Author: Chris Colby ( Title: FAQ: Introduction to Evolutionary Biology

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====================================================================== Author: Chris Colby ( Title: FAQ: Introduction to Evolutionary Biology ====================================================================== AN INTRODUCTION TO EVOLUTIONARY BIOLOGY -- BY CHRIS COLBY ********************************************************* INTRODUCTION ------------ Evolution is one of the most powerful theories science has ever known. For a variety of reasons, however, it is also one of the most misunderstood. One common misunderstanding is that the phrase "survival of the fittest" summarizes evolutionary theory. It does not. The phrase is both incomplete and misleading. Two other common misinterpretations are that evolution is progress and organisms can be arranged on an evolutionary ladder from bacteria to man. This post is an outline of the basics of evolutionary biology. It is intended to be an overview of the concepts and mechanisms of evolution and dispel pervasive misunderstandings about the theory. Creationist arguments are not addressed here; and many interesting topics in evolutionary biology are not covered (symbiosis and endosymbiosis, origins of life, evolution of sex, human evolution and much more) because I can't include everything and keep this down to a readable length. WHAT IS EVOLUTION? Evolution is a change in the gene pool of a population over time. 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, rare black variants spread through the population 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 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 called "microevolution". Larger changes (taking more time) are termed "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 phenomena. 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, 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 "average" moth did not get progressively darker. Indeed there were no "average" half-white/half-black moths ever in the population. I have defined evolution, here, 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 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. An organism's phenotype is determined by its genes and its environment. Phenotype is the morphological, physiological, biochemical, behavioral and other properties exhibited by a living organism. 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. 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. Organisms 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. An organism's success depends a great deal 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 each gene assorted entirely independently, the gene pool would be at linkage equilibrium. However, if some alleles were often found together in organisms (i.e. did not assort randomly) 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. 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 (i.e. they are at 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, biologists often, for the sake of brevity, refer to it that way. Selection is not a guided or cognizant entity; it is simply an effect. When supplied with genetic variation, natural selection allows organisms to adapt to their current environment. It does not, however, have any foresight. Structures or behaviors do not evolve for future utility. An organism must be, to some degree, 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 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). It is the individual organism that either reproduces or fails to reproduce. 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". 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. Helping closely related organisms can appear altruistic; but this is also a selfish behavior. An organisms reproductive success (or fitness) has two components; direct fitness and indirect fitness. An organism's direct fitness is a measure of how many alleles it contributes to the subsequent generation's gene pool by reproducing. An organism's indirect fitness is a measure of how many alleles identical to its own it helps enter the gene pool. An organism's direct fitness plus its indirect fitness is called its inclusive fitness. Natural selection favors behaviors that increase an organism's inclusive fitness. Closely related organisms share many of the same alleles. For example, in diploid species, siblings share at least 50% of their alleles -- the percent is higher if the parents are related. So, helping close relatives to reproduce gets an organisms own alleles better represented in the gene pool. The benefit of helping relatives increases dramatically in highly inbred species. In som 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 an attempt to maximize ones' own inclusive fitness; "altruistic" means behaving in an attempt to increase anothers fitness without regard to ones' own. This 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. For example, a steel shelled turtle would probably be an improvement. 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 most optimal set of traits (the global optima); but are probably several other sets of alleles that would yield a population almost as adapted (local optima). Transition from a local optima to the global optima 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 feather will therefore produce more offspring than the short feathered males. In the next generation, the average tail feather 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 feather 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 the only 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 most 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 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. Mutations occur at random with respect 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, with one exception. A new class of mutation has recently been documented in bacteria and yeast. It appears that unicellular organisms can undergo directed 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 mechanism of directed mutagenesis is unknown at this time, but it has been shown to be under genetic control - - i.e. directed 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. Biologists have not yet studied if directed mutations can produce novel solutions to environmental challenges. It is also unknown if it 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 in meiosis, 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. One interesting case of this involves genetic elements called P elements. In the genus _Drosophila_, P elements were transfered 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 transfered 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 edition, the overall pattern of macroevolution and evidence for common descent of all living species is presented. 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. Modern biologists hold that 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 living species of apes. 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 is now extinct and was not the same as present day apes (or humans for that matter). Our closest relatives are the chimpanzee and the pygmy chimp. 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) yeild 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 organism's ancestry sometimes remain even when an organisms ontogeny (development) is complete. These are called vestigal structures. Many snakes have rudimentary pelvic bones retained from their walking ancestors. This is an example of a vestigal 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 thorox. 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 criteria. 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. 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. 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 occured. 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 outcompeted 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); it is estimated that 96 percent of all species died out at this time. The sea animals that make up the so-called Paleozoic Fauna (among them crinoids, cephalopods, brachiopods and corals), suffered the worst. This assemblage did not reradiate after the event and remains at the level of diversity it sunk to after the extinction. In contrast, the sea animals that make up the Modern Fauna (gastropods, bivalves, crabs, echinoids and bony fishes) were barely affected and continued to increase in diversity after the event. The Permian extinction coincides with the formation of Pangea 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 sometime 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. 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 (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. 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 EVOLUTION TEXTS (IMHO) 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.


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