To: All Msg #138, Jun1593 11:47AM Subject: talk.origins evolution FYI I'm going to post my

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From: Chris Colby To: All Msg #138, Jun-15-93 11:47AM Subject: talk.origins evolution FYI Organization: animal -- coelomate -- deuterostome From: colby@bu-bio.bu.edu (Chris Colby) Message-ID: <123249@bu.edu> Newsgroups: talk.origins I'm going to post my "Introduction to evolutionary biology" file. The point has been raised on t.o. that the term FAQ (for "frequently asked questions") probably doesn't apply to many of the "FAQ"s posted. So I've decided to call mine a FYI (for "for your information") -- if anyone has any other possible acronyms, email me. This version of my FYI includes a section giving some events from the history of life. Other minor revisions are scattered throughout. I'll post it, as always, in two sections -- one labled "microevolution" and the other labeled "macroevolution". I'll mail this to Mr. Vickers as well so he can put it in the t.o. ftp site. EVOLUTIONARY BIOLOGY ******************** Introduction What is evolution? What isn't evolution? What evolution isn't Genetic variation How is genetic variation described? How much genetic variation is there? Evolution within a lineage -- anagenesis Mechanisms that decrease genetic variation Natural selection Sexual selection Genetic drift Mechanisms that increase genetic variation Mutation Directed mutagenesis Recombination Gene flow Overview of anagenesis Evolution among lineages -- cladogenesis The pattern of macroevolution Evidence for common descent and macroevolution Comparative genetics and biochemistry Comparative anatomy Developmental biology Vestigal structures Biogeography Natural selection and 'jury-rigged' design Fossils The nested pattern of biological diversity Predictions of evolutionary biology Scientific standing of evolution and its critics Mechanisms of macroevolution Speciation -- increasing biological diversity Modes of speciation Observed speciations Extinction -- decreasing biological diversity "Ordinary" extinctions Mass extinctions Punctuated equilibria A brief history of life RNA world The progenote and the three domains of life Evolution of metabolism Photosynthesis Respiration Endosymbiosis -- chloroplasts and mitochondria Cambrian and Ordovician radiations Invasion of the land Permian extinction Dinosaurs Angiosperms Mammals Overview Scientific Standing of Evolution and it's Critics Conclusion References Chris Colby --- email: colby@bu-bio.bu.edu --- "'My boy,' he said, 'you are descended from a long line of determined, resourceful, microscopic tadpoles--champions every one.'" --Kurt Vonnegut from "Galapagos" ======================================================================= From: Chris Colby To: All Msg #213, Jun-15-93 11:48AM Subject: microevolution -- t.o. FYI part one Organization: animal -- coelomate -- deuterostome From: colby@bu-bio.bu.edu (Chris Colby) Message-ID: <123250@bu.edu> Newsgroups: talk.origins AN INTRODUCTION TO EVOLUTIONARY BIOLOGY -- BY CHRIS COLBY ********************************************************* INTRODUCTION ------------ Evolution is one of the most powerful theories in science. It is not a difficult concept, but very few people -- the majority of biologists included -- have a satisfactory grasp of it. One mistake, common to TV nature shows, is that behaviors of individual organisms are aimed at perpetuating their species. Another common mistake is that species can be arranged on an evolutionary ladder from bacteria through "lower" animals, to "higher" animals and, finally, up to man. These mistakes, and many more, permeate popular science expositions of evolutionary biology and even filter into biology journals. All this confusion about evolution is very damaging to the study of evolution and biology as a whole. People who have a general interest in science are likely to dismiss evolution as a "soft" science after absorbing the pop science nonsense that abounds. The impression of it being a "soft" science is reinforced when many biologists in unrelated fields speculate publicly about evolution without having training in it. This essay is a brief introduction to evolutionary biology. As well as explaining the basics of the theory of evolution, I focus on explaining away many of the misconceptions about evolution. Creationist arguments are not directly addressed here. WHAT IS EVOLUTION? Evolution is a change in the gene pool of a population over time. A gene is a hereditary unit that can be passed on unaltered for numerous generations. The gene pool is the set of all genes in a species or population. The English moth, _Biston__betularia_, is a frequently cited example of observed evolution. In this moth there are two color morphs, light and dark. Black moths, which initially were rare, increased in frequency as a result of their habitat becoming darkened by soot from factories. Birds could see the lighter colored moths more readily and ate more of them. The moth population changed from mostly light colored moths to mostly dark colored moths. Since their color was primarily determined by a single gene, the change in frequency of dark colored moths represented a change in the gene pool. This change was, by definition, evolution. The kind of evolution documented above is "microevolution". Larger changes in a gene pool are called "macroevolution". Some biologists feel the mechanisms of macroevolution are different from those of microevolutionary change. Others, including myself, feel the distinction between the two is arbitrary. Macroevolution is cumulative microevolution. In any case, evolution is defined as a change in the gene pool. This means that evolution is a population level phenomenon. Only groups of organisms evolve. An individual organism does not evolve, nor do subunits of organisms evolve (with limited exceptions). So, when thinking of evolution, it is necessary to view populations as a collection of individuals with different traits. For example, in the example above the frequency of black moths increased, the moths did not turn from light to grey to dark in concert. I have defined evolution as a process and that is how I will use the term in this essay. Keep in mind, however, that in everyday use evolution refers to a variety of things. The fact that all organisms are linked via descent to a common ancestor is often called evolution. The theory that life arose solely via natural processes is often called evolution (instead of abiogenesis). And frequently, people use the word evolution when they really mean natural selection -- one of the many mechanisms of evolution. WHAT ISN'T EVOLUTION? For many, evolution is equated with morphological change, i.e. organisms changing shape or size over time. An example would be a dinosaur species evolving into a species of bird. It is important to note that evolution is often accompanied by morphological change, but this need not be the case. Evolution can occur without morphological change; and morphological change can occur without evolution. For instance, humans are larger now than in the recent past, but this is not an evolutionary change. Better diet and medicine brought about this change, so it is not an example of evolution. The gene pool did not change -- only its manifestation did. Phenotypic changes induced solely by changes in environment do not count as evolution because they are not heritable; in other words the change is not passed on to the organism's offspring. Phenotype is the morphological, physiological, biochemical, behavioral and other properties exhibited by a living organism. An organism's phenotype is determined by its genes and its environment. Most changes due to environment are fairly subtle (e.g. size differences). Large scale phenotypic changes (such as dinosaur to bird) are obviously due to genetic changes, and therefore are evolution. WHAT EVOLUTION ISN'T Evolution is not progress. Populations simply adapt to their current surroundings and do not necessarily become "better" over time. A trait or strategy that is successful at one time may be deleterious at another. Studies in yeast have shown that "more evolved" strains of yeast can be competitively inferior to "less evolved" strains. Any organism's success depends on the behavior of its contemporaries; for most traits or behaviors there is likely no optimal design or strategy, only contingent ones. HOW DOES EVOLUTION WORK? If evolution is a change in the gene pool; what causes the gene pool to change? Several mechanisms can change a gene pool, among them: natural selection, genetic drift, gene flow, mutation and recombination. I will discuss these in more detail later. It is important to understand the difference between evolution and the mechanisms that bring about this change. GENETIC VARIATION ----------------- Bringing about a change in the gene pool assumes that there is genetic variation in the population to begin with, or a way to generate it. Genetic variation is "grist for the evolutionary mill". For example, if there were no dark moths, the population could not have evolved from mostly light to mostly dark. In order for continuing evolution there must be mechanisms to increase or create genetic variation (e.g. mutation) and mechanisms to decrease it (e.g. natural selection and genetic drift). HOW IS GENETIC VARIATION DESCRIBED? Genetic variation has two components: allelic diversity and non- random associations of alleles. Alleles are different versions of the same gene at a given locus (locus means location). For example, at the blood group locus humans can have an A, B or O allele. Most animals, including humans, are diploid. This means they contain two alleles for every gene at every locus. If the two alleles are the same type (for instance two A alleles) the individual would be termed "homozygous" for that locus. An individual with two different alleles at a locus is called "heterozygous". Allelic diversity is simply the number of alleles at each locus scaled by their frequency in the gene pool. At any locus there can be many different alleles, more alleles than any single organism can possess. Linkage disequilibrium is a measure of association between alleles at different loci. If two alleles were found together in organisms more often than would be expected, these alleles would be in linkage disequilibrium. Linkage disequilibrium can be the result of physical proximity of the genes or maintained by natural selection if some combinations of alleles work better as a team. Assortative mating causes a non-random distribution of alleles at a single locus. Humans, for example, mate assortatively according to race; we are statistically more likely to mate with someone of own race than another. In populations that mate this way, fewer heterozygotes are found than would be predicted if the gene pool were randomly mixed. This mating effect can be the result of mate choice, or simply the result of population subdivision. Most organisms have a limited dispersal capability, so their mate will be chosen from the local population. HOW MUCH GENETIC VARIATION IS THERE? Considerable variation has been detected in natural populations. At 45 percent of loci in plants there is more than one allele in the gene pool. Any given plant is likely to be heterozygous at about 15 percent of its loci. Levels of genetic variation in animals range from roughly 15% of loci having more than one allele (polymorphic) in birds, to over 50% of loci being polymorphic in insects. Mammals and reptiles are polymorphic at about 20% of their loci - - amphibians and fish are polymorphic at around 30% of their loci. Most loci assort independently (this implies linkage equilibrium). In most populations, there are enough loci and enough different alleles that every individual (barring monozygotic (identical) twins) has a unique combination of alleles. EVOLUTION WITHIN A LINEAGE (ANAGENESIS) *************************************** The following sections deal with evolution within a population or lineage -- this is called anagenesis. Several mechanisms can bring about anagenetic change. I have grouped them into two classes -- those that decrease genetic variation and those that increase it. MECHANISMS THAT DECREASE GENETIC VARIATION ------------------------------------------ MECHANISMS OF EVOLUTION: NATURAL SELECTION Natural selection is the only mechanism of adaptive evolution; it is defined as differential reproductive success of pre-existing classes of genetic variants in the gene pool. In other words, some genotypes are (on average) better than others at contributing their alleles to the next generation's gene pool. Selection is not a force in the sense that gravity or magnetism is. However, for the sake of brevity, biologists sometimes refer to it that way. This often leads to some confusion when biologists speak of selection "pressures". This implies that something in the environment instructs the organism as to how to evolve, or "pushes" a population to more adapted state. This is not the case. Selection merely favors beneficial genetic changes when they occur by chance -- it does not contribute to their appearance. Also, when selection is spoken of as a force, it often seems that it is has a mind of it's own; or as if it was nature personified. This most often occurs when biologists are waxing poetic about selection. This kind of talk should be identified for the feebleminded crap it is and has no place in scientific discussions of evolution. Selection is not a guided or cognizant entity; it is simply an effect. A related pitfall in discussing selection is anthropomorphizing on behalf of living things. Often conscious motives are seemingly imputed to organisms, or even genes, when discussing evolution. This happens most frequently when discussing animal behavior. Animals are often said to perform thus and so behavior because selection will favor it. This could more accurately worded as "animals that, due to their genetic composition, perform this behavior tend to be favored by natural selection relative to those who, due to their genetic composition, don't." Such wording is cumbersome and to avoid this, biologists often anthropomorphize. This is unfortunate because it often makes evolutionary arguments sound silly. Keep in mind this is only for convenience of expression. When supplied with genetic variation, natural selection allows organisms to adapt to their current environment. It does not have any foresight. Structures or behaviors do not evolve for future utility. An organism must be adapted to its environment at each stage of its evolution. As the environment changes, new traits (new combinations of alleles) may be selected for. Large changes in populations are the result of cumulative natural selection -- numerous small changes are introduced into the population by mutation; the small minority of these changes that result in a greater reproductive output of their bearers are amplified in frequency by selection. If evolution proceeds without any foresight, it is logical to wonder how complex traits evolve? If half a wing is no good for flying, how did wings evolve? Half a wing may be no good for flying, but it may be useful in other ways. Feathers are thought to have evolved as insulation (ever worn a down jacket?) and/or as a way to trap insects. Later, proto-birds may have learned to glide when leaping from tree to tree. Eventually, the feathers that originally served as insulation now became co-opted for use in flight. This illustrates the point that a trait's current utility is not always indicative of its past utility. It can evolve for one purpose, and be used later for another. A trait evolved for its current utility is an adaptation; one that evolved for another utility is an exaptation. An example of an exaptation is a penguin's wing. Penguins evolved from flying ancestors; now they are flightless and use their wings for swimming. Natural selection works at the level of the individual. The example I gave earlier was an example of evolution via natural selection. Dark colored moths had a higher reproductive success because light colored moths suffered a higher predation rate. The decline of light colored alleles was caused by light colored individuals being removed from the gene pool (selected against). Individual organisms either reproduces or fails to reproduce and are hence the unit of selection. Genes are not the unit of selection (because their success depends on the organism's other genes as well); neither are groups of organisms a unit of selection. There are some exceptions to this "rule", but it is a good generalization. The individual organism reproduces or fails to reproduce. It competes primarily with others of it own species for its reproductive success. For this reason organisms do not perform any behaviors that are for the good of their species. Natural selection favors selfish behavior because any truly altruistic act increases the recipient's reproductive success while lowering the donors. Altruists would quickly disappear from a population as the non-altruists would reap the benefits, but not pay the cost, of any altruistic act. Of course, many behaviors appear to be altruistic. Biologists, however, can demonstrate (in the cases they have studied) that these behaviors are only apparently altruistic. Cooperating with or helping other organisms is often the most selfish strategy for an animal. Often this is called "reciprocal altruism" (an oxymoron if there ever was one). A good example of this is blood sharing in vampire bats. In these bats, those lucky enough to find a meal will often share part of it with an unsuccessful bat by regurgitating some blood into the other's mouth. Biologists have found that these bats form bonds with partners and help each other out when the other is needy. If a bat is found to be a "cheater", (i.e. he accepts blood when starving, but does not donate when his partner is) his partner will abandon him. The bats are thus not helping each other altruistically; they form pacts that are mutually beneficial. Helping closely related organisms can appear altruistic; but this is also a selfish behavior. Reproductive success (or fitness) has two components; direct fitness and indirect fitness. Direct fitness is a measure of how many alleles, on average, a genotype contributes to the subsequent generation's gene pool by reproducing. Indirect fitness is a measure of how many alleles identical to its own it helps to enter the gene pool. Direct fitness plus indirect fitness is inclusive fitness. Natural selection favors behaviors that increase a genotype's inclusive fitness. Closely related organisms share many of the same alleles. In diploid species, siblings share on average at least 50% of their alleles. The percentage is higher if the parents are related. So, helping close relatives to reproduce gets an organism's own alleles better represented in the gene pool. The benefit of helping relatives increases dramatically in highly inbred species. In some cases, organisms will completely forgo reproducing and only help their relatives reproduce. Ants, for example, have sterile castes that only serve the queen and allow her to reproduce. The sterile workers are reproducing by proxy. Keep in mind that the words "selfish" and "altruistic" have connotations in everyday use that biologists do not intend. "Selfish" simply means behaving in such a way that one's own inclusive fitness is maximized; "altruistic" means behaving in such a way that another's fitness is increased at the expense of ones' own. Use of the words "selfish" and altruistic" is not meant to imply that organisms consciously understand their motives. The opportunity for natural selection to operate does not induce genetic variation to appear -- selection only distinguishes between existing variants. Variation is not possible along every imaginable axis, so all possible adaptive solutions are not open to populations. To pick a somewhat ridiculous example, a steel shelled turtle might be an improvement over regular turtles. Turtles are killed quite a bit by cars these days because when confronted with danger, they retreat into their shells -- this is not a great strategy against a two ton automobile. However, there is no variation in metal content of shells, so it would not be possible to select for a steel shelled turtle. Natural selection does not necessarily produce individually optimal structures or behaviors. Selection targets the organism as a whole, not individual traits. So, specific traits are not optimized, but rather combinations of traits. In addition, natural selection may not necessarily even select for the the most optimal set of traits. In any population, there would be a certain combination of possible alleles that would produce the optimal set of traits (the global optimum); but there are probably several other sets of alleles that would yield a population almost as adapted (local optima). Transition from a local optimum to the global optimum may be hindered or forbidden because the population would have to pass through less adaptive states to make the transition. So, natural selection only works to bring populations to the nearest optimal point. SEXUAL SELECTION -- A SUBSET OF NATURAL SELECTION Darwin, and others, noticed that in many species males developed prominent secondary sexual characteristics. A few oft cited examples are the peacock's tail, coloring and patterns in male birds in general, voice calls in frogs and flashes in fireflies. Many/most of these traits are a liability from the standpoint of survival, mainly because any ostentatious trait or noisy, attention-getting behavior will alert predators as well as potential mates. How then could natural selection favor these traits? Natural selection can be broken down into many components, of which survival is only one. Sexual attractiveness is a very important component of selection, so much so that biologists use the term sexual selection when they talk about this subset of natural selection. Sexual selection occurs when the sexual attractiveness of a trait outweighs the liability incurred for survival. A male who lives a short time, but produces many offspring is much more successful than a long lived one that produces few. The former's genes will eventually dominate the gene pool of his species. In many species, especially polygynous species where only a few males monopolize all the females, sexual selection has caused pronounced sexual dimorphism. In these species males compete against other males for mates. The competition can be either direct (i.e. the largest males guarding their harems and fending off other males physically) or mediated by female choice. In species where females chose, males compete by displaying striking phenotypic characteristics and/or performing elaborate courtship behaviors. The females then mate with the males that most interest them, usually the ones with the most outlandish displays. There are many competing theories as to why females are attracted to these displays. One model, the "good genes" model, states that the display indicates some component of male fitness. A "good genes" advocate would say that bright coloring in male birds indicates a lack of parasites. The females are cueing on some signal that is correlated with some other component of viability. Another model, proposed by Fisher, is called the "runaway sexual selection" model. In his model he proposes that females may have a preference for some male trait (without regards to fitness) and then mate with these males when the trait appears. The offspring of these matings will therefore have the genes for both the trait _and_ the preference for the trait. Note, these genes would be expressed in the males and females respectively. As a result, the process snowballs out of control until natural selection brings it into check. Here is an example to clarify. Suppose that, due to some quirk of brain chemistry, female birds of one species prefer males with longer than average tail feathers. Mutant males with longer than average feathers will produce more offspring than the short feathered males. In the next generation, average tail length will increase. As the generations progress, feather length will increase because females do not prefer a specific length tail, but a longer than average tail. Eventually tail length will increase to the point were the liability to survival is matched by the sexual attractiveness of the trait and an equilibrium will be established. Note that in many exotic birds male plumage is often very showy and many species do in fact have males with greatly elongated feathers. In some cases these feathers are shed after the breeding season. A third model, called "the handicap hypothesis" states that males with the most costly displays (in terms of detriment to survival) are advertising the fact that, despite their "handicap", they still had what it took to survive. None of the above models are mutually exclusive. There are millions of sexually dimorphic species on this planet and the forms of sexual selection probably varies amongst them. Natural selection is a non-random mechanism of evolution. It is the only mechanism that causes adaptive evolution. The phrase "survival of the fittest" is often used synonymously with natural selection. IMHO, the phrase is both incomplete and misleading. For one thing, survival is only one component of selection -- and perhaps one of the less important ones in many populations. For example, in polygynous species, a number of males survive to reproductive age, but only a few ever mate. Males may differ little in their ability to survive, but greatly in their ability to attract mates -- the difference in reproductive success stems mainly from the latter consideration. Also, the word "fit" is often confused with physically fit. Fitness, in an evolutionary sense, is the average reproductive output of a class of genetic variants in a gene pool. Fit does not mean biggest, fastest or strongest -- sexiest might be closer to the truth in many animal species. Of all the mechanisms of evolution, natural selection has the potential to change gene frequencies the fastest. It usually acts to keep gene frequencies constant, however. This led a famous evolutionist, George Williams, to say "Evolution proceeds in spite of natural selection". MECHANISMS OF EVOLUTION: GENETIC DRIFT Another important mechanism of evolution is genetic drift. Drift is a binomial sampling error of the gene pool. What this means is, the alleles that form the next generation's gene pool are a sample of the alleles from the current generation. Drift is a rather abstract concept to some; I will try to explain it via an analogy. Imagine you had a swimming pool full of one million marbles. This will represent the parental gene pool -- half are red and half are blue. If you repeatedly picked ten marbles out, do you think you would get five red and five blue every time (assume you replaced your sample to the pool each time)? If you picked one hundred marbles out, do you think you would get fifty red and fifty blue out every time? In both cases the answer is no, some times the frequency of red marbles in the sample would deviate from 0.50. In the case of the 100 marble sample, the frequency of red marbles would deviate much less, however. If, after picking out ten or one hundred marbles, you refilled the pool with marbles at the frequency of that sample (for example, if you picked 6 red and four blue and refilled the pool with 600,000 red marbles and 400,000 blue) and repeated the process over and over; what do you think would happen? What would happen is that the frequency of red to blue would fluctuate over time. Eventually, there would be only one color marble left in the pool. This is roughly analogous to how genetic drift works. In small populations, the rate of change in the frequency of alleles is greater than in large populations. However, the overall rate of genetic drift is independent of population size. If the mutation rate is constant, large and small populations lose alleles to drift at the same rate. This is because large populations will have more alleles in the gene pool, but they will lose them more slowly. Smaller populations will have fewer alleles, but these will quickly cycle through. This assumes that selection is not operating on any of these alleles. Sharp drops in population size can greatly affect the gene pool. When a population crashes, the alleles in the surviving sample may not be representative of the pre-crash gene pool. This change in the gene pool is called the founder effect, because small populations of organisms that invade a new territory (founders) are subject to this. Many biologist feel the genetic changes brought about by founder effects may contribute to isolated populations developing reproductive isolation from their parent populations. Both natural selection and genetic drift decrease genetic variation. If they were the only mechanisms of evolution, populations would eventually become homogeneous and further evolution would be impossible. There are, however, mechanisms that replace variation depleted by selection and drift. These are discussed below. MECHANISMS THAT INCREASE GENETIC VARIATION ------------------------------------------ MECHANISMS OF EVOLUTION: MUTATION A mutation is a change in a gene. There are many kinds of mutations. A point mutation is a mutation in which one "letter" of the genetic code is changed to another. Lengths of DNA can also be deleted or inserted in a gene; these are also mutations. Finally, genes or parts of genes can become inverted or duplicated. Mutation is a mechanism of evolution because it changes allele frequencies very slightly. If an allele "A" mutates to another allele "a", the frequency of "a" has increased from zero to some small number (1/2N in a diploid population where N is the effective population size). The allele "A" will also decrease slightly in frequency. Evolution via mutation alone is very slow; for the most part, mutation just supplies the raw material for evolution -- genetic variation. Most mutations are slightly deleterious or neutral. The genome of most organisms (certainly all eukaryotes) contains enormous amounts of junk sequences. In addition, even in coding regions, many sites can undergo mutation and still maintain the original meaning. In other words, the genetic code is redundant. So, most mutations are neutral or nearly so; but, the overwhelming majority of mutations that produce any detectable phenotypic effect are deleterious. "Good" mutations, however, do occur. One example of a beneficial mutation comes from the mosquito _Culex_ _pipiens_. In this organism, a gene that was involved with breaking down organophosphates - common insecticide ingredients - became duplicated. Progeny of the organism with this mutation quickly swept across the worldwide mosquito population. There are numerous examples of insects developing resistance to chemicals, especially DDT - which was once heavily used in this country. And, most importantly, even though "good" mutations happen much less frequently than "bad" ones, organisms with "good" mutations thrive while organisms with "bad" ones die out. It has long been dogma that mutations occur without regard to their adaptive significance. Organisms cannot "decide" that they need a mutation and have it occur. The frequency of a mutation occurring is independent of the potential effect it would have. Recently, this notion has been challenged. A new class of mutation has recently been documented in bacteria and yeast. It appears that some unicellular organisms can undergo adaptive mutagenesis to repair "broken genes". The reversion mutation that restores a gene to normal functioning occurs several orders of magnitude more frequently when the gene is needed than when it isn't; the mutation rate at other loci is unaffected. The mechanism of adaptive mutagenesis is unknown at this time, but it has been shown to be under genetic control - - i.e. adaptive mutations are not errors like normal mutations are; they are actively created (or selectively retained) by the organism in response to the environment. The importance of directed mutagenesis is not yet known. The majority of evolution on this planet probably proceeded by natural selection sifting through random, spontaneous mutants, but, adaptive mutagenesis may have played a significant role in some microbe lineages. Biologists have not yet studied if directed mutations can produce novel solutions to environmental challenges. It is also unknown if they can occur in multi-cellular organisms with separate germ and somatic cell lines. In any case it appears that, in at least a few instances, the potential for selection to operate induces adaptive genetic variation to appear. MECHANISMS OF EVOLUTION: RECOMBINATION Recombination can be thought of as gene shuffling. Most organisms have linear chromosomes and their genes lie at specific location (loci) along them (bacteria have circular chromosomes). In most sexually reproducing organisms, there are two of each chromosome type in every cell. For instance in humans, there are two chromosomes number one (through 22 and two sex chromosomes), one inherited from the mother, the other inherited from the father. When an organism produces gametes, the gametes end up with only one of each chromosome per cell. Haploid gametes are produced from diploid cells by a process called meiosis. In meiosis, homologous chromosomes line up. The DNA of the chromosome is broken on both chromosomes in several places and rejoined with the other strand. Later, the two homologous chromosomes are split into two separate cells that divide and become gametes. But, because of recombination, both of the chromosomes are a mix of alleles from the mother and father. For example, let's say an organism has a chromosome with three genes, (A,B and C -- in that order). Assume that at each of these three loci there are at least two alleles. From the father, the organism inherited a chromosome with the alleles A1, B1 and C1. From the mother the organism inherited A2,B2 and C2 alleles. In meiosis the two chromosomes would line up and the two A alleles would line up, as would the B and C alleles. If recombination occurred between locus A and locus B, the resulting chromosomes in the two gametes would be; one chromosome carrying A1, B2 and C2 alleles and one chromosome carrying A2, B1 and C1 alleles. Real chromosomes carry many more than three genes and recombination occurs at many locations along the chromosome. The end result is that the two homologous chromosomes have "shuffled" alleles. Recombination can occur not only between genes, but within genes as well. Recombination within a gene can form a new allele. Recombination is a mechanism of evolution because it adds new alleles and combinations of alleles to the gene pool. A beneficial aspect of recombination is that beneficial mutants can be brought together onto the same chromosome, even if they arose in separate organisms. MECHANISMS OF EVOLUTION: GENE FLOW Gene flow simply means new genes added to a population by migration from another population. In some closely related species, fertile hybrids can result from interspecific matings. These hybrids can vector genes from species to species. Gene flow between more distantly related species occurs infrequently. This is called horizontal transfer. One interesting case of this involves genetic elements called P elements. In the genus _Drosophila_, P elements were transferred from some species in the _willistoni_ group, to _D. melanogaster_. These two species of fruit flies are distantly related and hybrids do not form. Their ranges do, however, overlap. The P elements were vectored into _D. melanogaster_ via a parasitic mite that targets both these species. This mite punctures the exoskeleton of the flies and feeds on the "juices". Material, including DNA, from one fly can be transferred to another when the mite feeds. Since P elements actively move in the genome (they are themselves parasites of DNA), one incorporated itself into the genome of a _melanogaster_ fly and subsequently spread through the species. Laboratory stocks of _melanogaster_ caught prior to the 1940's are devoid of P elements. All natural populations today harbor them. OVERVIEW OF EVOLUTION WITHIN A LINEAGE (ANAGENESIS) --------------------------------------------------- Evolution is a change in the gene pool of a population over time; it can occur due to several factors. Three mechanisms add new alleles to the gene pool: mutation, recombination and gene flow. Two mechanisms remove alleles, genetic drift and natural selection. Drift removes alleles randomly from the gene pool. Selection removes deleterious alleles from the gene pool. Natural selection can also increase the frequency of an allele (or combination of alleles) in the gene pool. Selection that weeds out harmful alleles is called negative selection. Selection that increases the frequency of helpful alleles is called positive, or sometimes positive Darwinian, selection. A new allele can also drift to high frequency. But, since the change in frequency of an allele each generation is random, nobody speaks of positive or negative drift. Except in rare cases of high gene flow, all new alleles enter the gene pool as a single copy. Most new alleles added to the gene pool are lost almost immediately due to drift or selection; only a small percent ever reach a high frequency in the population. Even most moderately beneficial alleles are lost due to drift when they appear. The fate of any new allele depends a great deal on the organism it appears in. This allele will be linked to the other alleles near it for many generations. A mutant allele can increase in frequency simply because it is linked to a beneficial allele at a nearby locus. This can occur even if the mutant allele is deleterious, although it must not be so deleterious as to offset the benefit of the other allele. Likewise a potentially beneficial new allele can be eliminated from the gene pool because it was linked to deleterious alleles when it first arose. An allele "riding on the coat tails" of a beneficial allele is called a hitchhiker. Eventually, recombination will bring the two loci to linkage equilibrium. But, the more closely linked two alleles are, the longer the hitchhiking will last. The effects of selection and drift are coupled. Drift is intensified as selection pressures increase. This is because increased selection (i.e. a greater difference in reproductive success among organisms in a population) reduces the effective population size, the number of individuals contributing alleles to the next generation. Adaptation is brought about by cumulative natural selection, the repeated "sifting" of mutations by natural selection. Small changes, favored by selection, can be the stepping-stone to further changes. The summation of large numbers of these changes is macroevolution. This is discussed below. EVOLUTION AMONG LINEAGES (CLADOGENESIS) *************************************** The following sections deal with how single populations ramify to become multiple populations and eventually separate species - this is called cladogenesis. In addition, the overall pattern of macroevolution and evidence for common descent of all living species is presented. Also, a brief history of life on the planet is given. THE PATTERN OF MACROEVOLUTION Evolution is not progress. The popular notion that evolution can be represented as a series of improvements from simple cells, through more complex life forms, to humans (the pinnacle of evolution), can be traced to the concept of the scale of nature. This view is incorrect. All species have descended from a common ancestor. As time went on, different lineages of organisms were modified with descent to adapt to their environments. Thus, evolution is best viewed as a branching tree or bush, with the tips of each branch representing currently living species. No living organisms today are our ancestors. Every living species is as fully modern as we are with its own unique evolutionary history. No extant species are "lower life forms", atavistic stepping stones paving the road to humanity. A related, and common, fallacy about evolution is that humans evolved from some living species of ape. This is not the case -- humans and apes share a common ancestor. Both humans and living apes are fully modern species; the ancestor we evolved from was an ape, but it is now extinct and was not the same as present day apes (or humans for that matter). If it were not for the vanity of human beings, we would be classified as an ape. Humanities closest relatives are, collectively, the chimpanzee and the pygmy chimp. Our next nearest relative is the gorilla. EVIDENCE FOR COMMON DESCENT AND MACROEVOLUTION ---------------------------------------------- Whereas microevolution can be studied directly, macroevolution is studied by examining patterns in biological populations and clades (groups of organisms) and inferring process from pattern. Given the observation of microevolution and the knowledge that the earth is billions of years old -- macroevolution could be postulated. But this extrapolation, in and of itself, does not really provide a compelling explanation of the patterns of biological diversity we see today. Evidence for macroevolution, or common ancestry and modification with descent, comes from several other fields of study. These include: comparative biochemical and genetic studies, comparative developmental biology, patterns of biogeography, comparative morphology and anatomy and the fossil record. Comparative genetic and biochemical data provide data supporting the inference of common descent. DNA sequence comparisons of closely related species (as determined by morphologists) yield similar sequences. Overall sequence similarity is not the whole story, however. The pattern of differences we see in closely related genomes is worth examining. Genes are sequences of nucleotides that code for proteins. There are four different kinds of nucleotides commonly incorporated into DNA: adenine (A), guanine (G), cytosine (C) and thymine (T) -- each block of three is called a codon. Each codon designates an amino acid (the subunits of proteins). The gene, or sequence of codons, is transcribed into RNA -- a nucleic acid similar to DNA. (RNA, like DNA, is made up of nucleotides although the nucleotide uracil (U) is used in place of thymine (T).) The RNA is then translated via cellular machinery into a string of amino acids -- a protein. All living organisms use DNA as their genetic material, although some viruses use RNA. The three letter code is the same for all organisms. The universal genetic code is redundant. There are 64 codons, but only 20 amino acids to code for; so, most amino acids are coded for by several codons. In many cases the first two nucleotides in the codon designate the amino acid. The third position can have any of the four nucleotides and not effect how the code is translated. In addition to showing overall similarity, gene sequences from closely related species show the same codon is often used for amino acids. In cases where there are differences, however, they are usually in these "silent" sites. In addition, the genome is loaded with 'dead genes' called pseudo-genes. Pseudogenes occupy the same location in the genome in closely related species. The same can be said for introns, sequences of DNA that interrupt a gene, but do not code for anything. Introns are spliced out of the RNA prior to translation, so they do not contribute information needed to make the protein. They are sometimes, however, involved in regulation of the gene. Third codon positions (silent sites), pseudo-genes and introns show more sequence differences between species than coding sections of a gene. This is because mutations that change the code of a gene, and hence the protein made, usually affect the organism adversely and are selected against. Mutations in non-coding regions do not affect the phenotype of the organism and get passed on. If two species shared a recent common ancestor one would expect genetic information, even information such as redundant nucleotides and the position of introns or pseudogenes, to be similar. Both species would have inherited this information from their common ancestor. The degree of similarity would be a function of divergence time. Studies in comparative anatomy also provide support for common descent. Groups of related organisms are 'variations on a theme' -- the same set of bones are used to construct all mammals. The bones of the human hand grow out of the same tissue the bones of a bat's wing or a whale's flipper does and they share many identifying features (muscle insertion points, ridges). The only difference is that they are scaled differently. Evolutionary biologists say this indicates that all mammals are modified descendents of a common ancestor which had the same set of bones. Evidence for common descent also comes from studying comparative developmental biology. Closely related organisms share similar developmental pathways, the differences in development are most evident at the end. This is, again, usually illustrated using mammalian (or sometimes vertebrate) examples. As organisms evolve, their developmental pathway gets modified. It is easier to modify the end of a developmental pathway than the beginning since changes early on have a cascading effect. Therefore, organisms pass through stages of early development that their ancestors passed through. These stages, however, are modified because selection "sees" all phases of an organism's life cycle. So, an organism's development mimics its ancestors although it doesn't recreate it exactly. Traces of an organisms ancestry sometimes remain even when an organisms ontogeny (development) is complete. These are called vestigial structures. Many snakes have rudimentary pelvic bones retained from their walking ancestors. This is an example of a vestigial structure. Biogeography also supports the inference of common descent. Organisms clustered spatially are frequently also clustered phylogenetically; this is especially true of organisms with limited dispersal opportunities. The mammalian fauna of Australia is often cited as an example of this; marsupial mammals fill most of the equivalent niches that placentals fill in other ecosystems. If all organisms descended from a common ancestor, species distribution across the planet would be a function of site of origination, potential for dispersal and time since origination. In the case of Australian mammals, their physical separation from sources of placentals means potential niches were filled by a marsupial radiation rather than a placental radiation or invasion. Natural selection can only mold available genetically based variation. In addition, natural selection provides no mechanism for advance planning. If selection can only tinker with what it has to work with and, if all organisms share a common ancestor, we should expect to see examples of suboptimal design in living species. This is indeed the case. In African locusts, the nerve cells that connect to the wings originate in the abdomen, even though the wings are in the thorax. When the insect send the message to fly from its brain to its wings, the nerve impulse travels down the ventral nerve cord past its target then backtracks to the wing. In _Cnenidophoran_ lizards, females reproduce parthenogenetically. Fertility in these lizards is increased when a female mounts another female and simulates copulatory behavior. This is because these lizards evolved from sexual lizards whose hormones were aroused by sexual behavior. Now, although the sexual mode of reproduction has been lost, the means of getting aroused (and hence fertile) has been retained. Fossils show hard structures of organisms less and less similar to modern organisms as you go down the strata (layers of rocks). In addition, patterns of biogeography apply to fossils as well as extant organisms. When combined with plate tectonics, fossils provide evidence of distributions and dispersals of ancient species. For example, South America had a very distinct marsupial mammalian fauna until the land bridge formed between North and South America. After that marsupials started disappearing and placentals took their place. This is commonly interpreted as the placentals wiping out the marsupials (but this may be an over simplification). Further strong evidence for macroevolution comes from the fact that suites of traits in biological entities fall into a nested pattern. For example, plants can be divided into two broad categories, non-vascular (mosses) and vascular. Vascular plants can be divided into seedless (ferns) and seeded. Vascular seeded plants can be divided into gymnosperms (pines) and flowering plants or angiosperms. And angiosperms can be divided into monocots and dicots. Each of these types of plants have several characters that distinguish them from other plants -- traits are not "mixed and matched" in groups of organisms. For example, flowers are only seen in plants that carry several other characters that distinguish them as angiosperms. This pattern arises due to lineages splitting (speciation), retaining ancestral traits and deriving new traits. Derived traits only appear in lineages descended from the population that first displayed the trait. This hierarchical pattern of diversity is what one expects to see if species branch into new species and are modified with descent. Thus, it is not just that similar species share similar traits (although that is evidence in and of itself); when you look at large groups of organisms, a pattern on a larger scale is seen. This hierarchical pattern can be produced even if the process responsible is not hierarchical. For example, microevolution leads to hierarchical patterns of genetic diversity even though it works at a single level. The question of hierarchical processes in evolution is still being debated. The real test of any scientific theory is its ability to generate testable predictions and, of course, have the predictions borne out. Evolution easily meets this criterion. In several of the above examples I stated, closely related organisms share X. If I define closely related as sharing X, this is a contentless statement. It does however, provide a prediction. If two organisms share (oh lets say) a similar anatomy (two birds, for ex.), I would then predict that their gene sequences would be more similar than a morphologically distinct organism (like a plant, for ex.). This has been spectacularly borne out by the recent flood of gene sequences -- the correspondence to trees drawn by morphological data is very high. The discrepancies are never too great and usually confined to cases where the pattern of relationship was hotly debated. MECHANISMS OF MACROEVOLUTION ---------------------------- The next three sections (speciation, extinction and punctuated equilibrium) deal with mechanisms of evolution above the species level. SPECIATION -- INCREASING BIOLOGICAL DIVERSITY --------------------------------------------- Speciation is the process of a single species becoming two or more species. Many biologists feel speciation is key to understanding evolution and that certain evolutionary phenomena apply only at speciation and macroevolutionary change cannot occur without speciation. Other biologists think major evolutionary change can occur without speciation. Changes between lineages are only an extension of the changes within each lineage. In general, paleontologists fall into the former category and geneticists in the latter. MODES OF SPECIATION Biologists recognize two types of speciation: allopatric and sympatric speciation. The two differ in geographical distribution of the populations in question. Allopatric speciation is thought to be the most common form of speciation. It occurs when a population is split into two (or more) geographically isolated subdivisions that organisms cannot bridge. Eventually, the two populations' gene pools change independently until they could not interbreed even if they were brought back together. In other words, they have speciated. Sympatric speciation occurs when two subpopulations become reproductively isolated without first becoming geographically isolated. Monophytophagous insects (insects that live on a single host plant) provide a model for sympatric speciation. If a group of insects switched host plants they would not breed with other members of their species still living on their former host plant. The two subpopulations could diverge and speciate. Some biologists call sympatric speciation microallopatric speciation to emphasize that the subpopulations are still physically separate at an ecological level. Biologists know little about the genetic mechanisms of speciation. Some think series of small changes in each subdivision gradually lead to speciation; others think there may be a few key genes that could change and confer reproductive isolation. One famous biologist thinks most speciation events are caused by changes in internal symbionts. Most doubt this, however. Populations of organisms are very complicated. It is likely that there are many ways speciation can occur. Thus, all of the above ideas may be correct, each in different circumstances. OBSERVED SPECIATIONS It comes as a surprise to some to hear that speciation has been observed. In the genus _Tragopogon_ (a plant genus consisting mostly of diploids), two new species (_T._ _mirus_ and _T._ _miscellus_) have evolved within the past 50-60 years. The new species are allopolyploid descendants of two separate diploid parent species. Here is how this speciation occurred. The new species were formed when one diploid species fertilized a different diploid species and produced a tetraploid offspring. This tetraploid offspring could not fertilize or be fertilized by either of its two parent species types. It is reproductively isolated, the definition of a species. Two other plant species have also arisen within the past 110 years in this manner, _Senecio_ _cambrensis_ and _Spartina_ _townsendii_. EXTINCTION -- DECREASING BIOLOGICAL DIVERSITY --------------------------------------------- "ORDINARY" EXTINCTION Extinction is the ultimate fate of all species. The reasons for extinctions are numerous. A species can be competitively excluded by a closely related species, the habitat a species lives in can disappear and/or the organisms that the species exploits could come up with an unbeatable defense. Some species enjoy a long tenure on the planet while others are short- lived. Some biologists believe species are "programmed" to go extinct in a manner analogous to organisms being destined to die. The majority, however, believe that if the environment stays fairly constant, a well adapted species could continue to survive indefinitely. MASS EXTINCTION Mass extinctions shape the overall pattern of macroevolution. If you view evolution as a branching tree, it's best to picture it as one that has been severely pruned a few times in its life. The history of life on this earth includes many episodes of mass extinction in which many taxa (groups of organisms) were wiped off the face of the planet. Mass extinctions are followed by periods of radiation where new species evolve to fill the empty niches left behind. It is probable that surviving a mass extinction is largely a function of luck. Thus contingency plays a large role in patterns of macroevolution. The most famous extinction occurred at the boundary between the Cretaceous and Tertiary Periods (the K/T Boundary- 65MYA). This extinction eradicated the dinosaurs. Some hypothesize that the K/T event was caused by environmental disruption brought on by a large impact on earth. Several lines of evidence point to a large collision at the time of the extinction, but attempts to link the two have not been convincing to all biologists. Following this extinction the mammalian radiation occurred. Mammals coexisted for a long time with the dinosaurs but were confined mostly to nocturnal insectivore niches. With the eradication of the dinosaurs, mammals radiated to fill the vacant niches. The largest mass extinction came at the end of the Permian (250MYA); and coincides with the formation of Pangaea II, when all the world's continents were brought together by plate tectonics. A worldwide drop in sea level also occurred at this time. Currently, human alteration of the ecosphere is causing a global mass extinction. PUNCTUATED EQUILIBRIA --------------------- Some paleontologists believe evolution is a hierarchical process. The theory of punctuated equilibria attempts to infer the process of macroevolution from the pattern of species documented in the fossil record. In the fossil record, transition from one species to another is usually abrupt in most geographic locales -- no transitional forms are found. In short, it appears that species remain unchanged for long stretches of time and then are quickly replaced by new species. However, if wide ranges are searched, transitional forms that bridge the gap between the two species are sometimes found in small, localized areas. For example, in Jurassic brachiopods of the genus _Kutchithyris_, _K. acutiplicata_ appears below another species, _K. euryptycha_. Both species were common and covered a wide geographical area. They differ enough that some have argued they should be in a different genera. In just one small locality an approximately 1.25m sedimentary layer with these fossils is found. In the narrow (10 cm) layer that separates the two species, both species are found along with transitional forms. In other localities there is a sharp transition. Gould and Eldredge, the authors of punctuated equilibria, interpret this in light of theories of allopatric speciation. They concluded that isolated populations of organisms will often speciate and then invade the range of their ancestral species. Thus at most locations that fossils are found, transition from one species to another will be abrupt. This abrupt change will reflect replacement by migration however, not evolution. In order to find the transitional fossils, the area of speciation must be found. They also argue that evolution can proceed quickly in small populations so that the tempo of evolution is not continuous. This has lead to some confusion about the theory. Some popular accounts give the impression that abrupt changes in the fossil record are due to blindingly fast evolution; this is not what the theory of punctuated equilibria says. Some PE proponents envision the theory as a hierarchical theory of evolution because they see speciation as analogous to mutation and the replacement of one species by another (which they call species selection) as analogous to natural selection. Speciation adds new species to the species pool just as mutation adds new alleles to the gene pool and species selection favors one species over another just as natural selection can favor one allele over another. This is the most controversial part of the theory. Most biologists agree with the pattern of macroevolution these paleontologists posit, but many disagree with the mechanism -- species selection. Critics would argue that species selection is not analogous to natural selection and therefore evolution is not hierarchical. The theory of punctuated equilibrium was designed to replace the theory of phyletic gradualism. Phyletic gradualists held that a species would slowly transform into another species over its entire range. Phyletic gradualism is often associated with the assumption of a uniform rate of evolution, but this need not be the case. A BRIEF HISTORY OF LIFE ----------------------- Biologists studying evolution do a variety of things: population geneticists study the process as it is occurring; systemetists seek to determine relationships between species and paleontologists seek to uncover details of the unfolding of life in the past. Discerning these details is often difficult, but hypotheses can be made and tested as new evidence comes to light. This section should be viewed as the "best guess" scientists have as to the history of the planet. The material here ranges from some issues that are fairly certain to some topics that are nothing more than informed speculation. For some points there are opposing hypotheses -- I have tried to compile a "consensus" picture. In general, the more remote the time, the more likely the story is incomplete or in error. Life evolved in the sea. It stayed there for the majority of the history of earth. The first replicating molecules were most likely RNA. RNA is a nucleic acid similar to DNA. In laboratory studies it has been shown that some RNA sequences have catalytic capabilities. Most importantly, certain RNA sequences act as polymerases -- enzymes that form strands of RNA from its monomers. This process of self-replication is the crucial step in the formation of life. The common ancestor of all life probably used RNA as its genetic material and was most likely a progenote -- an organism whose genes were not arranged into a genome. The progenote gave rise to three major lineages of life. These are: the prokaryotes ("ordinary" bacteria), archaebacteria (thermophilic, methanogenic and halophilic bacteria) and eukaryotes. Eukaryotes include protists (single celled organisms like amoebas and diatoms and a few multicelluar forms such as kelp), fungi (including mushrooms and yeast), plants and animals. Eukaryotes and archaebacteria are the two most closely related of the three. The process of translation (making protein from the instructions on a messenger RNA template) is similar in these lineages, but the organization of the genome and transcription (making messenger RNA from a DNA template) is very different in prokaryotes than in eukaryotes and archaebacteria. Scientists interpret this to mean that the progenote (common ancestor) was RNA based; it gave rise to two lineages that independently formed a DNA genome and hence independently evolved mechanisms to transcribe DNA into RNA. The first cells must have been anaerobic because there was no oxygen in the atmosphere. In addition, they were probably thermophilic ("heat-loving") and fermentative. Rocks as old as 3.5 Billion years old have yielded prokaryotic fossils. Specifically, some rocks from Australia called the Warrawoona series give evidence of bacterial communities organized into structures called stromatolites. Fossils like these have subsequently been found all over the world. These mats of bacteria still form today in a few locales (for example, Shark Bay Australia). Bacteria are the only life forms found in the rocks for long, long time -- eukaryotes (protists) appear about 1.5 BYA and fungi-like things appear about 900 MYA (0.9 Billion years ago). Somewhere along the way, photosynthesis evolved. Photosynthesis is a process that allows organisms to harness sunlight to manufacture sugar from simpler precursors. The first photosystem to evolve (PSI) uses light to convert CO2 and H2S to glucose. This process releases sulfur as a waste product. Later a second photosystem (PSII) evolved, probably from a duplication of the first photosystem. Organisms with PSII use both photosystems in conjunction to convert C02 and water (H2O) into glucose. This process releases oxygen as a waste product. Anoxygenic (or H2S) photosynthesis, using PSI, is seen in living purple and green bacteria. Oxygenic (or H2O) photosynthesis, using PSI and PSII, takes place in cyanobacteria. Cyanobacteria are closely related to and hence probably evolved from purple bacterial ancestors. Green bacteria is an outgroup. Since oxygenic bacteria are a lineage within a cluster of anoxygenic lineages, scientists infer that PSI evolved first. This also corroborates with geological evidence. Green plants and algae also use PSI and PSII for photosynthesis. In these organisms, photosynthesis occurs in organelles (membrane bound structures within the cell) called chloroplasts. These organelles originated as free living bacteria related to the cyanobacteria that were engulfed by ur-eukaryotes and eventually entered into an endosymbiotic relationship. This endosymbiotic theory of eukaryotic organelles was championed by Lynn Margulis. Originally very controversial, this theory is now virtually universally accepted. One key line of evidence in support of this idea came when the DNA inside chloroplasts was sequenced -- the gene sequences were more similar to free-living cyanobacteria sequences than to sequences from the plants the chloroplasts resided in. The advent of photosystem II brought about a large change in the atmosphere of earth -- the "oxygen holocaust". Oxygen is a very good electron acceptor and can be very damaging to living organisms. Many bacteria are anaerobic and die almost immediately in the presence of oxygen. Other organisms, like animals, have special ways to avoid cellular damage due to this element (and in fact require it to live.) Initially, when oxygen began building up in the environment, it was neutralized by materials already present. Iron, which existed in high concentrations in the sea was oxidized and precipitated. Evidence of this can be seen in banded iron formations from this time, layers of iron deposited on the sea floor. As one geologist put it -- "the world rusted". Eventually, it grew to high enough concentrations to be dangerous to living things. In response, many species went extinct, some continued (and still continue) to thrive in anaerobic microenvironments and several lineages independently evolved oxygen respiration. One lineage to evolve oxygen respiration was the purple bacteria. Purple bacteria also enabled the eukaryotic lineage to become aerobic. Eukaryotic cells have membrane bound organelles called mitochondria that take care of respiration for the cell. These are also endosymbionts just like chloroplasts. Mitochondria formed this symbiotic relationship very early in eukaryotic history, all but a few groups of eukaryotic cells have mitochondria. Later, a few lineages picked up chloroplasts. Red algae picked up ur-chloroplasts from the cyanobacterial lineage. Green algae, the group plants evolved from, picked up different ur- chloroplasts from a prochlorophyte, a lineage closely related to cyanobacteria. Prior to the Cambrian (~600 MYA), animals start appearing; the first animals dating from just before the Cambrian were found in rocks near Adelaide, Australia. They are called the Ediacarian fauna and have subsequently been found in other locales as well. It is unclear if these forms have any surviving descendents. Some look a bit like Cnidarians (jellyfish, sea anemones and the like); others resemble annelids (earthworms). All the phyla (the second highest taxonomic category) of animals appeared around the Cambrian. The Cambrian 'explosion' may have been a result of higher oxygen concentrations enabling larger organisms with higher metabolisms to evolve. Or it might be due to the spreading of shallow seas at that time providing a variety of new niches. In any case, the radiation produced a wide variety of animals. Some paleontologists think more animal phyla were present then than now. The animals of the Burgess shale are an example of Cambrian animal fossils. These fossils, from Canada, show a bizarre array of creatures, some which appear to have unique body plans unlike those seen in any living animals. Although creationists are fond of pointing to the Cambrian explosion as evidence of their views -- they ignore four things 1.) Evidence of life (including animals) prior to the Cambrian 2.) Although quick, the Cambrian explosion is not instantaneous in geologic time 3.) Although all the phyla of animals came into being, these were _not_ the modern, derived forms we see today. Our own phylum (which we share with other mammals, reptiles, birds, amphibians and fish) was represented by a small, sliver-like thing called _Pikaia_. 4.) Plants were not yet present. The Cambrian explosion is not evidence of a single creation event producing the current biota. Following the Cambrian, the number of marine families leveled off at a little less than 200. The Ordovician explosion (~500MYA) followed. This 'explosion', larger than the Cambrian, introduced numerous families of the Paleozoic fauna (including crinoids, articulate brachiopods, cephalopods and corals). The Cambrian fauna, (trilobites, inarticulate brachiopods, etc.) declined slowly during this time. By the end of the Ordovician, the Cambrian fauna had mostly given way to the Paleozoic fauna and the number of marine families was just over 400. It stayed at this level until the end of the Permian period. Somewhere in between these two points, plants and fungi (in symbiosis) invaded the land (~400 MYA). The first plants were moss- like and required moist environments to survive. Later, evolutionary developments such as a waxy cuticle and a vascular system allowed some plants (for example ferns) to exploit more inland environments. The first vascular land plant known is _Cooksonia_, a spiky, branching, leafless structure. At the same time, or shortly thereafter, arthropods (myriapods -- centipedes and millipedes) followed plants onto the land. By the Devonian period (~380 MYA) vertebrates had moved onto the land, _Ichthyostega_ is the among the first known land vertebrates, an amphibian. It was found in Greenland and was derived from lobe- finned fishes called Rhipidistians. Amphibians gave rise to reptiles, animals with scales to decrease water loss and a shelled egg permitting young to be hatched on land. Among the earliest well preserved reptiles is _Hylonomus_, from rocks is Nova Scotia. The Permian extinction (~250MYA) was the largest extinction in history. The last of the Cambrian Fauna went extinct. The Paleozoic fauna took a nose dive from about 300 families to about 50. It is estimated that 96% of all species in existence met their end. Some estimate that as many as 50% of all families went extinct (you have to kill of 100% of the species in a family before it goes extinct, hence the difference between the two numbers.) Following this event, the Modern fauna, which had been slowly expanding since the Ordovician, took over. The Modern fauna (including fish, bivalves, gastropods and crabs) was barely affected by the Permian extinction and increased to over 600 marine families at present. (The Paleozoic fauna held steady at about 100 families.) A second extinction event shortly following the Permian kept animal diversity low for awhile. The flora as well as the fauna changed following the Permian. During the Carboniferous (the period just prior to the Permian) and in the Permian the landscape was dominated by ferns and their relatives. After the Permian extinction, gymnosperms (ex. pines) became much more abundant. Gymnosperms had evolved seeds (which ferns lack) which helped their ability to disperse. Gymnosperms also evolved pollen, encased sperm which allowed for more outcrossing. In ferns, sperm must swim from the male organs to the female organs During the Jurassic (~200 MYA) and Cretaceous (~150MYA) periods the dinosaurs ruled and flowering plants (angiosperms), together with insects, diversified. Dinosaurs evolved from reptiles. One modification may have been a key splayed stance and walk with an undulating pattern because their limbs are modified from fins and their gait is modified from the movement a fish makes when swimming. These animals cannot sustain continued locomotion because they cannot breathe while they move; their undulating movement compresses their chest cavity. Thus, they must stop every few steps and breath before continuing on their way. Dinosaurs evolved an upright stance (similar to the upright stance mammals independently evolved) and this allowed for continual locomotion. In addition, dinosaurs evolved to be warm- blooded. Warm-bloodedness allows an increase in the vigor of movements in erect organisms. Splay stanced organisms would probably not benefit from warm-bloodedness. Recently, a very primitive dinosaur, _Eoraptor lunensis_ was found in Argentina. Angiosperms evolved two key adaptations that allowed them to displace gymnosperms as the dominant fauna -- fruits and flowers. Fruits allow for animal based seed dispersal (and deposition with plenty of fertilizer 8-). Flowers evolved to facilitate animal, especially insect, based pollen dispersal. Angiosperms currently dominate the flora of the world -- over three fourths of all living plants are angiosperms. Insects, who radiated a great deal along with angiosperms, dominate the fauna of the world. Over half of _all_ named species are insects. One third of this number are beetles. The end of the Cretaceous (~65 MYA) is marked by a minor mass extinction that was the demise of all the lineages of dinosaurs save the birds. Once the dinosaurs were out of the picture, mammals -- previously confined to nocturnal, insectivorous niches -- diversified. _Morgonucudon_ , a contemporary of dinosaurs, is an example of one of the first mammals. The study of the history of life on this planet reveals a planet in flux. The abundance of various lineages varies wildly across geologic time. New lineages can evolve and radiate out across the face of the planet, pushing older lineages to extinction, or relictual existences in protected refugia and/or suitable microhabitats. Organisms modify their environments, sometimes disastrously as in the case of the "oxygen holocaust" -- their modification of the environment can be the impetus for further evolutionary change. Overall, diversity has increased since the beginning of life. This increase is, however, interrupted numerous times by mass extinctions. Diversity appears to have hit an all-time high just prior to the appearance of humans. As the human population has increased, biological diversity has decreased at an ever-increasing pace. The correlation is probably causal. SCIENTIFIC STANDING OF EVOLUTION AND IT'S CRITICS The topics of evolution and common descent were once highly controversial in scientific circles; this is no longer the case. Although debates rage about how various aspects of evolution work and details of patterns of relationships are not fully worked out, evolution and common descent are considered fact by the scientific community. So-called "scientific" creationists do not base their objections on scientific reasoning or data. Nor do they have a testable, scientific theory to replace evolution with. "Scientific creationism" is a poorly disguised attempt to attack evolution because it contradicts the religious beliefs of some fundamentalists. CONCLUSION ---------- ARE WE STILL EVOLVING? Yes, evolution is still occurring; all organisms continue to adapt to their surroundings and "invent" new ways of better competing with members of their own species. In addition, allele frequencies are being changed by drift, mutation and gene flow constantly. Studying the process of evolution as it continues to occur is a major field of biology today. Although evolution has been observed and all the mechanisms have been shown to work, there is still no consensus on the relative contribution of each of the mechanisms to the overall pattern of evolution within a lineage. Likewise, although new species have been seen to arise; biologists have many questions about what influences the pattern of macroevolution. Are some groups "good" at speciating? Who survives mass extinctions and why? Evolution is the unifying theory of biology. The functions of biological entities at all levels (ecosystems, populations, organisms, genes) are the product of a non-random factor (e.g. natural selection) operating in conjunction with random factors (such as mutation and mass extinction) within a framework of historical constraint. Ecosystems, species, organisms and their component parts all have a long history. A complete explanation of any legitimate trait in biology must therefore have two components. First, a proximal explanation -- how does it work? And second, an ultimate explanation -- what was it modified from? For centuries humans have asked, "Why are we here?". A question such as that probably lies outside the realm of science. However, biologists can provide an elegant answer to the question, "How did we get here?" --------------------------------------------------------------------- SOME GOOD BOOKS ABOUT BIOLOGY AND EVOLUTION A good introductory text in evolutionary biology is: Evolutionary Biology, by Douglas Futuyma, 1986, Sinauer, Sunderland, Mass The text assumes some previous knowledge of biology, but reviews most critical background material. It contains numerous references to the primary literature. Most of the information in this file can be found (along with the references to the primary literature) in this text. A good introductory text into population genetics, the field that mathematically describes changes in the gene pool is: Principles of Population Genetics, by Hartl and Clark , 1989, Sinauer, Sunderland, Mass None of the math is very daunting (it's just an intro text after all) but it's really critical (IMHO) to understanding what evolution is all about. And again, lots of refs. A text that deals with the interface of molecular biology and evolution is: Fundamentals of Molecular Evolution, by Li and Graur, 1991, Sinauer, Sunderland, Mass A very concise introduction to this field. A text that deals with theories of macroevolution is: Macroevolutionary Dynamics, by Niles Eldredge, 1989, McGraw-Hill, New York A text that documents the history of life on earth is: History of Life, by Richard Cowen, 1990, Blackwell Scientific, Boston A readable introduction to the history of our planet and especially the changes that have occurred in the biota. A popular introduction to the field that also debunks the most common creationist arguments is: The Blind Watchmaker, by Richard Dawkins, 1987, Norton, New York Dawkins is (IMHO) a very engaging writer. A close look at the creation/evolution debate can be found in: Abusing Science, by Philip Kitcher, 1982, MIT, Cambridge, Mass A meticulous critique of creationism. A book about biodiversity is: The Diversity of Life, by E. O. Wilson, 1992, Harvard Belknap, Cambridge, Mass. This book deals with the current ecological crisis facing our planet and puts forward the strong case for preserving biological diversity. In addition, a brief explanation of evolutionary biology is presented. Numerous examples of the biology and natural histories of species and ecosystems are presented. There is a lot of information packed into this well written book.-- _very_ highly recommended.

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