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Evolution of Biology

"Nature, like a careful gardener, thus takes her seeds from a bed of a particular nature and drops them in another equally fitted for them."
– On The Origin of Species
Evolution of Evolution: Interview with Molecular Ecologist Richard Lenski. Most of us think about evolution in the past tense. After all, we were first exposed to the concept of evolution when we saw dinosaurs and other fossils at museums. But evolution has not stopped; it is an on-going process. Provided by National Science Foundation
 
Charles Darwin may be the naturalist most responsible for changing how the world views living organisms. His theory that species change over time by means of natural selection powerfully impacted the study of biology and its various subdivisions. But it may surprise people to know that Darwin's evolutionary thesis, "On the Origin of Species," didn't have all the answers, nor did the scientific community as a whole completely agree with him. During the last 150 years, new scientific data resulted in both major and minor modifications of his theory.

 
Evolution of Evolution: Interview with Ecologist Massimo Pigliucci. Darwin would be both be bewildered and delighted at what biologists have discovered from the end of the 19th century to the dawn of the 21st. Much of the research supported by the National Science Foundation over the past several decades has resulted in a spectacular explosion of knowledge. Provided by National Science Foundation
 
Audio:
Interview with Integrative Biologist Hopi Hoekstra
 
Interview with Evolutionary Geneticist Mohamed Noor
 

Essays


From Darwin to DNA: Mice, Molecules and the Struggle for Existence —
Understanding how natural selection acts on DNA base pairs


By Hopi Hoekstra

More than any other scientist, Charles Darwin changed the way we view the world.  In providing a simple mechanistic explanation of how biological diversity is generated, he not only revolutionized the field of biology, but also the way we think about ourselves.  He argued that the apparent design we observe in nature—the close fit of organisms to their environment—could be explained by what he called natural selection, the differential success of genetic variants in a population.  It is remarkable that Darwin was able to formulate his ideas without any knowledge of the mechanism of inheritance because evolution by natural selection is an explicitly genetic theory. The complete story would not be told until a century later, with the discovery of the DNA double helix, for in this four-letter DNA code we can dissect out the mechanistic specifics—the genetic nuts and bolts—of how biological diversity arises.  Oh, wouldn't Darwin be proud!

Natural selection can act on specific DNA base pairs to contribute to variation in form, physiology and behavior. Research in our lab is focused on understanding how organisms adapt to their environment by identifying the precise DNA base pairs responsible for these modifications. One of the traits we study is coloration.  Color and color pattern can be used to hide from predators, like the white winter coats of snowshoe hares, or to attract mates, like the brilliant blue-green tails of male peacocks—even small variations in color can have a large effect on an individual's ability to survive and reproduce.

In the southeastern United States, oldfield mice (Peromyscus polionotus) typically occupy overgrown fields with dark soil, and accordingly, have a dark-brown coat, which serves to camouflage the mice from predators.  In the last few thousand years, these mice have also colonized the brilliant-white sand dunes of Florida's coasts. Here, these beach-dwelling mice are almost completely white, blending perfectly into their new environment. Using a combination of field studies, classical genetics and modern molecular biology, we are working to understand how—through changes in pigmentation genes—these mice have adapted to their new environment.

Our work has revealed several interesting patterns.  First, we have found that most of the differences in mouse fur color are caused by changes in just a handful of genes; this means that adaptation can sometimes occur via a few large mutational steps. For example, we identified a single DNA base-pair mutation in a pigment receptor, the presence or absence of which accounts for about 30 percent of the color difference between dark mainland mice and light beach mice on Florida's Gulf Coast.  To date, this is one of the few examples of how a single DNA change can have a profound effect on survival of individuals in nature.

Second, we have shown that the same adaptive solution can evolve by different genetic pathways.  Beach mice are not just restricted to Florida's Gulf Coast, but are also found over 200 miles away on the Atlantic coast.  We have shown that mice on the eastern coastal dunes have also evolved light-colored fur, but through different mechanisms: the pigment-receptor mutation causing light color in Gulf Coast mice is absent from the eastern beach mice. Thus, similar evolutionary changes can sometimes follow a different path.

Using a variety of approaches—some, like molecular biology, way beyond Darwin's ken, and others, like fieldwork, rooted firmly in Darwin's own tradition of natural history,—we are discovering the genetic basis of what Darwin called "that perfection of structure and coadaptation which most justly excites our admiration," and in so doing, provide molecular evidence for Darwin's great theory.


Hopi Hoekstra received her B.A. in Integrative Biology from the University of California, Berkeley. She completed her Ph.D. in 2000 as a Howard Hughes predoctoral fellow at the University of Washington.  For her dissertation work, she received the Ernst Mayr Award from the Society for Systematic Biology. She then moved to the University of Arizona as an NIH postdoctoral fellow, where she studied the genetic basis of adaptive melanism in pocket mice and was awarded the American Society of Naturalists Young Investigator Prize. In 2003, Hoekstra became an assistant professor at the University of California, San Diego, and was named a Beckman Young Investigator. In 2007, she moved to Harvard University, where she is a John L. Loeb associate professor of biology in the Department of Organismic and Evolutionary Biology and the curator of mammals at the Museum of Comparative Zoology. She serves as an associate editor of Evolution, a member of Faculty of 1000, on the council of the Society for the Study of Evolution and the American Genetics Association, and the scientific advisory board of the National Evolutionary Synthesis Center.

Please see the Resources section for the Bibliography/Additional Reading list for this essay.

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From Darwin's Gemmules to Evolutionary Genomics
Study of inheritance improves understanding of hybrid organisms and species formation

By Mohamed Noor

One of Charles Darwin's problems in presenting the theory of evolution by natural selection was that he lacked a mechanism for how variants, or slight differences within a species, passed from parents to offspring.  The resemblance between relatives was obvious, illustrating that one's "essence" passes to children, but how such genetic information is transferred only became widely appreciated later.  Darwin's challenge was understanding how variation persisted if inheritance involved serial blending: if one goes to a paint store and combines all paints by pairs over many iterations, eventually everything will be the same color.

To address this deficiency, he proposed the idea of "gemmules," supposed particles of inheritance secreted by cells that ultimately find their way into the germline where they mix with gemmules from the offspring's other parent.  These gemmules could acquire characteristics directly from the tissues that produced them, consistent with the idea popularized by French naturalist Jean-Baptiste Lamarck's inheritance of acquired characters theory.  More importantly for Darwin, gemmules could explain how heritable variation might persist, upon which natural selection could act to produce evolutionary change.

Since Darwin's time, the ability to study inheritance and heritable variation in an evolutionary context has grown exponentially.  Progress began in the early 1900's with the rediscovery of Augustinian priest Gregor Mendel's concept of allelic inheritance, or paired gene copies.  Mendel's theory that gene pairs, or a series of pairs, determine the characteristics of an organism gave birth to modern genetics.  It was applied to evolution soon thereafter with the suggestion that "continuous" characters like human height may be explained by variations in the coding sequence.

The last 40 years have been equally transformative, if not more so.  Evolutionary biologists capitalized on advances in genetics to understand the processes of adaptation and species formation.  Protein variation documented in the 1960s led scientists to infer the operation of natural selection at the molecular level using the "neutral theory of molecular evolution."  Albeit imperfect, the theory served as a null or statistical hypothesis against which to compare patterns of variation within a species to random changes that could happen without the presence of natural selection.  Funded by the National Science Foundation, experimentalists surveyed protein variation, DNA sequence variation at focal genes and most recently, genome-wide DNA sequence variation.  Repeatedly, they found observed patterns were inconsistent with the null hypothesis, suggesting that natural selection plays a large and ubiquitous role shaping most genomes.

Progress is somewhat slower in understanding species formation, but recent genetic approaches are having an impact.  For example, large-scale surveys show that many "good" species exchange genes with other species, creating hybrids and suggesting that reproductive isolation—the lack of genetic exchange that separates species—may be leaky initially.  Recent work by my group and others suggests that certain regions of the genome may allow such leaky hybrid species to form constantly, unlike the paint example previously mentioned.  Distinct hybrid types persist because parts of the genome in which genetic exchange is rare or absent never really mix.  This hypothesis also explains the observation that closely-related, co-occurring species often differ by chromosomal rearrangements, but the rearranged genomic regions fail to blend in hybrids and thus allow the distinct parent species to continue unaltered.  Support for this model of species persistence comes from genetic mapping studies and, as already mentioned, examination of patterns of DNA sequence variation within and between species.

Overall, genetic studies of adaptation and species formation are flourishing, as evidenced by recent studies identifying some of the genes responsible.  Interestingly, a few examples of inheritance have been described, under the broad umbrella of "epigenetics," in which the experience of an individual alters features of its offspring for one or more generations.  This idea is similar to Darwin's gemmule concept.  If such inheritance proves common, then future theory and experimentation will integrate these ideas to test their evolutionary effects.  Once again, we'll be running in a direction initially signaled by Darwin.


Mohamed A. F. Noor is a professor and associate chair of biology at Duke University in Durham, N.C. He is a recipient of the 2008 Darwin-Wallace medal by the Linnean Society of London, an honor given for "major advances in evolutionary biology" once every 50 years.  He has been active in the evolution community, recently serving as editor of Evolution, and currently as a regular member in the National Institutes of Health Genetic Variation and Evolution study section, a council member for the Society for the Study of Evolution and American Genetics Association, and as associate editor for multiple journals.  The National Science Foundation supports his research on the role of chromosomal rearrangements in the persistence of species.

Please see the Resources section for the Bibliography/Additional Reading list for this essay.

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Evolution: Past, Present and Future
Scientific knowledge may permit humans to guide future evolution

By Richard Lenski

Most of us think about evolution in the past tense. After all, we were first exposed to the concept of evolution when we saw dinosaurs and other fossils at museums. But evolution has not stopped; it is an on-going process. Charles Darwin emphasized this point when he closed On the Origin of Species by saying: "… from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."

With patience and skill, one can even watch evolution in action in some organisms. Peter and Rosemary Grant have spent decades in the Galápagos Islands observing the evolution of beak shape in certain birds, known as Darwin's finches, in response to changes in seed availability caused by a fluctuating climate and competition. Microbiologists, too, observe evolution in action, including bacteria that become resistant to antibiotics.

Because bacteria reproduce so quickly, we use them in experiments to test evolutionary hypotheses. For over 20 years and 45,000 bacterial generations, my students and I have maintained twelve populations of E. coli in small flasks of sugar water. We measure the process that Darwin discovered – adaptation by natural selection – by competing 'modern' bacteria against their ancestors, which we store frozen and then revive for the tests. Imagine if we could bring Homo erectus back to life, and challenge them to games of football and chess! In our flasks, the modern bacteria outscore their ancestors in the struggle for existence.

You might wonder if the twelve lineages improved in the same or in different ways. Just how repeatable would evolution be if, in the metaphor of Stephen Jay Gould, we could replay the tape of life? On the one hand, mutations are random, so the lineages would tend to diverge. On the other hand, selection would favor the same adaptations because they live in identical environments. We have seen many cases of parallel evolution. The individual cells in all twelve lineages are larger than their ancestors, and all are more efficient at using the glucose in the culture medium we grow them in. Also, all twelve lines have similar mutations in several genes. In other ways, however, they have diverged, including a striking case where a single lineage evolved the ability to consume citrate, another source of energy in the medium, but one the ancestors could not exploit. In fact, a characteristic feature of E. coli as a species is that it cannot grow on citrate. We are now investigating the series of mutations that enabled this transcendent change.

What does evolution hold for the future? First, we humans have changed landscapes and climates, causing some species to go extinct, allowing others to colonize new habitats, and altering the selective pressures on those that survive. We have left a profound mark on the future evolution of life. Second, the increased density and mobility of our species provides new opportunities for pathogens to gain a foothold and evolve to exploit us. We ignore evolution at our peril. Third, we humans have acquired the scientific knowledge and technological tools to guide evolution in potentially useful ways. Researchers today can combine genes from distantly related species that cannot interbreed, synthesize genes that have never existed in nature, and evolve molecules in novel contexts. Moreover, and remarkably, the processes that allow evolution have been transported from nature into artificial realms. Self-replication, mutation, recombination and competition have been introduced into computer programs – 'digital organisms' – that can then evolve to solve computational problems. Similar approaches allow electronic circuits and even robots to evolve complex and interesting functions.

Darwin would be amazed to see where his ideas have led. Not only do we understand the history of life on Earth and the mechanisms of evolution far better than anyone in his day, we can directly observe the process of evolution and harness its power toward new ends.


Richard Lenski is the Hannah Distinguished Professor of Microbial Ecology at Michigan State University. His research attracts world-wide recognition and focuses on the genetic mechanisms and ecological processes that drive evolutionary change. Lenski is a Member of the National Academy of Sciences and a Fellow of the American Academy of Arts and Sciences. The National Science Foundation supports his long-term evolution experiment with E. coli.

Please see the Resources section for the Bibliography/Additional Reading list for this essay.

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What Would Darwin Think?
An evolutionary biologist ponders Darwin's take on modern biology

By Massimo Pigliucci

With the approaching 150th anniversary of the publication of "The Origin of Species," which also happens to be Charles Darwin's 200th birthday, I am often asked, "What would Darwin think of modern biology if he were alive today?" It is a wonderful question, because of course there is no wrong answer to it. Darwin would, I think, both be bewildered and delighted at what biologists have discovered from the end of the 19th century to the dawn of the 21st. Much of the research supported by the National Science Foundation (NSF) over the past several decades has resulted in a spectacular explosion of knowledge in fields as varied as molecular genetics and genomics, physiology, developmental biology, evolutionary biology, systematics, phylogenetics and ecology. Not only have we recently decoded entire genomes of a variety of organisms, but we are moving toward modeling the complex interactions among networks of genes, trying to understand how they mold the intricate process of development. We have studied natural selection, arguably Darwin's principal contribution to science, in his beloved Galapagos finches as well as in plants, microbes and even human beings. And we have developed sophisticated views of ecological interactions from studies of populations, communities of species, and entire ecosystems.

Nonetheless, there are some major puzzles in evolutionary biology that are still largely open to inquiry, and to which I am compelled to think Darwin would turn his attention. What distinguished Charles Darwin as a scientist was a rare combination of traits that helped make him one of the most influential scientists in the history of humanity. On the one hand he was a very keen naturalist, capable of spending years carefully collecting observations and conducting experiments about the natural world. On the other hand, he was always interested in the big ideas, bent on building a comprehensive theory that explains the history and diversity of living organisms.

In this sense, Darwin would feel right at home were he alive today. Biology is not only going through an impressive period of empirical discoveries, but many think it is at the threshold of major new theoretical insights. The current version of evolutionary theory is referred to as "the Modern Synthesis," and was achieved during the 1930s and 1940s as a way to bring together Darwin's original ideas (common descent of all organisms and natural selection) with the discoveries of the new science of genetics. It was an intellectual feat that took shape over a period of decades and set the agenda for evolutionary research ever since.

According to an increasing number of biologists, we may be approaching the formulation of a new, extended evolutionary synthesis for similar reasons. The molecular biology revolution has taken place entirely after the Modern Synthesis, and has brought us a wealth of novel and often unexpected information about the inner workings of living organisms. A new field of evolutionary developmental biology (so-called "evo-devo") began to take shape as late as the 1990s, specifically to integrate developmental and evolutionary biology, something that was left out of the synthesis of the 1940s. Recent research focussed on a host of novel concepts, such as the idea that the evolutionary process itself changes over time ("evolvability"), the existence of non-genetic (so-called "epigenetic") systems of inheritance, and the fact that natural selection acts at many levels of biological organization, from genes to individuals, from populations to entire species.

All of this poses exciting challenges for evolutionary biologists engaged in both empirical and theoretical research funded by the NSF. And Charles Darwin would be delighted to be alive today.


Massimo Pigliucci is a professor of ecology and evolution at Stony Brook University in New York. He is the recipient of the Society for the Study of Evolution's 1997 Dobzhansky Prize, which recognizes the accomplishments of outstanding young evolutionary biologists.  He is a Fellow of the American Association for the Advancement of Science where he was elected "for fundamental studies of genotype by environmental interactions and for public defense of evolutionary biology from pseudoscientific attack."  Pigliucci writes regularly for Skeptical Inquirer and Philosophy Now and his essays can be found online at www.rationallyspeaking.org. The National Science Foundation supports his research on evolutionary genetics and gene-environment interactions.

Please see the Resources section for the Bibliography/Additional Reading list for this essay.

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Any opinions, findings, conclusions or recommendations presented in this material are only those of the presenter grantee/researcher, author, or agency employee; and do not necessarily reflect the views of the National Science Foundation.