An Introduction to EVOLUTIONARY BIOLOGY

An Introduction to EVOLUTIONARY BIOLOGY
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Table of Contents What is Evolution? History and Development of a Unifying Discipline Latin America and Evolutionary Biology Taxonomy, Classification, and Species Mechanisms of Genetic Variation and Earth’s Diversity Select Topics in Evolutionary Biology

What is Evolution? Evolution and the Nature of Science
In this section: Evolution and the Nature of Science The Rise of Evolutionary Biology The Development of Evolutionary Theory Modern Synthesis

Evidence for Evolution
Paleontologists study fossils that give clues to evolutionary processes Tiktaalik is one such fossil (early tetrapod) Many other scientific fields support the theory of evolution Tiktaalik is a link between fish and the earliest amphibians (and possibly all mammals, reptiles, dinosaurs, and birds). It is 375 million years old, which is when shallow water fish were first making the transition to land. This discovery, as well as a long series of others over the last 150 years, supports the theory of evolution.

Evolution and Biology Evolution provides an explanation for the diversity of life The passing down of traits is now explained by both evolution and genetics Mutations and natural selection change populations across multiple generations Evolution is a main principle of biology today; without its systems and mechanisms, many occurrences would go unexplained. Not only does it explain the diversity of life on the planet, but it also helps explain how organisms acquire traits and how lineages work. The latter concerns are also addressed in genetics, which is a relatively new field (under 100 years old). Additionally, there are mechanisms within evolution that explain why offspring are not always like their parents; mutation, for example, changes traits on a genetic level (changes can be good, bad, or neutral). Natural selection, another mechanism, is the process by which better-adapted organisms have greater breeding success while those which are not as well-adapted do not have as much success (and do not contribute as much, if at all, to the gene pool). Important note: evolution only applies to populations, never to individual organisms.

Small and Large Evolutionary Changes
Evolution produces small-scale changes over short periods of time Example: Bacteria with antibiotic resistance Large-scale changes occur over longer periods of time (speciation) Speciation and other large-scale changes can help organisms inhabit new environments Example: The amniotic egg Transitions like these, both large and small, can be found in the fossil record Small-scale changes, while limited by definition, can have significant impacts in the organisms themselves and the environment around them. In the case of some bacteria developing resistance to antibiotics, medical researchers are now forced to come up with new ways to fight these potentially deadly infections. Larger changes, though difficult to spot in intermediate stages, have just as much (if not more) significance for the organisms involved. One such large change, speciation, occurs when one species splits into two distinct species (such as when two populations become geographically separated). Often times, the populations will become better adapted to their respective environments and pass on different traits to subsequent generations, giving rise to gradually differing gene pools. One such change is the development of the amniotic egg, which allowed for the development of many reptiles (not having to go back to the water to reproduce meant they could spend more time on land, which in turn led to adaptations to a terrestrial environment).

Evolution in Various Fields
Medicine: genetic analysis of SARS virus Agriculture: artificially selecting wheat for preferred traits Industry: selecting molecules for preferred traits In medicine, knowing the genetic profile of the SARS virus allowed scientists to look at related viruses for information on treatments, vaccines, cures, and other important facts. In agriculture, wheat can be artificially selected for traits like resistance to drought, heat, and insects. In industry, chemists can select molecules that perform a certain task more efficiently or with better results and then reproduce that particular molecule for widespread use (like converting agricultural waste into ethanol).

Accepting Evidence of Evolution
Science relies on natural phenomena and testable explanations Some see the differing natures of science and religion as being in conflict Many scientists and theologians find no conflict They can reconcile the two explanations of the world Evolution is still considered a theory, but has been widely accepted as a fact Science has strict requirements about what is considered “scientific”, in that all scientific concepts must be based on natural, observable phenomena and questions must be testable (not only to be potentially proven, but also potentially disproven). In religion, there are no such stringent criteria, and many religious concepts are accepted as fact within a denomination without being testable or observable. Despite these differences, a person who can understand the distinctions and accept science and religion as fundamentally different is often able to reconcile the two ways of thinking. In terms of the categorization of evolution, is it still considered a theory in a technical sense, but the overwhelming evidence in support of evolution (and long-standing scientific acceptance of it) mean it is often treated as or called a fact.

Descent with Modification
Dobzhansky says, “nothing in biology makes sense except in the light of evolution” Evolution means change between generations, or “descent with modification” A lineage is dependent on an ancestor-descendent relationship Theodosius Dobzhansky ( ), one of the most famous evolutionary biologists of the twentieth century, believed that the theory of evolution connected everything in biology and explained phenomena that were previously unexplainable. The exact definition of evolution has shifted in the last 150 years, but is generally accepted to be “descent with modification”, or the change that occurs between multiple generations of a population. The concept of a lineage is important in this definition, because a given lineage is the history of populations through time (a theme of major importance in evolution).

Adaptation Adaptation is “design” in living things
Adaptation allows organisms to survive and reproduce Examples include the woodpecker’s beak and camouflage Adaptation is what allows organisms to be “fit” in a given environment. The woodpecker evolved its beak in order to reach its food; better beaks meant more food, which meant healthier birds, which meant more offspring. This influx of “well-beaked” woodpeckers into the gene pool meant that the entire population would shift towards having better beaks. The same is true for camouflage and for millions of other adaptations.

Evolution Before Darwin
Jean-Baptiste Lamarck wrote Philosophic Zoologique in 1809 Lamarck argued that animals “strived” to adapt (in place to natural selection) Others before Darwin believed in species fixity The idea that species never change Jean-Baptiste Lamarck was a scientist who attempted to explain changes in organisms over time. His theory is known as “transformism”; in it, animals change through conscious effort. The most famous example of this is the giraffe: Lamarck’s theory states that the giraffe got its long neck after “willing” itself to reach higher and higher branches. Each successive generation would start out with longer necks, stretching them over the life of the giraffes, then passing on these even longer necks to the next set of offspring. As wrong as this concept is known to be today, even further from what we know to be true today was the popular belief that species each came from unique origins and never changed. That would mean that giraffes were placed on Earth as we know them today and have not changed ever. This concept was easily reconcilable with the Biblical version of creation, and was widely accepted.

Charles Darwin’s Arrival and Reception
After his voyage on the Beagle ( ), Darwin failed to reconcile all current theories with the concept of adaptation Darwin created his own theory, which included the concept of natural selection; Alfred Wallace also arrived at this conclusion on his own Darwin and Wallace presented their findings in 1858 The theory seemed to contradict the Bible and was controversial among laymen, but was somewhat less so among scientists The voyage on the HMS Beagle was pivotal in the life and career of Charles Darwin. The five years he spent traveling the world allowed him to observe many different environments and thousands of species of plants and animals. Particularly important was his stay at the Galapagos Islands off the Pacific coast of South America; there, he was able to see speciation and adaptation taking place across several islands. This, along with many other observations, led to Darwin’s development of the theory of evolution. Incorporating adaptation and change over time (as well as concepts like extinction) made Darwin’s theory very different from the other ideas of the time. In a strikingly similar theory, Alfred Wallace came to the same conclusions that Darwin did, and the pair presented their combined theory to the Linnaean Society in While most non-scientists were offended on a religious level, scientists had concerns about the theory that were of a different nature.

Flaws in the Theory of Evolution
Darwin’s theory of evolution lacked a means of heredity, meaning that there was no mechanism to explain the passing down of traits Natural selection insufficiently explained intermediate forms in evolution (like proto-wings), which were seen as better explained by directed variation Charles Darwin’s theory proved an interesting one for scientists to study, but they soon began to pick it apart when it became obvious that the theory could not sufficiently explain heredity. Though Darwin made it clear that traits were passed down and that this led to variation between generations, he could not explain what mechanism or force was causing these traits to be passed down and why there were always changes between generations (which, cumulatively, led to evolution). Scientists were also reluctant to take on natural selection as the driving force of change because it appeared to be a random processes (not true, but they thought so) and it couldn’t explain where some morphological changes came from. A popular example is that of the bird’s wing: if having a fully-developed wing is beneficial but having a partially-developed (or proto-) wing is not beneficial, why would natural selection choose to keep passing on the partial wing trait? If natural selection did not act with foresight (and it doesn’t), then there would be no reason for it to keep developing a wing if only the finished product was helpful. When Darwin was unable to explain this phenomenon, scientists turned to directed variation, which stated that there was a force behind these changes and that offspring would evolve in the direction that their parents had “strived” for (Lamarck again).

Mendelian Genetics Gregor Mendel explained how traits were passed down from one generation to the next His pea plant experiments ( ) explored concepts of hybridization, and dominant and recessive phenotypes Mendel mailed his findings to Darwin, who never looked at them A rediscovery of Mendelian inheritance in the early 1900s led to a marriage between that theory and Darwin’s theory of evolution Mendelian genetics (also known as Mendelian inheritance) is a theory in biology concerning how traits are passed down in diploid organisms. In short, each offspring has half of its genetic material from one parent and the other half from the other parent. Color is frequently used as an example; if one parent is red and one is blue, there are four possible outcomes: rr, bb, rb, and br. If one allele is dominant, meaning that it can hide other non-dominant alleles. If red is dominant, the outcomes could be: RR, bb, Rb, bR. In all except the “bb” offspring, the red color would be apparent while the blue color would be hidden (if present). Only two parents who are homozygous with the recessive allele will be guaranteed to produce offspring with the recessive trait (in our example, only two “bb” parents will definitely have “bb” offspring). If neither the red nor blue traits expressed dominance, there would be one red, one blue, and two purple outcomes in the breeding of two heterozygous parents. Mendel discovered this and other aspects of genetics. Originally, there was much scientific resistance to his theories, and his work went largely unappreciated at the time. In the early twentieth century, however, Mendel’s work was rediscovered and subsequently combined with Darwin’s theory of evolution. This combination is known as the Modern Synthesis.

The Modern Synthesis Fisher, Haldane, and Wright all published materials supporting a connection between Darwinian evolution and Mendelian genetics Combined with natural selection, Mendelian inheritance answered all the questions initially raised in 1858 Publications of Interest: R.A. Fisher – a 1918 paper and The Genetical Theory of Natural Selection (1930) J.B.S. Haldane – The Causes of Evolution (1932) Sewall Wright – “Evolution in Mendelian populations” (1931) and a four-volume treatise ( ) These three scientists, along with Julian Huxley, are considered to be the “founding fathers” of the Modern Synthesis. In their various papers and books, they explored the relationships between Mendelian genetics and Darwinian evolution, with special focus placed on natural selection and adaptation. These publications made two major contributions: they finally answered all of the questions initially raised when Darwin’s theory was first published, and they reconciled two apparently distinct theories into one combined area (the Modern Synthesis).

Further Development of Evolutionary Biology
Dobzhansky, Ford, Kettlewell, Mayr, Huxley, and many others published materials on genetics and evolution The concepts of genotypes and gene pools were incorporated into the new way of thinking Publications of interest: Julian Huxley – Evolution: the Modern Synthesis (1942) Theodosius Dobzhansky – Genetics and the Origin of Species (1937) E.B. Ford – Ecological Genetics (1964) G.C. Robson and O.W. Richards – The Variation of Animals in Nature (1936) Richard Goldschmidt – The Material Basis of Evolution (1940) Ernst Mayr – Systematics and the Origin of Species (1942) Jepsen et al. – Genetics, Paleontology, and Evolution (1949) -> this was the publication of the Princeton Symposium Following the first connections between Mendelian inheritance and Darwinian evolution, a great number of books was published to make connections between these fields and other areas of science (as well as to recount specific studies that supported aspects of the Modern Synthesis). Additionally, genetic concepts like genotype (an individual genetic profile) and gene pool (the genetic information for an entire population) were incorporated into the theories as more detailed genetic information became available through widespread research.

Pre-Darwinian Evolutionary Thought
Ancient Greeks had theories on evolution James Ussher calculated the earth’s age to be roughly 6,000 years old according to Genesis Hutton, Lyell, Linnaeus, Buffon, E. Darwin, W. Smith, Werner, Cuvier, and Lamarck all contributed to evolutionary theory Anaxiamander (Greece) and Lucretius (Rome) first proposed the concept of all life being related and changing over time, and Aristotle later supported this concept with his Scala Naturae or Ladder of Life. Following this time period, there was a lack of development in this area because of the seeming incompatibility of evolution with biblical timelines (such as James Ussher’s October 22, 4004 B.C. “birth date” for Earth). James Hutton developed the Theory of Uniformitarianism, which was later refined by Charles Lyell in the 1800s. Carl Linne (or Linnaeus) attempted to categorize all living things into groups. Georges-Louis Leclerc, Comte de Buffon released a massive work in which he provided evidence for descent with modification and other key evolutionary concepts, but was concerned about making too many waves and did not present his ideas with the forcefulness or staunch support that would have been needed to make them stand out. Erasmus Darwin, Charles Darwin’s grandfather, published his own works on botany and zoology, and though he believed in evolution, he had no mechanism to explain the process. William Smith developed the Principle of Biological Succession (as seen in stratigraphy). Abraham Gottlob Werner and Baron Georges Cuvier supported catastrophism (along with Louis Agassiz). Jean-Baptiste Lamarck came up with the theory of transformism as an explanation of evolution.

Darwin and the Wallace-Darwin Theory
Darwin’s Theory The Wallace-Darwin Theory Adaptation Variation Over-reproduction Natural selection Variability in traits Over-reproduction Variability in fitness Fitness determines success Heritable traits and change between generations Darwin’s theory had four major points: organisms adapt to their environments, organisms are variable in their traits, populations will always tend to reproduce beyond the environment’s capacity (this concept was based on the work of Thomas Malthus), and that the variability in fitness would lead to natural selection. The combined Wallace-Darwin theory shares many of these facets, though it separates Darwin’s point #2 into two sections: variability in traits and variability in fitness. The second set’s final two points include both the concepts of adaptation and natural selection, which are organized differently in Darwin’s list. The use of Thomas Malthus’ work by both lists displays his deep influence, and Darwin and Wallace were also influenced by Charles Lyell, the famous geologist.

Concepts in the Modern Synthesis
Genetic definition of evolution: “changes in allele frequencies within populations” Alleles are different versions of the same gene Sources of these changes include genetic drift (random changes), gene flow (exchanges between populations), mutation pressure (copying errors in genetic replication), and natural selection (“survival of the fittest”) Mendelian genetics added a great deal of information to Darwin’s theory of evolution; this marriage allowed for the development of many concepts. An important one is that of the allele: each gene has multiple versions called alleles, and which alleles get passed on to future generations will decide what traits show up in those generations. For example, if the gene is “hair color”, the alleles can be “red”, “black”, “light brown”, and so on. Knowing what these allele frequencies can do to a population, it is important to know how gene frequencies can change. Genetic drift is the random change that occurs within a population (for example, an allele will fail to make it to future generations for no particular reason, or an allele will become fixed at 100% simply by chance). Gene flow is the exchange of material between populations. Mutation pressure is the force exerted on a population when mutation comes into play (mutation, as far as evolution is concerned, is the erroneous copying of genetic material from parent to offspring). Finally, natural selection selects certain alleles to become more or less frequent depending on the alleles’ relationship to fitness.

Darwin and the Galapagos
In this section: The Voyage of the HMS Beagle Chapter XVII: Galapagos Archipelago (excerpt from Darwin’s journal) Adaptive Radiation of Darwin’s Finches

Darwin’s Background Raised in the Anglican Church
Loved science, went to medical school (1825) Dropped out after witnessing surgery on a child with no anesthesia Joined Christ’s College at Cambridge to study religion and pursue science in his spare time Born in 1809, Darwin had two famous grandfathers: Erasmus Darwin (physician and scientist) and Josiah Wedgwood (manufacturer of fine pottery). When Darwin was young, he enjoyed spending time in the outdoors, which was considered a suitable hobby for a young man; however, his inclination towards science was thought of as a past time, not a career option. In 1825, Darwin went to Edinburgh University to study medicine, which his family thought would suit him given his scientific leanings. However, Darwin left medical school after he saw surgery being performed on a child; this was before anesthesia was invented, and Darwin was horrified at the procedure. In 1827, he was sent to Christ’s College at Cambridge to study to join the Anglican clergy. This left him enough leisure time to explore the world of science.

Before, During, and After the Beagle
Two watershed events for Darwin: he re-read his grandfather’s book and later witnessed his professor, Adam Sedgwick, making a scientific error Professor Henslow recommended Darwin for the Beagle Darwin got along with Captain FitzRoy most of the time During the voyage, Darwin collected many specimens of flora and fauna Back in England, he married and had 10 children Darwin returned in poor health and stayed that way until his death in 1882 Darwin had two important experiences between his enrollment at Christ’s College and his trip on the Beagle. First, he re-read his grandfather’s book, Zoonomia, and realized that Erasmus had presented many theories without any direct evidence. Second, he watched while his professor, Adam Sedgwick, disregarded evidence that did not fit with his theory (in this case, a tropical shell found in Wales, which is not a tropical place). Darwin saw both of these men’s actions as grievous errors, and vowed to collect as much evidence as possible before creating a theory and not to ignore any evidence that may contradict his theory. His chance to collect enormous amounts of data came when he was recommended to the HMS Beagle by professor John Henslow. Captain Robert FitzRoy took Darwin aboard, where the crew nicknamed Darwin “flycatcher”. The captain and Darwin got along well at most times, but there was a famous incident in which the pair argued about slavery, after which Darwin was banned from the captain’s table for a short period of time. During the voyage, Darwin took ill, and was bedridden for several weeks following the bite of a disease-carrying insect. His health never fully returned. Despite this, Darwin was able to collect a great deal of information, particularly at the Galapagos Islands off the coast of South America; the small size of the islands and their relative isolation made them a good place to study changes in species and other evolutionary mechanisms. Darwin studied tortoises, lizards, and a wide variety of finches. Finally, when the ship returned in late 1836, Darwin settled down to organize his notes and start a family. He married and had ten children. It took him twenty years to publish his thoughts in On the Origin of Species, which was published 24 years before his death at the age of 73.

The Voyage of the Beagle
The Beagle left England and went to the following areas: Tenerife, Cape Verde, Bahia, Rio de Janeiro, Montevideo, the Falkland Islands, Valparaiso, Lima, the Galapagos Islands, Sydney, Hobart, King George’s Sound, Cocos Island, Mauritius, Cape Town, Cape Verde again, the Azores, and then back to England (Falmouth).

Darwin’s Journal: Introduction
The text in the guide has been condensed He gives credit to Owen, Waterhouse, Gould, Jenyns, and Bell for influencing his work He thanks several colleagues, especially Professor John Henslow, who helped him (from London) during the voyage Darwin’s introduction reads like an acknowledgements page rather than a true introduction: he thanks nearly a dozen scientists, colleagues, writers, friends, and others who helped him either through their own works or by directly assisting Darwin in his own studies. He does, however, note that the journals presented here are condensed and edited, which is surprising after one reads the amazing details and lengthy descriptions of various plants and animals on the islands.

The Galapagos The Galapagos Islands are a group of volcanically-created islands off the Pacific coast of South America. They are closest to the modern country of Ecuador. The island names above are the designations Darwin used, though they are now referred to by their Spanish names.

September 15th-23rd There are ten Galapagos islands, all south of the Equator, spotted with many craters, and volcanic in origin Chatham Island had relatively few plants, only giant tortoises and some dull-colored birds Charles Island had been frequented by buccaneers and whalers, now inhabited by political exiles and others Darwin’s assessment of the Galapagos islands is not warm at first: he notes that the plant and animal life that he encounters early on is dull and not “equatorial” in nature, and that most of the sea-level life is scarce. He attributes this to the lack of rainfall, and notes that higher elevations on the islands have much more lush and interesting life forms because there is more moisture up there. In his specific assessments of Chatham and Charles Islands, he notes that Chatham is rather boring in biological terms, but Charles has a greater variety of life. The inhabitants who live on Charles Island are mainly those who have been exiled from Ecuador; he states (with some incredulity) that they claim to be poor, yet only have to hunt for two days in order to eat for the rest of the week. In addition to local fruits, the people eat tortoise meat.

September 29th Darwin visited Albemarle Island and Narborough Island
Both were covered with black lava formations and much of the islands was sterile There were black lizards on Albemarle, as well as yellow-brown ones While all the islands in the Galapagos supported some life, a few of the islands were not as lush or interesting as Darwin would have preferred. Albemarle and Narborough were of this type; though there was life, it was not varied or strange enough to make Darwin want to stay on these islands for an extended period of time; part of that, however, may be related to the Beagle nearly being stuck with no wind in between these two islands. Darwin was also disappointed to find that a large portion of these islands did not have any life at all.

October 8th – James Island
Darwin came across a group of Spaniards, as well as other small groups Darwin learned that tortoise meat can be prepared a number of ways, and also visited a salina Measured the temperature in various instances: the sand was at least 137º F James Island provided Darwin with a great deal of information, even though he did not spend much of his time studying the wildlife. He learned about various ways in which tortoise meat is prepared (the Spaniards there were salting it for transport), and also went to a salina, or lake from which salt is procured. Darwin’s writings include a section on the oppressive heat on this island: when the winds died down, it became unbearably hot. It could reach 93º inside a tent, but the sand was at least 137º (the thermometer would not go any higher). Following these observations, Darwin moved away from island-specific chronicles and began to look at his data more specifically.

Mice, Land Birds, and Water Birds
Mus Galapagoensis was the only indigenous terrestrial mammal (and mouse) Darwin caught 26 land birds, 25 of which were unique to the archipelago He also caught 11 water birds, only 3 of which were new species Mammals and water birds did not seem to excite Darwin nearly as much as the land birds did, presumably because there were so many new species of land birds to be found. He documented hawks, buzzards, Polybori, owls, wrens, doves, swallows, thrushes, and finches. It was the last of these, the finches, that caught Darwin’s special attention. All of these were new species, and there were 13 different varieties on the islands. Later analysis of these species shows that the finches are a perfect example of adaptive radiation.

Reptiles – the Tortoise
Darwin discovered snakes, lizards, tortoises, and sea turtles He was surprised to find no toads or frogs at all, even though the environment seemed ideal for them (perhaps egg differences?) Tortoises travel to water sources, sometimes four miles a day The inhabitants believed the tortoises to be deaf Darwin spends several paragraphs discussing the absence of frogs from the Galapagos. Though he thinks that the environment is suitable for them, he comes to the conclusion that lizards may be able to survive here because their eggs are more easily transported across bodies of salt water, while the frogs may have difficulty doing the same. As for the tortoises, Darwin spends a great deal of time observing them, including measuring their traveling speed and even riding them multiple times (he was unable to do so successfully). The locals believed that the tortoises were totally deaf because it was so easy to sneak up on them without arousing any reaction until the person passed the tortoise.

Galapagos Lizards Amblyrhynchus cristatus Amblyrhynchus Demarlii
Aquatic: lives on rocky sea beaches About a yard long Eats only seaweed When frightened, it will allow itself to be captured rather than jump in the ocean When thrown in, it will come out and return to the previous spot Terrestrial: lives in burrows Confined to the central islands Smaller than the aquatic ones Eats cactus and other vegetation Will fight another lizard if held next to it Darwin provides great detail on both the Amblyrhynchus lizards on the Galapagos Islands. The aquatic lizard fascinated him because it survived entirely on marine vegetation. He was also interested in the lizard’s behavior when cornered: when Darwin would scare it and trap it on a cliff, it would rather face the consequences on land than dive into the ocean. Darwin also noted that when he threw the lizards into the ocean, they would swim right back and go to the exact spot they had been before. With the terrestrial species, Darwin also experimented with annoying the lizards. In one case, he kept pulling them out of their burrows by the tail, but they did not retaliate. When he held two lizards together and did not let them escape, they would bite each other, even though they never tried to bite him.

Shells, Insects, and Plants
Darwin collected 90 shells, of which 47 were previously unknown Also collected several insects, most of which were new species, but was surprised by how few there were Collected 100 new species of flowering plants Was extremely surprised that fewer American species of flora had not arrived at the islands through natural means, given the short distance between the two locations After the detailed analysis of reptiles, Darwin provides fewer details for other animal and plant types. He documents that he found many new types of shells, insects, and plants, but at this point in his journals he begins to make more broad generalizations (and ask broad questions) rather than stick to the extreme level of detail in earlier sections. He muses about the amazing variety between the islands, and wonders why the species on each island are so different if the environments are so similar (and the distances between them are so small).

The Tameness of Birds Darwin noted that birds were not afraid of humans The birds could be killed from close range even after other birds had been killed nearby Darwin believed this to mean that an instinct to avoid humans would have to be passed down through multiple generations From his journals, it seems that Darwin spent a great deal of time annoying, harming, and even killing the animals of the Galapagos (though, to be fair, biological studies at the time were always conducted by first killing the animals to be studied). His dealings with birds are no different; he experimented by killing them in various ways, including many close-range methods. It seemed that no matter how many birds he killed, other nearby animals became no more afraid of him and were not aware of any rising danger. Darwin concludes that a fear of humans must be passed down after several generations of contact between animals and humans, and cannot be learned by individuals and passed around as a warning within the same generation.

Adaptive Radiation Adaptive radiation is the diversification of populations into ecological niches Four key concepts: Origins Speciation Diversity Disparity Adaptive radiation is typically shown in the diagram of the tree of life. The branches, radiating out and up, represent the process of speciation, with each new branch representing a new line, and twigs representing species. The process of new species radiating out to fill ecological niches is known as adaptive radiation. The tree of life also helps visualize concepts like extinction, which can be represented by branches that don’t continue to develop. Adaptive radiation brings up four key questions: “Where did the ancestors come from, when and how? How and why are new species formed? Why are there x number of species? Why are these species as different, or as similar, as they are?” (USQRG, pg. 46)

Finches and Speciation
Darwin’s finches are unique because of their rapid diversification and relative youth (3 MYA) Allopatric speciation: geographic separation Sympatry can lead to interbreeding with or without fitness loss or no interbreeding Compared to animals on Hawaii and other island chains, the Galapagos finches are unique because they underwent speciation so rapidly and because the process began so recently (3 million years ago). The exact species of bird that began the process is unknown, but it likely came from the mainland of South America and then colonized the Galapagos. Mitochondrial DNA studies have helped pin down all of these facts. When compared to the Hawaiian honeycreeper, the finches have a much faster species doubling time (.75 million years vs. over 1 million years for the honeycreeper). The model that best explains the rapid diversification of the finches is the allopatric model. In allopatry, different populations of the same species are separated geographically (in this case, by flying to different islands). Once separated, each population adapts to its respective environment and begins to change. When (and if) the populations encounter each other again (known as sympatry), there are three possibilities: interbreeding with no fitness loss (no speciation), interbreeding with fitness loss (no speciation), and no interbreeding (speciation). Though the ability to interbreed is the cornerstone to the definition of species, there is still no agreed-upon all-purpose definition, which poses a problem in biological studies.

Environmental Factors
Sympatry is not required for speciation Not all islands might have existed when speciation began A changing environment has significant effects on adaptive radiation Sympatry, the geographic combination of different populations, is not required in the new model of allopatric speciation. It was originally assumed that when different populations had diversified enough, they could co-exist in the original environment; while this might be true, it is not necessarily a fundamental step in the speciation process. Additionally, the model for allopatric speciation must be changed to account for environmental changes that take place during the process. If new islands appeared, climates changed, or food sources shifted, those changes would have far-reaching consequences for all populations involved in the speciation being studied.

Adaptation and Reproductive Isolation
1977 drought: populations of small finches decreased (no small seeds) c drought: populations of large finches decreased (no large seeds) Dynamic equilibrium Medium ground finches respond to cues from their own species even when genetically able to hybridize Two droughts took place on the Galapagos in recent years (1977 and nearly 10 years later). The first drought happened to reduce production of small seeds, which meant that the primary food source for small-beaked finches was removed and hence their populations decreased. The second drought had the inverse effect, in which larger seeds were absent and larger-beaked finches suffered. This set of circumstances displays the effects of environmental factors on evolution and adaptive radiation. The idea that, even with short-term changes like these, populations will more or less even out is known as dynamic equilibrium. Another important concept in speciation is the reproductive isolation of populations that co-exist. Even in situations where two different species can hybridize, they will often seek out mates of their own species, often by visual cues or songs. This behavior leads to further separation and speciation.

Finch Songs Songs are learned traits passed down from parent to offspring Songs are particular to populations, not necessarily entire species Changes in environment can lead to natural selection of different songs than those of a parent species Some changes to songs are by chance, not natural selection alone Finches learn the songs of their parents and subsequently seek out mates that know the same song. When a population moves to a new environment, such as colonizing a new island, there are many factors that may change that song: a random sampling from the original “home” population means that some will be left out, there will be some random errors (like a social mutation) in transmitting the song, rare variants may increase through selection or random chance, and morphological changes (like bigger bodies or different beaks) may change the voice box and hence change the song. All of these factors lead to shifts in finch songs.

Adaptive Landscapes Genotype and phenotype frequencies can be plotted on a 3D landscape to determine fitness Areas of best fitness are known as peaks An adaptive landscape is a 3D graph that uses two morphological (or phenotypic) qualities for two axes with fitness as the third axis. In the case of finches, beak size and body size provide good axes. Relatively big bodies and big beaks constitute a peak of fitness, while those in the medium range may not be as fit. A different type of visualization for evolution is the river of life. Instead of a tree, which is a helpful but limited metaphor, the river includes concepts like hybridization, twigs never becoming branches (species never spawning larger groups), and other ideas within evolution.

Adaptive Landscape and the River of Life
Genotype and phenotype frequencies can be plotted on a 3D landscape to determine fitness Areas of best fitness are known as peaks The river of life is a visual metaphor that may replace the tree of life (accuracy) An adaptive landscape is a 3D graph that uses two morphological (or phenotypic) qualities for two axes with fitness as the third axis. In the case of finches, beak size and body size provide good axes. Relatively big bodies and big beaks constitute a peak of fitness, while those in the medium range may not be as fit. A different type of visualization for evolution is the river of life. Instead of a tree, which is a helpful but limited metaphor, the river includes concepts like hybridization, twigs never becoming branches (species never spawning larger groups), and other ideas within evolution.

Taxonomy, Classification, and Species
In this section: Classification Taxonomy

Taxonomy, Traditional Classification, and Cladograms
Aristotle, John Ray, Carolus Linnaeus, and Robert Whittaker all made significant contributions to taxonomy Classifications from largest to smallest: Kingdom, Phylum, Class, Order, Family, Genus, Species Traditional classification focuses on common ancestry and amount of divergence (major characters) Cladograms focus on derived characteristics and incorporate parsimony Taxonomy belongs to the larger scientific study of systematics. The goal of systematics is to determine phylogeny. For each organism, there are specific nested categories (listed in the slide) that create a map of the interconnectedness of all living things. Linnaeus came up with the key concept of binomial nomenclature, which gives all organisms two names (genus and species) that are not dependent on the spoken language of the scientist. One type of classification, traditional, focuses on the apparent characteristics of species in order to classify them. For example, the amniotic egg would be considered a major character, and would be used to unite related species together under one larger taxon. Cladograms, used in cladistics, also uses major characters, but does not focus on the overall similarity of any organisms. Otherwise dissimilar organisms might be placed together in a cladogram because they share one important derived character. An important concept in cladograms, parsimony, means that the fewest number of evolutionary steps is usually correct. For example, a bird would have developed a wing along a series of changes that get to the final result as efficiently as possible; it would not make evolutionary sense for the bird to have developed arms then flippers then wings.

Cladistics vs. Phenetics
Uses one or more derived characters Focuses on lineages and common ancestry Does not include overall similarity Uses algorithms to determine similarity Mathematical and objective Not used very often, but helpful in objective studies Cladistics is a classification method that uses one or more derived characters to group organisms together. “Derived characters” refer to those that come from a shared ancestry. Unlike traditional classification and phenetics, cladistics does not focus on overall similarity. Phenetics is very different from both traditional classification and cladistics in that it uses mathematical formulas to calculate overall similarity. Though this particular method is not used very often, the algorithm approach has proved very useful in the computer age.

Nomenclature According to the International Code of Botanical Nomenclature: All taxa belong to a higher taxonomic group The first name for a new species to be published is considered valid (the “dibs” rule) All new taxa must have an author In any worldwide classification system, there needs to be clear policies so that naming and classification can be consistent. According to the International Code of Botanical Nomenclature, all taxa (species) must belong to a higher group, the first name for a species to be published gets “dibs” on that species, and all species must have an author. For example, Homo sapiens L. is the designation for modern humans, where Homo is the genus, sapiens is the species, and L. stands for Linnaeus, who first put a Latin name to the species.

Definition of a Species
Unlike all other categories (e.g. Kingdom), species are not an artificial construct, and actually exist in nature Reproductive compatibility typically defines a species (can these two animals have fertile offspring?) Asexual reproduction and grey areas make this definition imperfect Because there is a biological mechanism that creates the distinction of “species”, the taxon is unique among all classification groups in that it is not a human construct. Unfortunately, other than knowing that species are naturally occurring groups, it is difficult to pin down an exact definition. Some animals asexually reproduce, and sometimes two different species produce fertile offspring, so how is reproductive compatibility the definition of a species? Ultimately, a combination of the biological definition and morphological characteristics help scientists determine which organisms are separate species, but the lack of a concrete definition is still very frustrating to those in the field.

Nomenclature and Classification
Taxonomic keys help scientists determine which species an organism is Evolution and lineages determine the closeness of relationships in classifying multiple organisms Taxonomic keys help standardize the way scientists classify organisms. One such way, the dichotomous key, uses specific “this or that”-style choices which help scientists distinguish between different species. The relative simplicity of the dichotomous key is the reason it is so successful. Additionally, scientists use the evolutionary histories of organisms to help determine how they should be classified. Derived characters come into play here.

Example of Dichotomous Key
Dichotomous keys use technical language in simple steps to help classification This is one example of a dichotomous key, which is used to determine exactly what an organism is. By answering a series of this-or-that questions, the scientist can determine the taxonomy of a particular organism.

Methods of Classification
Phenetics (numerical taxonomy) uses algorithms for an objective classification Cladistics is the most popular and focuses on lineages Evolutionary taxonomy is a combination of the two, but considered arbitrary by most scientists Phenetics and cladistics (already discussed) are two of the most popular methods, with cladistics being the most widely used. Evolutionary taxonomy, though it seeks to bridge the gap between the two methods, fails to do so successfully because the classification method is far too arbitrary to produce reliable results.

Kingdom Systems Kingdoms, ranging in number from three to thirteen in some systems, are the largest taxonomic group The most common is a five kingdom system, but it is being replaced by a six kingdom model The organization of kingdoms dictates how all other groups will be organized further down the taxonomic ladder. The three kingdom system only has the groups Archaebacteria, Eubacteria, and Eukaryota. Many find this to be insufficient. The five kingdom system includes Monera, Protista, Fungi, Plantae, and Animalia. In the six kingdom model, Monera is divided into Eubacteria and Archaebacteria. The five kingdom system has recently come under fire because it is not based on evolutionary lineages. Cladistic taxonomists seek to solve this problem with the three kingdom system.

Mechanisms of Genetic Variation and Earth’s Diversity
In this section: The Evidence for Biological Evolution Evolutionary Mechanisms Introduction to Evolutionary Biology On the Many Origins of Species Speciation Standing in Place

Contributions From Other Areas
Paleontology: fossils Genetics: DNA Astrophysics and geology: age of the earth Physics and chemistry: dating methods Anthropology: human origins In addition to the contributions of evolutionary biologists, there have been many developments in other areas of science. Paleontology has provided information about life forms of the past and how they relate to surrounding rocks, genetics has decoded hundreds of genomes, astrophysics and geology have revealed information about the age of the earth and the universe, physics and chemistry have developed dating methods (like radiometric dating), and anthropology has revealed insight into human origins.

Origins of the Universe and Earth
Georges Lemaitre: the Big Bang theory Background radiation and distances allow for dating of the universe Universe: 14 BYA Earth: 4.6 BYA Moon: BYA A Roman Catholic priest, Georges Lemaitre, came up with the idea of the Big Bang: a massive explosion that started the universe as we know it. The Big Bang began with a singularity, an infinitely small, hot, and dense mass containing all the matter and energy in the universe. The singularity expanded and began to cool, which allowed for chemical reactions to occur. This was approximately 14 billion years ago; our Milky Way galaxy was formed just shortly following this. It took almost ten billion years for the earth to coalesce into a planet. Shortly following this event, the moon was formed.

Life’s Formation on Earth
Life is at least 3.5 billion years old Life required three conditions to form: self- reproducing molecules (RNA?), enough molecules for variation, and heritable variations Protocells with variations led to natural selection Life on Earth dates back to 3.5 billion years ago, only 1.1 billion years after the planet was formed. In order for the process to begin, there had to be molecules that could reproduce themselves, there had to be a large enough number of molecules for there to be variation, and that variation had to be heritable. When the first protocells on the earth formed, they exhibited variation, which kick-started natural selection (when there is variation, that means some variants are fitter than others). Some scientists believe that RNA may have had the qualities necessary to be involved in the development of the first life on the planet.

The Fossil Record Newer sediment deposits are closer to the surface (and those fossils resemble modern organisms) 540 MYA: hard-bodied organisms begin to dominate the fossil record Tiktaalik is a transitional form Archaeopteryx: dinosaur-bird? The fossil record includes the remains of many millions of species that have inhabited the earth. Fossils closer to the surface are more recent and more closely resemble living things today, while fossils buried deeper are older and do not as closely resemble today’s organisms. About 540 million years ago, the first hard-bodied organisms became the dominant life forms in the fossil record, replacing simpler soft-bodied organisms. This move is one of many transitions that have taken place in the history of the planet. One such transition, the move from aquatic to terrestrial life, is represented by Tiktaalik, an early tetrapod that had traits appropriate for both land and sea survival. Another transition, that from dinosaurs to birds, may be represented by the fossil Archaeopteryx, which appears to be a feathered dinosaur-bird.

Homologous and Analogous Structures
Homologous structures look similar and come from a common lineage. For example, the forelimbs of several animals (humans, dogs, whales, birds) have similar bone structures and all developed in a common ancestor of all these modern species. Analogous structures may also look similar, but do not come from a common lineage. Often, structures of this nature appear similar because the two organisms share an environment and have each adapted a similar solution to dealing with that environment. An example of one such structure of the dolphin’s flipper and the shark’s fin. Although they look very similar, the two animals evolved along different lines and just happen to have developed an effective appendage for the oceans in which they life. Homologous structures are morphological characteristics in multiple organisms that come from a single ancestral lineage (like human arms and dog forelimbs) Analogous structures look similar but do not come from a common ancestral origin (like a dolphin’s and shark’s front fins/flippers)

Evolution and Geographical Distribution
There is a great deal of variation in living things because there is so much variation in the environment. Adaptive radiation functions to allow organisms to become highly specialized and fill ecological niches; this specialization means that organisms that began as one species can rapidly become two or more species because they are changing to be better fit to their environments (as seen in the splitting of branches on the tree diagram). Often times there is a colonizing species that arrives at an environment with many available niches, and different populations splinter off to colonize different areas, thus beginning the adaptive radiation. There are many factors that dictate how a species will evolve, some of which include precipitation levels, elevations, and soil types.

Evolution and Geographical Distribution
Organisms live in so many different places because evolution (via adaptive radiation) produces a variety of life forms suited to ecological niches Variations in precipitation levels, elevations, soils, and other factors lead to rapid speciation in colonizing species There is a great deal of variation in living things because there is so much variation in the environment. Adaptive radiation functions to allow organisms to become highly specialized and fill ecological niches; this specialization means that organisms that began as one species can rapidly become two or more species because they are changing to be better fit to their environments (as seen in the splitting of branches on the tree diagram). Often times there is a colonizing species that arrives at an environment with many available niches, and different populations splinter off to colonize different areas, thus beginning the adaptive radiation. There are many factors that dictate how a species will evolve, some of which include precipitation levels, elevations, and soil types.

The Impact of DNA DNA provides clues to past genetic changes
According to genetic information, humans are closely related to chimpanzees, but increasingly far from gorillas, mice, chickens, and puffer fish DNA shows how much all life on Earth has in common Looking at DNA, scientists have been able to find out a great deal about current life forms, past life forms, evolution, and the commonalities of all life on Earth. Humans are genetically only about 2% away from chimpanzees, though that small amount obviously counts for a lot. Other organisms, like mice and fish, are much farther away in genetic terms. The greatest surprise that has come from all of this research is not how different all organisms are, but how much DNA everything has in common. All life on Earth shares a surprisingly large amount of genetic material. The graph on this slide shows a comparison between several different animals based on the gene for cystic fibrosis. Chimpanzees are extremely close to humans, but each successive animal is further and further away.

Humans and Chimps Humans are 98% genetically identical to chimpanzees
In the case of one gene, all of the differences between humans and chimps (only 5 out of 250 nucleotides) could be matched on one side by gorilla DNA Chimpanzees are the closest modern relative to humans. It should be noted here that humans did NOT evolve from monkeys, but rather modern monkeys and modern humans shared a common ancestor 6-7 million years ago. However, in that time period, there have been relatively few genetic changes between the two groups. In one study of a specific gene, there were only 5 nucleotides that differed between humans and chimps out of 250 total (2%). For each one that differed, one of the nucleotides matched with the same nucleotide position in gorilla DNA (showing their relatively close relation to both species).

Human Evolution Timeline
6-7 MYA last common ancestor of humans and chimps 4.1 MYA Australopithecus afarensis (southern ape) 2.3 MYA Homo habilis (skillful man) 1.8 MYA Homo erectus (upright man) 200,000 years ago Homo sapiens (wise man) Human evolution truly begins when our lineage broke with that of modern chimpanzees. Following that, our descendants evolved into Australopithecus afarensis, demonstrated by the fossilized remains of Lucy. These animals were far shorter than modern humans and spent a significant portion of their lives in trees, though they were able to walk upright (as demonstrated by the Laetoli footprints). Australopithecus evolved into the first early human, Homo habilis. Following that came Homo erectus, then Homo sapiens, also known as modern man.

Evolutionary Mechanisms
Mutation, recombination, and gene flow increase genetic variation Mutations can be beneficial, deleterious, or neutral Genetic drift and natural selection decrease genetic variation Natural selection can be directional, stabilizing, or disruptive Mutations are copying errors during genetic replication. They can be beneficial (in which case they are more likely to be passed on), deleterious (in which case they are less likely to be passed on), or neutral (in which case they are neither especially likely or unlikely to be passed on). Recombination is essentially “allele shuffling” that takes place during replication. Gene flow is the exchange of genetic material between populations (in one direction or back and forth). Genetic drift is a random sampling error of genetic material that occurs naturally in all sexually-reproducing populations. It decreases genetic variation because alleles can be left out of the gene pool or fixed at 100%. Natural selection also decreases genetic variation because it weeds out less fit alleles. Directional natural selection means an extreme phenotype is selected for (like a giraffe’s long neck), stabilizing natural selection favors a middle-of-the-road phenotype, and disruptive natural selection occurs when the middle phenotype is not fit, but the two extremes are.

Case Study: Manchester Moths
Before 1848 Biston betularia moths were mainly light-colored The Industrial Revolution Soot covered the birch trees Rapid natural selection occurred Soon after 1848 The moths were primarily dark-colored The case of the Biston betularia in Manchester, England is particularly important in understanding how natural selection works. Prior to 1848, most of the moths were light because they spent their time on birch trees, which were also light in color (this provided them some camouflage). After the start of the industrial revolution, soot began to cover the birch trees and make them darker, meaning that light moths stood out. These moths were then eaten by predators, leaving the darker moths to survive and contribute offspring to future generations. Within only 50 years, the light moths were down to 5% of the total population. In the rural areas, where soot had less of an impact, the light moths did not fare as poorly.

The Evolutionary Process
Gene mutation leads to individuals being selected which leads to population evolution Microevolution: gene mutations, small changes Macroevolution: speciation, big changes Abiogenesis is the theory of how living things first appeared (this is NOT evolution) Gene mutation, a primary cause of genetic variation, begins the “cycle” of evolution. Once there are variable traits in a population, individuals in that population are selected as more or less fit and contribute to the gene pool accordingly. This process repeated over time leads to evolution of populations. Individuals NEVER evolve, only populations evolve. Evolution can be split into two groups: microevolution and macroevolution. While some think that big and small changes function by different mechanisms, others believe that the same mechanisms are in place in both but function on different scales. Finally, abiogenesis is often confused with evolution because both theories deal with where life came from; however, abiogenesis deals with the origins of life from non-living matter whereas evolution deals with the history of life since its development. Pictured is an example of a mutation in a dog; the animal was born with one upper body that diverged into two lower bodies.

Misconceptions Morphological change and evolution are not always bound to one another Tiny changes might be the environment acting on an organism, and not really evolution Organisms act on the environment just as much as the environment acts on organisms Morphological changes (appearances) are not always caused by evolution, and evolution can occur without showing any morphological changes. Additionally, small changes (like body size) can be the environment acting on an organism instead of evolutionary forces (for example, humans today are taller than humans 500 years ago because we have higher quality food and better medical care). Environments are also affected by organisms, which can change landscapes and create modifications to fit the environment to the organisms (like beavers building a dam).

Genetic Variation Mutation types: deletion, duplication, inversion, insertion, translocation Most animals are diploid (two alleles for every gene at each locus) Homozygous: same alleles Heterozygous: two different alleles Linkage disequilibrium alters allele frequency There are five types of mutation. Deletion removes a piece of code, duplication copies a piece of code twice, inversion flips a piece of code, insertion adds a piece of code, and translocation swaps two pieces of code. In most animals, there are two alleles at every location (locus) for every gene (one from the mother and one from the father), making the animal diploid. If the two alleles at a given locus are the same, the individual is called homozygous. If the two alleles are different, the individual is heterozygous. A measurement known as linkage disequilibrium determines how closely associated alleles of two different genes are. Sometimes alleles will become associated through natural selection or other processes, meaning the pair will be passed on as a set more frequently. This non-random sorting is considered disequilibrium.

Mating Assortative mating creates a non-random distribution of alleles at a given locus Non-random mating disrupts the Hardy- Weinberg equilibrium (allele frequencies) Humans tend to mate with individuals of the same race, meaning there are fewer heterozygotes than predicted in the Hardy- Weinberg equilibrium Like in the case of Papilio memnon, a species of moth, some animals will prefer to mate with certain morphologies within that species. The moths are capable of producing bright and dark colors and a tail or no tail. There should be four morphologies, but instead there are only two that appear in nature (bright with tails and dark with no tails). This is an example of assortative mating. When moths of one of the rare morphologies appear in nature, they are quickly eaten by predators because they do not mimic the appearance of a bad-tasting moth (bright with tail) and are not cryptic (dark with no tail). The Hardy-Weinberg equilibrium predicts allele frequency in natural populations, but is thrown off when mating of this type occurs. It is the same for human populations: not only do people tend to mate with those in their local population (meaning similar racial make-up, typically), but humans also tend to mate within their race, leading to assortative mating. Because of this, there are fewer heterozygotes in human populations than would be predicted in the Hardy-Weinberg equilibrium.

Natural Selection Sometimes heterozygotes are more fit than either homozygotes (malaria) Reproductive success: direct, indirect, and inclusive fitness Traits can end up used for something other than their original purpose This process is called exaptation Sometimes heterozygotes are more fit for a particular reason than either version of the homozygotes. One such case is the malaria resistance afforded by the sickle cell anemia gene. People with the homozygous version with sickle cell anemia are sick, and people with the homozygous version without sickle cell anemia have no resistance to malaria. People with one allele from each, however, have some natural resistance to malaria without the deleterious effects of sickle cell. This heterozygousy is most common in Africa, where malaria is most prevalent. Natural selection is linked with reproductive success, which is broken down into two categories. Direct fitness is the amount of genetic material an individual successfully puts into the gene pool. Indirect fitness is the amount of genetic material identical to the individual that the individual helps make it into the gene pool (“I may not survive, but I’ll make sure all my identical siblings do!”). Inclusive fitness is the combination of these figures. In evolution, sometimes traits can be used for something other than their original purpose. For example, a penguin’s wing was once developed for flying, but is now used for swimming. This is called exaptation.

Sexual Selection Fitness is not always related to being big, fast, or strong; reproductive success is more important Females often select males based on secondary characteristics (peacock’s tail, flashes in fireflies) These characteristics may reveal “good genes” or other desirable qualities in males Though natural selection is often referred to as “survival of the fittest”, they are not completely synonymous. Survival is one aspect of fitness, but sexual success is far more important (an animal that lives a very short amount of time but leaves many offspring is far more successful than his inverse). Females of many species will often select males that have secondary sexual characteristics that are impressive in some way. Bigger and brighter plumage on a peacock will attract more mates than average plumage, and so on. Humans have their own versions of this type of selection, such as females often selecting males who are taller, more muscular/fit, and have a full head of hair. However, social pressures and personal preference play a large role in human sexual selection, often putting trait-based natural selection on the back burner. Regardless of the species, though, there is still the question of why these secondary characteristics attract mates. Some argue that the most impressive secondary sexual characteristics indicate that the male has good genes, meaning he would produce more fit offspring. Whatever the reason, sometimes this selection gets stuck in a loop, meaning that the impressive trait gets a male selected, and his offspring have that trait and later get selected, and so on. In the case of a species wherein large antlers are preferable, this may lead to males developing antlers that are so large that they can no longer run away from predators or move efficiently, making them less fit than males with smaller antlers. This point is where natural selection steps in and removes the grossly oversized antlers from the population and keeps the sexual selection process in check.

Genetic Drift Genetic drift is a random sampling error that occurs naturally in all sexually-reproducing populations Mutations and genetic drift generally balance each other (mutations adding and drift subtracting) Fisher and Wright disagreed on the importance of drift: Fisher said it had a negligible effect on large populations, while Wright said it was important in all populations Unlike drift, the founder effect represents the remaining genetic material after a population “crash” Genetic drift is one of two mechanisms that cause a decrease in genetic variation (natural selection being the other). Mutation, a process that adds variation to a population, generally balances with genetic drift regardless of the size of the population (small populations have fewer alleles in total but cycle through them quickly while large populations have more alleles in total but lose them very slowly). Allele frequencies can change rapidly after a sudden event, like a population crash. The remaining genotypes will be the only alleles available, meaning the variation will decrease suddenly and create a new population based only on the remaining individuals. This is known as the founder effect (a similar process occurs when a population migrates to a new area and begins to colonize; the colonizing population is only a sampling of the original population). Wright and Fisher did not agree on the importance of genetic drift. Wright maintained that drift had an effect on all populations regardless of size, and could even help populations bridge the gaps between fitness peaks. Fisher believed that when a population became large enough, the effects of drift would be minimal to the point of not being worth consideration.

Mutation and New Alleles
Most mutant alleles are neutral Some are harmful The smallest proportion are beneficial Most new mutations are lost from the gene pool within one generation Neutral mutations lost due to random drift, deleterious ones often selected against, and beneficial ones selected for (but still often lost) Beneficial mutations happen less frequently but thrive most often Mutations occur when genetic material is copied erroneously. Though most mutations are neutral, meaning they have no effect on the organism, there are some that do cause noticeable changes. Deleterious or “bad” mutations cause some sort of harm to the organism and are often selected against (the organism is infertile or is unsuccessful in finding a mate, the organism cannot get food effectively or run away quickly, etc.). Beneficial or “good” mutations are the most rare, but are more often than not selected for (the organism is better at finding a mate or getting food or avoiding predators, etc.) because they help an organism to survive and reproduce.

Recombination and Gene Flow
Recombination is the mixing of maternal and paternal alleles during cell replication It increases variation by shuffling genetic material Gene flow is the addition of new genes via population mixing Gene flow between distantly related species is horizontal transfer Horizontal transfer is rare Recombination is a process that increases genetic variation. It combines genetic material into new patterns (shuffling the genes themselves and material within genes). These new patterns are not the same as mutation, which is an error in copying. Gene flow is the transfer of genetic material between populations; it can occur in one direction or back and forth between two populations. Gene flow between two distantly related populations is rare. Known as horizontal transfer, one such occurrence took place in two Drosophila populations. One species contained P elements, and when a mite fed on these flies and then fed on the other species of flies, the P elements were transferred to the second species. The P elements spread to the rest of the population. Even though these two species cannot form hybrids, they still were able to exchange genetic information via third party (the mite).

Evolutionary Mechanisms – More
Genetic variation in a population is determined by the balance of mechanisms Natural selection can be positive or negative Genetic drift is random, so it cannot be positive or negative Recurrent mutation of a beneficial allele will help it reach fixation An allele that “catches a ride” with a beneficial allele is a hitchhiker Natural selection, one mechanism of evolution, can be positive or negative. Negative selection is the weeding out of a deleterious allele, while positive selection is the increase of a beneficial allele. Positive selection is sometimes called positive Darwinian selection. Genetic drift is not referred to as positive or negative, regardless of its effect, because it is random. There is no “purpose” behind it, unlike in natural selection. In mutation, most mutations are lost immediately, even though some of them may be beneficial. The recurrent mutation of a beneficial allele will make that allele more likely to make it into the gene pool and eventually reach fixation in a population. Sometimes an allele will associate itself to a beneficial allele, meaning it will be more likely to get selected for, even though it is not beneficial itself. This type of allele is known as a hitchhiker.

Evolutionary Theory and Genetics
Lamarck’s theory and Darwin’s studies are two early contributions to the new field Mendel mailed Darwin his paper but Darwin never opened it Mendel’s work was not accepted early on because he only studied discrete traits Fisher’s Fundamental Theorem of Natural Selection states that adaptive change in a given population is proportional to the genetic variation present Before Darwin, there were several scientists who had proposed the theory of evolution or concepts relating to it, namely Lamarck. Darwin read his work and sought to improve upon it with his own studies. Darwin was unable to explain exactly how traits were passed down through generations, a problem which was solved within his lifetime. Though Gregor Mendel mailed Darwin the paper explaining genetics and inheritance, Darwin never opened it and so he never found out that his big question was potentially answered. Mendel had his share of critics though, namely those that did not think his theory could explain continuously varying traits. Mendel only studied discrete traits (things that were one way or another, with no grey area), which made people think that his theory was only a partial explanation of genetic variation. In another study, R.A. Fisher theorized that adaptive change is directly proportional to the genetic variation present in a population (Fundamental Theorem of Natural Selection).

DNA and RNA DNA nucleotides: adenine, guanine, cytosine, thymine
RNA: uracil instead of thymine; used in transcription Introns do not code, exons do Silent and replacement sites evolve at different rates DNA (deoxyribonucleic acid) contains all the genetic information for an individual. It has four nucleotides which create the genetic code for that individual. Each block of three nucleotides is known as a codon. Codons code for amino acids. A gene in use gets transcribed into RNA (ribonucleic acid). Sequences of DNA that interrupt a gene but are not used in coding are called introns, while those that do code are known as exons. Silent sites are nucleotide positions that can be changed without an amino acid substitution. Replacement sites require amino acid substitution when they are changed. Replacement sites do not evolve as frequently as silent sites do, so their rates of evolution are far slower.

Evolution and Development
Vestigial structures are traces of ancestry in modern animals Example: the human appendix Common descent and macroevolution are supported by the organization of traits (nested patterns of evolution) Vestigial structures (like the appendix in humans) are body parts that used to have a distinct function but no longer perform it. They are generally not necessary for survival or fitness (though some, like the appendix housing immune cells, have a limited usefulness). Common descent and macroevolution have many pieces of evidence supporting them (such as patterns of known instances of evolution, the mirroring of embryonic development and evolutionary development, and homologous traits), but a large example is the nesting of traits into a clear organizational pattern. Looking at plants, they can be divided into vascular and non-vascular, vascular into seedless and seeded, vascular seeded into gymnosperms and angiosperms, and vascular seeded angiosperms into monocots and dicots. These traits do not “mix and match”, and serve as evidence that each group shares traits with a common ancestor, while each subgroup has traits of its own.

Speciation Allopatric speciation occurs with geographic separation (most common) Sympatric speciation (sometimes called microallopatric speciation) occurs without geographic separation Allopatric speciation, believed to be the most common variety of speciation, occurs when a population of organisms becomes split into two or more groups that can no longer interact because of some geographic factor (a body of water, for example). The two populations adapt to their respective environments, changing to fit their new niches. Eventually, the change will be significant enough that the two populations will no longer be able to interbreed (and hence, speciation has occurred). In sympatric speciation, no geographical barrier is needed. The populations become separate for some other reason (food preferences, timing of reproductive cycles, etc.) and practice assortative mating until the two populations can no longer interbreed. Some scientists call this microallopatric speciation to point out that there is still an ecological barrier, even if the two populations are still able to come into contact.

Extinction Normal extinction occurs for many reasons
Competition, disappearing habitat, loss of food source, etc. Mass extinction follows large-scale events Asteroid impact, climate change, humans Mass extinction is followed by huge periods of adaptive radiation because there are empty niches to fill Largest mass extinction: end of the Permian Most famous mass extinction: Cretaceous- Tertiary boundary Extinction is the dying out of one species. It occurs for many reasons and is the fate of all species, past, present, and future. Extinction can be the result of competition from a closely-related species, the loss of the organism’s habitat, or the loss of a major food source. Mass extinctions occur far less often but have far-reaching consequences. Mass extinctions are caused by global events that change the ecology on a huge scale. About 250 million years ago, at the end of the Permian period, the largest mass extinction in history killed most of the world’s species. The most famous extinction, known as the K-T extinction, is the one that killed the dinosaurs. It occurred about 65 million years ago. All mass extinctions are followed by periods of rapid radiation and evolution, and the K-T extinction was no exception; after the extinction of all the dinosaurs, mammals experienced a long period of evolutionary development in the absence of the previously-ruling dinosaurs.

Punctuated Equilibrium
Punctuated equilibrium theory states that evolution is not a steady process Instead, long periods of relatively little evolution and change are broken up by bursts of rapid change Proposed by Stephen Jay Gould and Niles Eldredge Gould and Eldredge proposed that, according to the fossil record, transitions between species are usually abrupt and there are often few or no transitional forms found. This would mean that, instead of human ancestors slowly moving from ape-like creatures to upright early humans, there would have likely been a very sudden shift from tree-dwellers to ground-dwellers in a short period of time. This theory is known as punctuated equilibrium. Many proponents of this theory see relationships between micro- and macroevolution: speciation is analogous to mutation and one species replacing another is analogous to natural selection (known as species selection). While many scientists agree with the general outline of punctuated equilibrium, few are quick to support species selection as a viable natural event.

Evolution’s Importance
Evolution unites disparate fields of biology It explains the distribution of traits across multiple lineages and the variation of life on Earth It helps explain how modern species came to be Theodosius Dobzhansky famously said that “nothing in biology makes sense except in the light of evolution.” Biology is united by the concept of evolution, which connects the history of all living things with the history of the planet and the universe, the environment and ecological concerns, geological and paleontological studies, and especially genetics. Evolution, combined with genetics, explains why life on Earth is so diverse and how it came to be so. Though evolution cannot answer the question “why are we here?”, it can answer “how did we get here?”

Rhagoletis: A Case Study
The apple maggot Rhagoletis is diverging into two species Speciation began without geographic separation Cause appears to be mating habitat preference (apple and hawthorn plants) Studied first by Benjamin Walsh, then by Guy Bush The two populations of Rhagoletis, according to Walsh and Bush, were originally from the same species. Even after the start of the speciation event, they continued to look and behave the same, as though they were still part of the same population. However, they do not interbreed. This speciation is thought to be occurring because one population began using a new host plant (apple tree) for mating and reproductive purposes, which effectively cut off one population from the other. By separating into two plant groups, the flies began to breed only within their own “races” (assortative mating), which further separated the two populations. This is leading to speciation, specifically a process known as sympatric speciation (sympatric comes from the Greek words for “together” and “fatherland”).

Diversity in the Amazon
Speciation in the Amazon was originally thought to occur according to river separations Research revealed that ancient ridges were responsible for some speciation Mitochondrial DNA helped separate the two causes James L. Patton, an evolutionary biologist from UC Berkeley, studied the patterns of evolution in the Amazon river basin. Originally, scientists believed that the ever-shifting rivers were the cause of the frequent speciation in the basin, but Patton’s studies of the mitochondrial DNA showed that this was only half the story. While some animals, like the tamarinds, had indeed separated into distinct species because of river separation, other animals did not have the same geographical pattern. One explanation for these patterns is that there were arches or ridges present at the time of speciation that have since eroded away. One such structure, the Iquitos arch, follows exactly along the line of divergence between the two sets of species. The research team is continuing to search for other arches and ridges to determine what impact they might have had on local organisms.

Sympatric Speciation and Frequency
Sympatric speciation is an explanation for speciation that occurs with no apparent physical separation Has occurred with other flies, fish, butterflies The theory is established; now the focus is on how and why Further evidence for sympatric speciation is coming from many sources and studies, with animals ranging from moths to butterflies to salmon to cichlids to sea urchins. This new evidence suggests that sympatric speciation is no longer just a possibility, but rather a reality. Most scientists do not dismiss the concept entirely, but now there is a new question: why does this type of speciation occur, and how often does it happen?

Sympatric Speciation Examples
Indigobirds – prefer mates that know the same song Cichlids – exist at different depths within one lake Palm Trees – initially separated by soil differences, now kept apart by flowering timing Sympatric speciation is now considered to be a real possibility in evolution, but only now are many potential examples of the phenomenon being studied seriously. One such example, the indigobirds in Cameroon, shows that mating preferences alone can be enough to drive populations apart. The indigobirds lay eggs in finch nests and allow the finches to raise the young as their own. When the birds grow up, they incorporate the finch songs into their repertoire, and then seek out mates that know the same finch song. This assortative mating can eventually lead to speciation. In the case of the cichlids in Cameroon, that may have already occurred. When populations of the fish separated, possibly to exploit various food sources at different depths, they began to adapt to those depths and food sources, eventually splitting into several different species while still remaining in the same lake. In the case of the palm trees, Lord Howe Island (off the coast of Australia) houses two distinct species that may have separated from a small variation in soil types on the island. Now that they are distinct species, their flowering times keep them entirely separate from one another.

Sympatry: How Significant?
Some argue that the examples are still allopatric on a small scale Others argue that sympatry exists but is very minor in the big picture of evolution Some “clear cut” cases of allopatry are now attributed to sympatry Though scientists now generally accept the concept of sympatry as a possibility and reality in natural evolution, many still question how significant a force it is in the world. Some of the examples, like the cichlids and palm trees, have been called “microallopatric” speciation because there are some environmental separations in play (depths of water, soil types), even if the physical barrier does not entirely prevent the species from coming into contact with each other. Even those that do not question sympatry as a force do not always find it to be a particularly important piece of the evolutionary puzzle. Regardless of the varying opinions, there is no question that sympatry exists and has had some impact on the world today. It may even be the case that some speciation events that were previously attributed to allopatry might be cases of sympatry. The jury is very much still out.

Select Topics in Evolutionary Biology
In this section: Jurassic Genome Turn On: A Revolution in the Field of Evolution? Evolution and Tinkering

Genome Sizes Big genomes are found in animals with big bone cells
Small genomes are found in animals with small bone cells Junk DNA: non-coding material (98.5% of human DNA) Genome sizes were originally believed to correlate to the complexity of a given animal, but science is now discovering that this is not the case. The T-Rex had a relatively small genome considering its size (1.9 billion base pairs), and much smaller animals have been discovered to have large genomes (the mountain grasshopper has 16.5 billion bp, the marbled lungfish has 130 billion bp). These huge expanses of genome real estate seem to be filled with something called junk DNA. Junk DNA is non-coding genetic material that takes up a large portion of most organisms’ DNA profiles. In humans, it makes up 98.5% of the genome.

Fossils and Genomes Birds evolved from theropods, which had relatively small genomes This contradicted the assumption that small genomes evolved with flight Genome sizes may be affected by natural selection According to Chris Organ, modern birds evolved from a group of dinosaurs known as theropods. These animals had small genomes compared to other dinosaur lineages. Discovering that birds did not develop small genomes at the same time that they began to fly changed how scientists related genomes with the lineage of modern birds. There is some evidence that there is a relationship between genome sizes and natural selection, but the question of causality versus correction remains.

Embryos and Evolution Recapitulation: “ontogeny recapitulates phylogeny” Two kinds of change Through a lifetime Through a lineage Is embryonic development a small- scale model of evolution? In the field of evolutionary developmental biology, researchers believe that the process of embryonic development (ontogeny) reveals many insights into the larger picture of evolution (phylogeny). They believe that the lifetime of an organism can sometimes mirror or mimic the lineage of an organism. The decoding of many genomes may provide more information on this developing theory. The picture is a controversial drawing of eight species’ embryological development. Ernst Haeckel created the drawings in the 1870s to show the similarities between many different animals. Critics state that the drawings were fabricated entirely, or at least drawn in such a way as to overstate the similarities. Though Darwin did not rely on these drawings for his theory of evolution, those looking to discredit Darwin and Haeckel at the same time attempted to link the two. Developments in science over the last 130+ years have made this controversy all but moot.

Evo Devo’s Findings Evo Devo is short for evolutionary developmental biology All animals are built from essentially the same genes (including Hox genes) Differences in animals are caused by the same genes expressed at different times and places Evolution is mostly a matter of “throwing switches” Carroll and his colleagues have come up with three major findings in the field of evolutionary developmental biology. First, all animals are built from pretty much the same genetic material. One specific type of material, known as Hox genes, controls development of appendages and other body parts. Altering Hox genes can create bizarre-looking creatures of horror movie fame. Interestingly enough, when the Hox gene for ear development is transplanted from a person to a mouse, the mouse doesn’t grow a human ear, it grows a mouse ear. These types of genes are also known as “tool kit” genes. Evo devo has also found that the differences between animals (morphologically speaking) are not caused by different genes being present in the animals but by the same genes being expressed differently. This “throwing switches” concept has raised a lot of eyebrows in the scientific community, especially since Carroll has suggested that evolution is far more concerned with throwing switches than eliminating or adding genes to populations.

“Throwing Switches” Gene expression, not gene presence, is the guiding force of evolution Secret to this might lie in the non-coding or “junk” DNA This may explain the wide variation of life with so few genes Carroll and his colleagues believe that the key to evolution is not the addition and subtraction of genetic material from populations, but rather the activation of specific genetic material in different times and places. The solution might lie in the junk DNA, where non-coding material can potentially control these switches. If this is the case, there can be nearly infinite variation among living things even though there are only a few thousand genes to go around.

Evo Devo: A Revolution? Evo devo may be more of a paradigm shift than a revolution Darwin’s theory of evolution and Mendel’s theory of inheritance were revolutions Evo devo is not quite as significant a breakthrough, but still important Evolutionary developmental biology, though an important area of study, is not quite significant enough to be heralded as the next revolution in biology. Unlike true revolutions like those of Darwin and Mendel, evo devo represents a major shift but not a complete change in all areas. It is better described as a paradigm shift, or a huge change of perspective, than a revolution.

The Nature of Science Science follows a method
Hypotheses have to be testable Science gives provisional answers to limited questions Religion and mythology can offer comprehensive answers Science is actually a very strict matter. Firstly, all experiments must follow the scientific method in order to be considered properly tested (define a problem, form a hypothesis, make observations and perform experiments, analyze data, compare data with hypothesis, retest if necessary, draw conclusions, and transmit results). Scientific questions must be testable in order to be considered valid, and those questions are typically limited in scope. Science cannot provide big answers to big questions; science only gives provisional answers to small questions. Given this limitation, people have often turned to religion or systems of mythology to explain the big questions.

Hierarchy of Objects and Constraints
Sciences can be arranged in order of complexity (physics to psychosociology) Successive integrations in nature: analyzing complex objects at all levels and determining predictability Constraints and history dictate evolutionary systems In trying to organize scientific fields into a hierarchy of complexity, the objects of study are considered. Physics is considered simplest because it deals with the simplest materials. Psychosociology, however, is extremely complex. This same type of hierarchy can occur in nature, but it requires a great deal of analysis at every level. Additionally, the question of predictability must be considered: if something is true at one level of complexity, it is also true at other levels? Can an event or condition be predicted at one level using information from other levels? Constraints at each level and the cumulative effects of history dictate how these systems function.

Natural Selection Natural selection is the result of two constraints
Reproduction Ongoing interaction with the environment Natural selection gives direction to changes Two constraints create the need for natural selection. The first is the requirement for reproduction, which is a basic function of all organisms. The second is permanent interaction with the environment. Because all organisms must live in the environment and interact with it constantly, the environment must always be considered when analyzing those organisms. In the case of natural selection, the environment is just as important as the organisms themselves in understanding evolution. Natural selection does not just provide change in populations, but it also gives a direction to those changes.

Natural Selection as a Tinkerer
Natural selection is not an engineer Engineers use specific tools to achieve a planned result with an ideal outcome in mind It is a tinkerer It does the best it can with what is available Some evolutionary changes appear to be constant, small-scale improvements (not long term “projects”) Evolution and natural selection can be thought of as tinkerers, constantly improving upon previous designs by using the best available materials to create the best possible result for that time and place. Unlike engineers, who use tools designed for a specific task, materials suited to that task, and plans for an ideal outcome, tinkerers use whatever materials are available to create a “good enough for now” design in life. One such example of this style is the lung, which was improved upon over many successive generations until it became efficient and useful.

Results of Tinkering Human females spontaneously abort nearly all malformed fetuses before the first 3 weeks of pregnancy Humans have developed an association between pleasure and sex to spur them to reproduce Tinkering in humans has led to several developments. One such result is the human reproductive system and its method for expelling poorly-formed offspring before they can be brought to term. Approximately 50% of all pregnancies result in spontaneous abortion. This usually occurs within the first three weeks, which means the female is typically unaware that she was ever pregnant. This system is in place to prevent evolutionarily “unfit” individuals from entering the population. Of course, the system is not foolproof, and some of these fetuses still come to term. This means that the tinkering has not perfected the process. Another example is that of the human sexual drive. Because the sexual act is pleasurable, humans are driven to do it more often, which increases the overall success of human beings. Besides being valuable in reproduction, pleasure also helps humans distinguish between “good” and “bad” things because good things typically bring pleasure and bad things bring pain.

Tinkering and the Human Brain
New structures superimposed over old ones Conflicts between the “visceral” brain and the logical brain occur because of these additional structures and connections The human brain appears to be an excellent example of tinkering in that it has many new structures superimposed over older ones. Instead of scrapping an old design and making an entirely new one, evolution has continuously improved and added to the brain’s design. While this has achieved a large measure of success, the process has still created a somewhat-flawed product: there are still conflicts within the brain that are caused by the juxtaposition of two main drives, the visceral brain and the logical brain (essentially, instinct versus logic). The brain is not a perfect system, but it functions well enough for humans today; this level of efficiency is the hallmark of the tinkerer.

Conclusions Darwin, Wallace, and many others represent the foundation of the unifying theory of evolution Theories about evolution are shifting because of new genetic information and breakthroughs in other fields Though most scientists agree evolution is a fact, there are still questions about types of evolution (sympatric vs. allopatric), its speed, and how exactly it occurs Developing fields like genetics and evo devo are uncovering new information and raising even more questions While 1858 is a very long time ago in terms of scientific theories, the original studies aboard the HMS Beagle and Darwin’s landmark paper On the Origins of Species still resonate across all of biology today. New fields of science and new theories are developing all the time, not to replace the theory of evolution, but to add to it and tweak it to match what we now know of genetics and the development of populations over time. Though there is a vast library of information available to us today, there are just as many questions as ever, if not more, and scientists are still working to discover the secrets of evolution. For questions concerning this guide or the materials contained herein, please contact the author at

An Introduction to EVOLUTIONARY BIOLOGY

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