05-31. Iceland’s founding fathers underwent a rapid, 1000-year genetic shift. By Michael Price, Science Magazine. Excerpt: If modern Icelanders came face-to-face with their founding fathers, they’d be hard-pressed to see much family resemblance, according to a new study. That’s because today’s Icelanders have a much higher proportion of Scandinavian genes than their distant ancestors did, suggesting the islanders underwent a remarkably rapid genetic shift over the past thousand years. …Medieval histories suggest Iceland was first settled between 870 C.E. and 930 C.E. by seafaring Vikings and the people they enslaved, who possessed a mélange of genes from what is now Norway and the British Isles. For the next thousand years, the population of Iceland remained relatively small and isolated, hovering between about 10,000 and 50,000. Impeccable genealogical records and broad genetic sampling have made Icelanders—who now number 330,000—a model population for geneticists hoping to connect the dots between gene variants and traits. …Sequencing revealed that the settlers had a roughly even split of Norse (from what are today Norway and Sweden) and Gaelic (from what are now Ireland and Scotland) ancestry. But when the researchers compared the ancient genomes to those of thousands of modern people in Iceland and other European countries, they found that contemporary Icelanders, on average, draw about 70% of their genes from Norse ancestry. That suggests in the approximately 1100 years between Iceland’s settlement and today, the population has undergone a surprisingly quick genetic shift, the researchers report today in Science….

2018-03-13. Should Some Species Be Allowed to Die Out? By Jennifer Kahn, The New York Times. Excerpt: …Under the rules of the Endangered Species Act, once a species is discovered to be at risk of extinction, government agencies are required by law to take steps to save it. For years, critics have challenged that mandate, arguing that it undercuts the ability to weigh a species’ value or to consider the economic impact of its preservation — for instance, the cost of prohibiting logging in a valuable tract of forest. …there are currently six bills pending in Congress, all aimed at overhauling (some would say gutting) the Endangered Species Act. …One arguably legitimate criticism of the Endangered Species Act is that trying to save every creature is both unrealistic and inefficient. Because the act requires that we help all species at risk of extinction, the argument goes, agencies end up spending vital resources on less-important species, rather than concentrating on the most critical ones. Assigning value to species is a nearly impossible undertaking, because it involves a bewildering number of variables, including ecological importance, utility (coral reefs can act as breakwaters during coastal storms), the species’ place in our heritage, even its beauty or symbolism. Conservation has no formula for weighting these factors, either alone or in combination, and it’s hard to imagine one that people could agree on. How do we decide whether the wolf or the snow leopard is more valuable? In response, some conservation groups have argued that we should put our efforts toward saving the most genetically diverse species, with the goal of increasing our long-term ecological resiliency. …Others have suggested prioritizing “functional diversity”: the preservation of key species, like predators and pollinators, whose presence can radically affect an ecosystem….

2018-03-08. Why does evolution sometimes repeat itself? Spider-eating spiders may hold the answer. By Elizabeth Pennisi, Science. Excerpt: Discovering something for the second time might sound like a letdown. Not for ecologists in Hawaii, who have found that spider-eating spiders on four islands there independently evolved the same colors: gold, black, and white. This rare example of parallel evolution, which has also been seen in one other Hawaiian spider, could help clarify one of biology’s biggest mysteries: how and when evolution repeats itself….

2017-11-28. Things Looked Bleak Until These Birds Rapidly Evolved Bigger Beaks. By Douglas Quenqua, The New York Times. Excerpt: Conservationists have been sounding the alarm over invasive species for years, warning of the damage they can cause to habitats and native animals. But in Florida, an invasive snail might be helping an endangered bird species come back from the brink, researchers say. The population of North American snail kites — birds that use curved beaks and long claws to dine on small apple snails in the Florida Everglades — had been dwindling for years, from 3,500 in 2000 to just 700 in 2007. Things began to look particularly bleak in 2004, when a portion of the Everglades was invaded by a species of larger snail that the birds had historically struggled to eat. Ornithologists assumed the shift would hasten the snail kite’s decline. But the number of snail kites in the Everglades grew over the decade following the invasion of the larger snails. The reason, according to a study published Monday in Nature Ecology and Evolution, is that the snail kites have rapidly evolved larger beaks and bodies to handle the bulkier snails. “We were very surprised,” said Robert Fletcher, Jr., an ecologist at the University of Florida and an author of the study. “We often assume these large-bodied animals can’t keep up with changes to the system, like invasions or climate change, because their generation times are too long. And yet we are seeing this incredibly rapid change in beak size of this bird.”…

2017-05-29. Challenging Mainstream Thought About Beauty’s Big Hand in Evolution. By James Gorman, The New York Times. Excerpt: …Richard O. Prum, a Yale ornithologist and evolutionary biologist, … in a new book, “The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World — and Us…” …writes about one kind of beauty — the oh-is-he/she-hot variety — and mostly as it concerns birds, not people. And his answer is, in short: That’s what female birds like. …when they are choosing mates — and in birds it’s mostly the females who choose — animals make choices that can only be called aesthetic. They perceive a kind of beauty. Dr. Prum defines it as “co-evolved attraction.” They desire that beauty, often in the form of fancy feathers, and their desires change the course of evolution. …Darwin famously proposed the idea of evolution by natural selection, what is often called survival of the fittest. To put it simply, living things vary in their inherited traits, from speed to color to sense of smell. The traits of the individuals who survive longer and have the most offspring become more common. So, over time, the faster antelope have more young, the fastest of them have more offspring, and antelope end up very speedy. …But reproduction isn’t just about surviving and staying healthy long enough to mate. You have to find a mate. And in many species, your mate must choose you. This process is sexual selection. Female birds are often the ones choosing. And their choices can produce male birds that are incredibly colorful, …. If, for example, females like males with long tails, then long-tailed males have more offspring, and the longest-tailed of those offspring reproduce more. In the end, that species becomes known for its long tails. …survival might not have anything to do with it….

2017-04-03. What Makes a City Ant? Maybe Just 100 Years of Evolution. By Steph Yin, The New York Times. Excerpt: It can often take millenniums for organisms to evolve. But for crumb-size acorn ants in Cleveland, a single human life span may have been enough for them to become adapted to city living. In a recent study published in The Biological Journal of the Linnean Society, scientists found that city acorn ants were more tolerant of heat, and less tolerant of cold, than their rural counterparts. Because Cleveland became significantly urbanized only in the last century, this adaptation would have arisen in no more than 100 years, or 20 acorn ant generations, said Sarah Diamond, an assistant professor of biology at Case Western Reserve University and an author of the study…. 0

2017-02-01. Finding the Speed of Evolution in a Study of Bird Beaks. By Steph Yin, The New York Times. Excerpt: When the ancestors of Darwin’s finches arrived on the Galápagos two million years ago, they gained access to a world of new morsels, untapped by other animals. In a relatively short period, 14 species of finches evolved, specializing in different diets through different beak shapes: short for crushing seeds, sharp for catching insects, long for probing cactus flowers and so on. This rapid diversification in the presence of new opportunity is called adaptive radiation. Studies of small island bird and lizard populations describe a fast burst of evolution, followed by a slowdown. But broader research has failed to find this fast-then-slow pattern of evolution on a global scale. …In the case of birds, it is not that evolution slows over time, but rather it switches from generating major changes in beak shape to producing smaller iterations of the same basic shapes, said Gavin Thomas, a professor of animal and plant sciences at the University of Sheffield in Britain and an author of the paper. In their study, Dr. Thomas and collaborators collected 3-D scans of bird beaks from museum specimens representing more than 97 percent of present-day birds. Through a website called Mark My Bird, they asked the public to help mark out specific features on the scans, including the tip, midline and curvature of each bill. …the scientists were able to infer ancestral bill shapes and rates of evolution going back more than 80 million years. Their data suggested that most of the variation we see in beaks today evolved long ago, in a relatively short period of time….

2016-08-17. From Fins Into Hands: Scientists Discover a Deep Evolutionary Link. By Carl Zimmer, The New York Times. Excerpt: To help his readers fathom evolution, Charles Darwin asked them to consider their own hands. “What can be more curious,” he asked, “than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?” Darwin had a straightforward explanation: People, moles, horses, porpoises and bats all shared a common ancestor that grew limbs with digits. …On Wednesday, a team of researchers at the University of Chicago reported that our hands share a deep evolutionary connection not only to bat wings or horse hooves, but also to fish fins. …The fossil record shows that we share a common aquatic ancestor with ray-finned fish that lived some 430 million years ago. Four-limbed creatures with spines — known as tetrapods — had evolved by 360 million years ago and went on to colonize dry land. …For over two decades, Neil H. Shubin, an evolutionary biologist, has investigated this transition in two radically different ways. …In 1996, a team of French researchers studying mice discovered genes that are essential for the development of their legs. When the scientists shut down two genes, called Hoxa-13 and Hoxd-13, the mice developed normal long bones in their legs. But their wrist and ankle bones failed to appear, and they did not grow any digits. This discovery suggested that Hoxa-13 and Hoxd-13 genes tell certain cells in the tetrapod limb bud that they will develop into hands and feet. Dr. Shubin knew that fish have genes related to Hoxa-13 and Hoxd-13. He wondered what those genes were doing, if anything, in developing fins. An experiment on fish might give him and his colleagues a clue. “But we didn’t have the means to do it until technology caught up with our aspirations,” Dr. Shubin said. …thanks to a new gene-editing technology called Crispr. Scientists can use it to readily alter genes in virtually any species. …Andrew R. Gehrke, a graduate student… engineered zebrafish so that he could follow individual cells during the development of embryos. …cells that switched on the Hox genes started to glow. They kept glowing throughout development, until they reached their final location in the fish’s body. …When the fins were fully developed, …the fin rays were glowing. In a similar experiment on mice, the digits and wrist bones lit up. “Here we’re finding that the digits and the fin rays have some sort of equivalence at the level of the cells that make them,” Dr. Shubin said….

2016-02. Inside the Eye: Nature’s Most Exquisite Creation. By Ed Yong, National Geographic. Excerpt: …In his lab at Lund University in Sweden, Dan-Eric Nilsson is contemplating the eyes of a box jellyfish. …the box jelly boasts 24 eyes, which are dark brown and grouped into four clusters called rhopalia. …“When I first saw them, I didn’t believe my own eyes,” says Nilsson. “They just look weird.”  …The fossil record tells us nothing about how sightless animals first came to see the world. This mystery flustered Charles Darwin. “To suppose that the eye, with all its inimitable contrivances … could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree,” he wrote in Origin of Species. Creationists like to end the quotation there, with the great man doubting his own theory. But in the very next sentence, Darwin solves his own dilemma: “Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist … then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.” …Nilsson…created a simulation that starts with a small, flat patch of pigmented light-sensitive cells. With each yearlong generation, it becomes a little thicker. It slowly curves from a sheet into a cup. It gains a crude lens, which gradually improves. Even under the most pessimistic conditions, with the eye improving by just 0.005 percent each generation, it takes just 364,000 years for the simple sheet to become a fully functioning camera-like organ. As far as evolution goes, that’s a blink of an eye….

2015-11-24. Odd creature was ancient ancestor of today’s giraffes. By  Sid Perkins, Science. Excerpt: A distant relative of today’s giraffes was a bit of an odd creature: It was about the size of a bull moose, but it had a long neck that could stretch both up to eat tree leaves and down to eat grass. That’s the conclusion of the first comprehensive analysis of a complete set of fossilized neck bones from the animal, known as Samotherium major…. Samotherium, which lived in the open woodlands of Eurasia about 7 million years ago, had a neck about 1 meter long—about half the length of that of today’s giraffes. …the researchers report online today in Royal Society Open Science….

2015-04-17. How the wolf became the dog. By David Grimm, Science (AAAS). Excerpt:  …Most experts now think dogs domesticated themselves. Early humans left piles of discarded carcasses at the edges of their campsites—a veritable feast, the thinking goes, for wolves that dared get close to people. Those wolves survived longer and produced more pups—a process that, generation by generation, yielded ever-bolder animals, until finally a wolf was eating out of a person’s hand. Once our ancestors realized the utility of these animals, they initiated a second, more active phase of domestication, breeding early canines to be better hunters, herders, and guardians. …A comparison of thousands of ancient dog and wolf skeletons, for example, has revealed flattening of the dorsal tips of ancient dog vertebrae, suggesting that the animals hauled heavy packs on their backs. The team has also spotted missing pairs of molars near the rear of the jaw in ancient dogs, which may indicate that the animals wore some sort of bridle to pull carts. These services, in addition to dogs’ hunting prowess, may have proved critical for human survival, potentially allowing modern humans to outcompete our Neandertal rivals and even eventually settle down and become farmers. …a study in this week’s issue of Science helps explains how man and dog took the next step to become best friends. Takefumi Kikusui, an animal behaviorist at Azabu University in Sagamihara, Japan, and his colleagues have found that when dogs and humans gaze into each other’s eyes, both experience a rise in oxytocin—a hormone that has been linked to trust and maternal bonding. The same rise in oxytocin occurs when human mothers and infants stare at each other, suggesting that early dogs may have hijacked this response to better bond with their new human family…. – see also How dogs stole our hearts and Solving the mystery of dog domestication.

2014-12-01. Ability to consume alcohol may have shaped primate evolution. By Sarah C. P. Williams, Science. Excerpt: …desire to consume alcohol, as well as your body’s ability to break down the ethanol that makes you tipsy, dates back about 10 million years, researchers have discovered. The new finding not only helps shed light on the behavior of our primate ancestors, but also might explain why alcoholism—or even the craving for a single drink—exists in the first place. …the human ability to metabolize ethanol—allowing people to consume moderate amounts of alcohol without getting sick—relies on a set of proteins including the alcohol dehydrogenase enzyme ADH4. …Matthew Carrigan, a biologist at Santa Fe College in Gainesville, Florida, and colleagues sequenced ADH4 proteins from 19 modern primates and then worked backward to determine the sequence of the protein at different points in primate history. …the most ancient forms of ADH4—found in primates as far back as 50 million years ago—only broke down small amounts of ethanol very slowly. But about 10 million years ago, the team reports online today in the Proceedings of the National Academy of Sciences, a common ancestor of humans, chimpanzees, and gorillas evolved a version of the protein that was 40 times more efficient at ethanol metabolism. “Around this same time, the Earth cooled off, food sources changed, and this primate ancestor started to explore life on the ground,” Carrigan says. And this new way of life meant that, for the first time, primates started eating not only fruit picked from trees, but also the fallen fruits below. And fallen fruits, when they’re exposed to bacteria in the environment that convert sugars to alcohols, will begin to accumulate ethanol. “If you were the ancestor without this new mutation in ADH4, the ethanol would quickly build up in your blood and you’d get inebriated much faster,” Carrigan says. “You’d be a cheap date.” This easy inebriation, he says, would have been a disadvantage to the monkeys without the mutation, making them more easily get sick—or drunk—off fruit, enough so that they couldn’t defend their territory and seek out food. Primates with the new mutation could get more food, his group hypothesizes, and the gene was selected for in the human and chimpanzee lineage….

2014-09-11. Changing how we farm can save evolutionary diversity, study suggests. Excerpt: A new study by biologists at Stanford University and UC Berkeley highlights the dramatic hit on the evolutionary diversity of wildlife when forests are transformed into agricultural lands. …The researchers studied nearly 500 species of birds in Costa Rica in three types of habitat, and calculated the birds’ phylogenetic diversity, a measure of the evolutionary history embodied in wildlife. …The study, to be published in the Sept. 12 issue of the journal Science, found that the phylogenetic diversity of the birds fared worst in habitats characterized by intensive farmlands consisting of single crops. Such intensive monocultures supported 900 million fewer years of evolutionary history, on average, compared with untouched forest reserves. The researchers found a middle ground in diversified agriculture, or farmlands with multiple crops adjoined by small patches of forest. Such landscapes supported on average 600 million more years of evolutionary history than the single crop farms. “The loss of habitat to agriculture is the primary driver of diversity loss globally, but we hadn’t known until now how agriculture affected diversity in an evolutionary context,” said study co-lead author Daniel Karp, UC Berkeley postdoctoral research fellow in environmental science, policy and management. “We found that forests outperform agriculture when it comes to supporting a larger range of species that are more distantly related, so by maintaining patches of tropical trees and multiple crops on their land, farmers can enhance evolutionarily distinct species.”… By Sarah Yang, UC Berkeley News Center.

2013-11-07. Fast-Paced Evolution in the Andes. Excerpt:   In 1799 the great naturalist Alexander von Humboldt and his companions set out from Caracas, Venezuela, to climb the Andes. They struggled up a mountainside enveloped in mist so thick they had to clamber over rocks by hand. When the fog cleared, von Humboldt was left astonished by the view. Vast grasslands stretched all around him, home to an astonishing number of different trees, shrubs and flowers. …Von Humboldt had stumbled into a remarkable ecosystem, known as a Páramo. Páramos blanket the Andes in Venezuela, Ecuador and Colombia, growing at altitudes 9,200 to 14,800 feet above sea level.  “They’re like islands in a sea of forest,” said Santiago Madriñán, an expert on Páramos at the University of the Andes in Colombia. All told, Páramos cover about 13,500 square miles — an area the size of Maryland. In that small space, Dr. Madriñán and other researchers have found 3,431 species of vascular plants, most of them found nowhere else on Earth. …the Páramos are even more remarkable than von Humboldt could have realized. They are the fastest evolving place on the planet…. Carl Zimmer, The New York Times.

2013-09-26.  In Galápagos, An Insidious Threat to Darwin’s Finches.  Excerpt: The birds that have come to be known as Darwin’s finches have long intrigued students of evolution. But now a parasitic fly introduced to the Galápagos Islands is threatening the future of one or more of these iconic finch species…. by Elizabeth Kolbert, Environment360.

2013 Feb 04.  Pigeons Get a New Look. By Carl Zimmer, The New York Times. Excerpt: In 1855, Charles Darwin took up a new hobby. He started raising pigeons. [Read What Charles Darwin Wrote About Pigeons in ‘On the Origin of Species’ – LINK:] …“The diversity of the breeds is something astonishing,” he wrote a few years later in “On the Origin of Species” — a work greatly informed by his experiments with the birds. Pigeon breeding, Darwin argued, was an analogy for what happened in the wild. Nature played the part of the fancier, selecting which individuals would be able to reproduce. Natural selection might work more slowly than human breeders, but it had far more time to produce the diversity of life around us. …Now Michael D. Shapiro, a biologist at the University of Utah, …reports that it has delved into a source of information Darwin didn’t even know about: the pigeon genome. So far, they have sequenced the DNA of 40 breeds, seeking to pinpoint the mutations that produced their different forms. …The new work supports Darwin’s original claim that all pigeon breeds descend from the rock pigeon, whose range stretched from Europe to North Africa and east into Asia. [Times Topic: Charles Darwin – LINK:] …humans bred the birds to carry messages. By the eighth century B.C., Greeks were using pigeons to send the results of Olympic Games from town to town. Genghis Khan used pigeons to create a communication network across his empire in 12th century A.D.  …pigeon breeders produced crests on the birds on five separate occasions. The scientists …found that all of them shared precisely the same mutation in precisely the same gene, EphB2. …The new research suggests that the crested version of EphB2 arose in a surprising way. It mutated only once, rather than five separate times…. 

2012 July 02. A Giant Tortoise’s Death Gives Extinction a Face. By Carl Hulse, The NY Times. Excerpt: George, the last giant tortoise of his subspecies in this archipelago, was found dead in his corral at the Charles Darwin Research Station here the morning of June 24 — to the shock of his devoted caretakers, who had hoped he would survive for decades to continue his line…The Galápagos is home to other types of giant tortoises, though their numbers remain low and their populations vulnerable…“We were expecting to have George another 50 years,” he said as he stood before the pen, which houses a heart-shaped pool in which the tortoise’s caretakers had hoped to entice him to produce an heir with two biologically close female tortoises who remain. “It feels kind of empty.” George’s death was a singular moment, representing the extinction of a creature right before human eyes — not dinosaurs wiped out eons ago or animals consigned to oblivion by hunters who assumed there would always be more….

2011 September 21.  A Knack for Bashing Orthodoxy. By Michael Powell, The NY Times.  Excerpt: “…Prominent scientists and intellectuals cast Professor Richard Dawkins as the herald angel of a selfish culture, accusing him and his fellow sociobiologists of setting the cultural stage for the “I got mine” age of Ronald Reagan and Margaret Thatcher. The evolutionary biologist Richard Lewontin, a man of the political left, painted a picture out of a George Orwell novel. “If biological determinism is a weapon in the struggle between classes,” he wrote with two other scientists, “then the universities are weapons factories, and their teaching and research faculties are the engineers, designers.”
To Professor Dawkins, this badly distorted his science and his political leanings, which are resolutely liberal… He was writing about the behavior of genes, not about psychological and emotional states….
…Professor Dawkins’s great intellectual conviction is that evolution is progressive, and tends to lead to more and more complexity. Species, in his view, often arrive at similar solutions to evolutionary puzzles — the need for ears, eyes, arms or an octopus’s tentacle. And, often although not invariably, bigger brains. So the saber-toothed tiger shows up as a cat in Europe and Asia, and as a marsupial in South America. Different species seized on the same carnivorous solution…. [See also a video interview with Professor Dawkins]

2011 August 8. A Colorful Way to Watch Evolution in Nebraska’s Sand Dunes. By Hillary Rosner, The New York Times. Excerpt: Nebraska’s sandhills are the largest sand dunes in North America, spreading for more than 20,000 square miles, over more than a quarter of the state…
For a team of evolutionary biologists and geneticists from Harvard University who spent part of their summer in Valentine, on the sandhills’ northern edge, the draw is not the quartz itself, but a particular mouse whose coat color matches it. They’re using pigmentation to study a central question of biology: How do organisms adapt to their environments?
…Today, the Harvard group, run by Hopi Hoekstra, professor and curator of mammals for the university’s Museum of Comparative Zoology, is studying color to piece together evidence of how genetic diversity occurs, and how natural selection acts on that diversity.
They want to understand the specific genetic mechanisms that lead to changes in physical appearance, and then how those physical changes affect an organism’s fitness — how likely it is to survive and reproduce…

2010 October 9. On Guadalcanal, Studying Evolution. by Chris Filardi, The New York Times. Excerpt: …We used to think islands received colonists through a one-way flow of diversity from overflowing continental systems. Molecular analyses are now revealing that island evolution is a two-way street, with colonists arriving on islands, evolving into wonderfully unique forms, and then often backtracking to reinvigorate continental diversity. This means that islands are engines of diversification in their own right and far more important to global patterns of diversity than we once thought… 

2010 July 19. Discovery Could Help Date Monkey-Ape Spilt. By Sindya N. Shanoo, The New York Times. Excerpt: Scientists agree that Old World monkeys and apes share a common ancestry, but at some point two lineages diverged, one giving rise to the Old World monkeys and another to both apes and humans. Eactly when the split happened is a matter of debate.
A primate skull unearthed outside of Mecca in Saudi Arabia is the closest common ancestor to apes and Old World monkeys, researchers say, and helps date the split. Sediment records indicate that the fossil is 25 million to 29 million years old, making 24 million to 29 million years ago the window in which the monkey-ape split may have occurred. The ape and human lineages split later.
…Based on the skull, the primate was medium-sized and weighed about 30 pounds to 40 pounds. It had broad upper molars and a long, baboonlike snout. 

2010 Summer. An Inordinate Fondness for Tropical Species. By Kathleen M. Wong, Science Matters @ Berkeley. Excerpt: The tropics are hotbeds of biodiversity. Compared to other regions, the variety of birds, insects, plants and other species in the steamy forests of the equator is off the charts. 
…“In the Amazon, an area the size of a football field can have 300 different species of trees. You’re lucky in California if you get 10 or 15,” says Paul Fine, a Berkeley professor of integrative biology. “How can all of these species coexist? Why don’t they outcompete each other?” Fine is experimenting with rainforest trees to find the answers. In the process, he aims to identify the factors that help generate biological diversity.
…Much of his research takes place in Iquitos, Peru. Over the eons, rivers have carried soils to this portion of the Western Amazon from many corners of South America. Today, soil mosaics of white sand, clay, and flooded forests (habitats that are inundated for several months of the year) are found within a few hectares of one another.
…These conditions make Iquitos an ideal place to study how habitat variety affects speciation. To do so, Fine has been transplanting trees from one habitat to another. He is observing, for example, whether slow-growing trees associated with poor nutrient soils will grow faster on richer soils. “We want to see whether plants can turn these strategies on and off, whether they have the genetic makeup to deal with a variety of different environments,” Fine says.
…Fine is [also] now examining the chemical defenses trees produce in certain habitats… “We’re guessing that widely separated populations are not likely to have the same kinds of insect assemblages eating them. If we are right, we predict that this is going to drive selection for different kinds of plant defenses. It would be a kind of local adaptation to an ‘enemy environment.’” … He is also attempting to cross-pollinate the tree populations from different localities and habitats, to compare what insect-repelling chemicals the hybrids produce versus their parents. 

2010 May 19. All Life Forms Share Single Genetic Inheritance. IANS, The Times of India. Excerpt: …More than 150 years ago, Darwin proposed the theory of universal common ancestry (UCA), linking all forms of life by a shared genetic heritage from single-celled micro-organisms to humans.
…Over the last century and a half, qualitative evidence for this theory has steadily grown, in the numerous, surprising transitional forms found in the fossil record, for example, and in the identification of sweeping fundamental biological similarities at the molecular level.
…Harnessing powerful computational tools and applying specialized statistics, Theobald found that the evidence overwhelmingly supports UCA, regardless of horizontal gene transfer or multiple origins of life. 

2009 September 7. Where Did All the Flowers Come From? By Carl Zimmer, The NY Times. Excerpt: Throughout his life, Charles Darwin surrounded himself with flowers. …But despite his intimate familiarity with flowers, Darwin once wrote that their evolution was “an abominable mystery.”
…The fossil record…offered Darwin little enlightenment about the early evolution of flowers. At the time, the oldest fossils of flowering plants came from rocks that had formed from 100 million to 66 million years ago during the Cretaceous period. Paleontologists found a diversity of forms, not a few primitive forerunners.
Long after Darwin’s death in 1882, the history of flowers continued to vex scientists. But talk to experts today, and there is a note of guarded optimism….
The discovery of new fossils is one source of that new excitement. But scientists are also finding a wealth of clues in living flowers and their genes. They are teasing apart the recipes encoded in plant DNA for building different kinds of flowers. Their research indicates that flowers evolved into their marvelous diversity in much the same way as eyes and limbs have: through the recycling of old genes for new jobs…. 

2009 February 9. On Darwin’s ‘On the Origin of Species’. The NY Times. In addition to being the 200th anniversary of Darwin’s birth, 2009 is the 150th anniversary of the publication of his fundamental work, “On the Origin of Species.” As with many original sources, it is known mostly by reputation. Few people who are not biologists read Darwin in the original. But his writing can still offer surprises, insights and pleasures, and it can be sampled here, with selections by prominent scientists of their favorite passages and discussions of why these passages are important…. 

2009 February 9. Darwin, Ahead of His Time, Is Still Influential. By Nicholas Wade, The New York Times. Excerpt: Darwin’s theory of evolution has become the bedrock of modern biology. But for most of the theory’s existence since 1859, even biologists have ignored or vigorously opposed it, in whole or in part.
It is a testament to Darwin’s extraordinary insight that it took almost a century for biologists to understand the essential correctness of his views.
Biologists quickly accepted the idea of evolution, but for decades they rejected natural selection, the mechanism Darwin proposed for the evolutionary process….
And biologists are still arguing about group-level selection, the idea that natural selection can operate at the level of groups as well as on individuals….
It is somewhat remarkable that a man who died in 1882 should still be influencing discussion among biologists…. 

2009 February 9. Genes Offer New Clues in Old Debate on Species’ Origins. By CAROL KAESUK YOON, The New York Times. Excerpt: Charles Darwin called it the “mystery of mysteries,” a problem so significant and one he was so sure he had solved that he named his world-changing work after it: “On the Origin of Species.” So he might be surprised to learn that 150 years after the publication of his book, the study of how species originate, a process known as speciation, is not only one of the field’s most active areas of study, but also one of its most contentious….
…“A decade ago, the joke was that spell-checkers regularly attempted to substitute the word ‘speciation’ with ‘speculation,’” Mohamed Noor, an evolutionary biologist at Duke University, wrote in a commentary in the journal Nature. But he added, “Speculation in this area will soon be a thing of the past.”
To support such optimism, researchers point to the recent discovery of so-called speciation genes. Most biologists define a species as a group that is reproductively isolated — it cannot interbreed or exchange genes with any other. The newly discovered genes cause reproductive isolation between two groups by causing their offspring, or hybrids, to be infertile or die…. 

2009 February 9. Darwinism Must Die So That Evolution May Live. By Carl Safina, The New York Times. Excerpt: Charles Darwin gets so much credit, we can’t distinguish evolution from him.
Equating evolution with Charles Darwin ignores 150 years of discoveries, including most of what scientists understand about evolution. Such as: Gregor Mendel’s patterns of heredity (which gave Darwin’s idea of natural selection a mechanism — genetics — by which it could work); the discovery of DNA (which gave genetics a mechanism and lets us see evolutionary lineages); developmental biology (which gives DNA a mechanism); studies documenting evolution in nature (which converted the hypothetical to observable fact); evolution’s role in medicine and disease (bringing immediate relevance to the topic); and more.
By propounding “Darwinism,” even scientists and science writers perpetuate an impression that evolution is about one man, one book, one “theory.”… 

2009 February 9. Crunching the Data for the Tree of Life. By Carl Zimmer, The New York Times. Excerpt: Michael Sanderson…, a biologist at the University of Arizona, is part of an effort to figure out how all the estimated 500,000 species of plants are related to one another. For years now the researchers have sequenced DNA from thousands of species…. The pace of their progress gives Dr. Sanderson hope that they will draw the entire evolutionary tree of plants within the next few years….
There’s just one problem. “We have no way to visualize such a tree at the moment,” he said….
… Biologists have responded to the problem by enlisting the help of computer scientists and software designers from companies like Google and Adobe to find a new way of looking at evolution. Their goal is to create a program that allows scientists and nonscientists alike to fly through evolutionary trees…. 

2009 February 9. Seeing the Risks of Humanity’s Hand in Species Evolution. By CORNELIA DEAN, The New York Times. Excerpt: …human predation is causing target species to evolve to reproduce at younger ages and smaller sizes, to their short-term benefit but to the long-term harm of the species.
…Because humans discovered fire, the benefits of hunting in teams and the bounties of agriculture, people have been changing the natural landscape, causing plants and animals to evolve in response….
…Human behavior has affected human evolution as well…. Since the beginning of the Industrial Revolution, humanity’s collective ability to change the world has been powered by fossil fuels and multiplied by machines. Often, the result has been evolutionary change at a fast pace and on a broad scale…. 

2009 February 9. Darwin the Comedian. Now That’s Entertainment! By JOHN TIERNEY, The New York Times. Excerpt: …Officially, he is a science historian named Richard Milner, but he regularly turns into his hero on stage — complete with white beard, bowler and cape — in a one-man musical, “Charles Darwin: Live & In Concert.”…
“Everyone should find his own Darwin,” Mr. Milner says. “The man was so large. He was a zoologist, a botanist, an explorer, a travel writer, a philosopher, an abolitionist, a doting father, a radical intellectual revolutionary with an utterly conservative and blemish-free lifestyle. He revolutionized every field he touched, and he was trained in none of them.”
…Mr. Milner has turned the shy naturalist into a suavely bemused performer doing patter songs about trilobites, garfish and tortoise shells. (You can see excerpts at…. 

2007 June 29. Study Traces Cat’s Ancestry to Middle East. By Nicholas Wade. The New York Times. Excerpt: … [Carlos A. Driscoll of theNational Cancer Institute and his colleagues have] spent more than six years collecting species of wildcat in places as far apart as Scotland, Israel, Namibia and Mongolia. He then analyzed the DNA of the wildcats and of many house cats and fancy cats. Five subspecies of wildcat are distributed across the Old World. … Their patterns of DNA fall into five clusters. The DNA of all house cats and fancy cats falls within the Near Eastern wildcat cluster, making clear that this subspecies is their ancestor… Wheat, rye and barley had been domesticated in the Near East by 10,000 years ago, so it seems likely that the granaries of early Neolithic villages harbored mice and rats, and that the settlers welcomed the cats’ help in controlling them. Unlike other domestic animals, which were tamed by people, cats probably domesticated themselves, which could account for the haughty independence of their descendants. … Until recently the cat was commonly believed to have been domesticated in ancient Egypt, where it was a cult animal. But three years ago a group of French archaeologists led by Jean-Denis Vigne discovered the remains of an 8-month-old cat buried with its human owner at a Neolithic site in Cyprus. … 

2007 June 26. Fast-Reproducing Microbes Provide a Window on Natural Selection. The New York Times. By Carl Zimmer. Excerpt: 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. 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. 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. 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. … 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. … 

2007 June 26. From a Few Genes, Life’s Myriad Shapes. The New York Times. By Carol Kaesuk Yoon. Excerpt: Since its humble beginnings as a single cell, life has evolved into a spectacular array of shapes and sizes… But just how such diversity of form could arise out of evolution’s mess of random genetic mutations … 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. “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.” 

2007 June 26. The Human Family Tree Has Become a Bush With Many Branches. By John Noble Wilford. The New York Times. Excerpt: 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 … 

2007 June 26. Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift. By Douglas H. Erwin. The New York Times. Excerpt: É Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science. The discovery of DNA marked one such shift, the theory of plate tectonics another. Éour evolutionary framework … was constructed from the 1930s to 1950s by early geneticists, paleontologists and others, who disagreed about the efficacy of natural selection in driving evolutionary change (Darwin’s big idea) and about the nature of the underlying genetic variation upon which natural selection could act. What they came to agree on was called the modern synthesis Éthat mutations to DNA create new variants of existing genes within a species. Natural selection, driven by competition for resources, allows the best-adapted individuals to produce the most surviving offspring. So adaptive variants of genes become more common. ÉIn the past few years every element of this paradigm has been attacked. Concerns about the sources of evolutionary innovation and discoveries about how DNA evolves have led some to propose that mutations, not selection, drive much of evolution, or at least the main episodes of innovation, like the origin of major animal groups, including vertebrates. The Achilles’ heel of the modern synthesis, as noted by the philosopher Ron Amundson, is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history. ÉMost species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.
Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it…. 

4 December 2006. The American Geological Society website about American education and the topic of evolution

21 February 2006. Few Biologists but Many Evangelicals Sign Anti-Evolution Petition. By KENNETH CHANG. NY Times. Excerpt: In the recent skirmishes over evolution, advocates who have pushed to dilute its teaching have regularly pointed to a petition signed by 514 scientists and engineers. The petition, they say, is proof that scientific doubt over evolution persists. But random interviews with 20 people who signed the petition and a review of the public statements of more than a dozen others suggest that many are evangelical Christians, whose doubts about evolution grew out of their religious beliefs. And even the petition’s sponsor, the Discovery Institute in Seattle, says that only a quarter of the signers are biologists, whose field is most directly concerned with evolution. The other signers include 76 chemists, 75 engineers, 63 physicists and 24 professors of medicine. …The petition makes no mention of intelligent design, the proposition that life is so complex that it is best explained as the design of an intelligent being. Rather, it states: “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.” A Web site with the full list of those who signed the petition was made available yesterday by the institute at The signers all claim doctorates in science or engineering. The list includes a few nationally prominent scientists like James M. Tour, a professor of chemistry at Rice University; Rosalind W. Picard, director of the affective computing research group at the Massachusetts Institute of Technology; and Philip S. Skell, an emeritus professor of chemistry at Penn State who is also a member of the National Academy of Sciences….

22 November 2005. In Give and Take of Evolution, a Surprising Contribution From Islands. By CARL ZIMMER. NY Times. Excerpt: Islands hold a special place in the hearts of evolutionary biologists. When Charles Darwin visited the Galápagos Islands in 1835, he was stunned by the diversity of birds, which helped guide him to his theory of evolution by natural selection. Beginning in the middle of the last century, the ornithologist Ernst Mayr laid the foundation for the modern understanding of the way new species evolve, arguing that they mainly emerged when populations became geographically isolated. Mayr based his theory on his studies of birds from Pacific islands. Yet islands have generally been considered evolutionary dead ends. After animals and plants emigrated from the mainland, it was believed that they became so specialized for island life that they could not leave. They eventually became extinct, only to be replaced by new arrivals from the mainland….But Dr. Filardi and Robert Moyle, a colleague at the museum, have found evidence that islands can act as engines of evolution instead of dead ends. Animals can spread from island to island, giving rise to an explosion of new species, and even colonizing the mainland again. The results suggest that conserving biodiversity on islands is vital for the evolution of new species in the future.
Dr. Filardi made this discovery by studying a group of Pacific island birds, known as monarch flycatchers, …In one lineage, the monarch flycatchers tripled their body size in less than a million years. “This stuff can happen really fast,” Dr. Filardi said. This evolutionary wave returned to its origins when flycatchers from the Solomon Islands colonized Australia and New Guinea.

24 May 2005. New Rule on Endangered Species in the Southwest. By FELICITY BARRINGER. NY Times. Excerpt: WASHINGTON, May 23 – The southwestern regional director of the United States Fish and Wildlife Service has instructed members of his staff to limit their use of the latest scientific studies on the genetics of endangered plants and animals when deciding how best to preserve and recover them. At issue is what happens once a fish, animal, plant or bird is included on the federal endangered species list as being in danger of extinction and needing protection. Dale Hall, the director of the southwestern region, in a memorandum dated Jan. 27, said that all decisions about how to return a species to robust viability must use only the genetic science in place at the time it was put on the endangered species list – in some cases the 1970’s or earlier – even if there have been scientific advances in understanding the genetic makeup of a species and its subgroups in the ensuing years. His instructions can spare states in his region the expense of extensive recovery efforts. Arizona officials responsible for the recovery of Apache trout, for example, argue that the money – $2 million to $3 million in the past five years – spent on ensuring the survival of each genetic subgroup of the trout was misdirected, since the species as a whole was on its way to recovery. …Six weeks later, his counterpart at the mountain-prairie regional office, in Denver, sent a sharp rebuttal to Mr. Hall. “Knowing if populations are genetically isolated or where gene flow is restricted can assist us in identifying recovery units that will ensure that a species will persist over time,” the regional director, Ralph O. Morgenweck, wrote. “It can also ensure that unique adaptations that may be essential for future survival continue to be maintained in the species.” Mr. Hall’s policy, he wrote, “could run counter to the purpose of the Endangered Species Act” and “may contradict our direction to use the best available science in endangered species decisions in some cases.” …That would make it easier for officials to approve actions – like construction, logging or commercial fishing – that could reduce a species’s number. …Bruce Taubert, the assistant director for wildlife management at the Arizona Game and Fish Department, said of the new policy, “We support it,” adding, in the case of the endangered Apache trout, “Why should we spend an incredible amount of time and money to do something with that species if it doesn’t add to the viability and longevity of the species that was listed? By not having to worry about small genetic pools, we can do these things faster and better,” Mr. Taubert said. But Philip Hedrick, a professor of population genetics at Arizona State University, said that it made no sense to ignore scientific advances in his field. “Genetics and evolutionary thinking have to be incorporated if we’re going to talk about long-term sustainability of these species,” he said. “Maybe in the short term you can have a few animals closely related and inbred out there, but for them to survive in any long-term sense you have to think about this long-term picture that conservation biologists have come up with over the last 25 years.”

March 2004. Exploring Evolution — Comprehensive website on evolution developed especially for teachers — from UC Museum of Paleontology — history of life, as well as the evolutionary mechanisms responsible for that history; what science is and is not; A History of Evolutionary Thought; importance of evolution to society, focusing on concerns of health, welfare, and economics; Misconceptions.

Cover of Losing Biodiversity online book

Non-chronological resources

Understanding Evolution
 – one-stop source for information on evolution. 

Howard Hughes Medical Institute Holiday Lectures

Ken Miller’s website.

National Center for Science Education –  articles on evolution

The Shape of Life – videos about the evolution of the animal kingdom on earth.

Teaching About Evolution and the Nature of Science
National Academy Press 

New York Times articles on evolution

PBS-NOVA videos and resources on evolution.

Univ of Calif Paleontology Dept. – Evolution teaching materials

NSTA evolution links, publications, position statements

PBS – 2007 NOVA video about the Dover, PA “trial”