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Chapter 10 GENETIC DRIFT: EVOLUTION AT RANDOM
Purposes and goals are unique to human thought. Natural phenomena do not have purpose. Scientists use chance or randomness , to mean that when physical causes can result in any of several outcomes, scientists cannot predict what the outcome will be in any particular case. Scientists may b e able to specify the probability , and thus the frequency, of one or another outcome. Genetic drift and natural selection are the two most important causes of allele substitution – evolutionary change – in populations. A sequence of random events in succession can change the frequency of an allele: this is called random genetic drift. Allele frequency is changed from one generation to the next: allele fluctuation. The genes in one generation do not end up in the same ratio in the next generation. This is a case of non-adaptive evolution: genetic drift does not necessarily results in adaptation. We should not assume that a characteristic or a difference between populations and species, is adaptive or has evolved by natural selection unless there is evidence for this conclusion.
THE THEORY OF GENETIC DRIFT
GENETIC DRIFT AS SAMPLING ERROR
The genes included in any generation, whether in newly formed zygotes or in offspring that survive to reproduce, are a sample of the genes carried by the previous generation. Any sample is subject to random variation or sampling error. The proportions of different kinds of items in a sample are likely to differ, by chance, from the proportions in the set of items from which the sample is drawn. Over long periods of time, variation is more easily maintained in large populations than in small ones. Random genetic drift reduces variation and leads eventually to the random fixation of one allele and the loss of other, unless it is countered by other processes, such as gene flow or mutation. COALESCENCE Not all members of a generation leave equal number of descendants. Some do not leave any. As time goes on, more and more alleles of a particular gene become extinct, so that the population consists of descendants of fewer and fewer of the original gene copies. Eventually all gene copies in the population are descended form a single ancestral gene copy.
The genes in the present population have coalesced back to a single common ancestor. The smaller the population, the more rapidly all gene copies coalesce back to a single ancestral copy. A population will eventually become monomorphic for one allele or the other, and that the probability that one allele will be fixed rather than the other, is equal to the initial frequency of that allele. A 1 = 0.8, the probability of A 1 to become fixed is 80%. A 2 = 0.2, the probability of A 2 to become fixed is 20%. “In genetics, coalescent theory states that all genes or alleles in a given population are ultimately inherited from a single ancestor shared by all members of the population, known as the most recent common ancestor. If the inheritance relationships are written in the form of a phylogenetic tree, termed a gene genealogy, the gene or allele of interest is said to undergo coalescence to the common ancestor… Coalescent theory seeks to reconstruct the ancestral relationship of individuals and is therefore of great utility in reconstructing the phylogenetic relationships of species based on information at the molecular level.” http://en.wikipedia.org/wiki/Coalescent_theory This does not mean that the population of a single common ancestor had only one member at that time. This model does not include the evolution of adaptive traits, those that evolve by natural selection. RANDOM FLUCTUATIONS IN ALLELE FREQUENCIES Small independent populations of a species are called demes , and the grouping of all these population is a metapopulation. An allele is selectively neutral if selection neither favors it or not. Neutral alleles may change by mutation over time allowing the calculations of the molecular clock. Example of random fluctuation of an allele: A deme has an allele frequency of 0.5; in the next generation the frequency may be 0.47; in the following generation it will change again from 0.47 to some other higher or lower value. This process of random fluctuation continues over time. Since no stabilizing force returns the allele to 0.5, the frequency will wander (drift) to either 0 or 1: the allele is either extinct or fixed. Once an allele has reached either 0 or 1, it cannot change unless another allele is introduced into the population, either by mutation or by gene flow from another population. The allele frequency may increase in some demes of the metapopulation and decrease in some others. The variance in allele frequency among the demes continues to increase from generation to generation. The number of demes fixed for on or another allele continues to increase, until all demes have become fixed. Thus, demes that initially are genetically identical evolve by chance to have different genetic constitutions.
The genetic drift that occurs when a new population is established by few colonists is called founder effect. The founder effect was defined by Ernst Mayr in 1963. The founders carry only a small fraction of the genes found in the original population. There is a loss of genetic variation. The new population will be genetically different from the parent population: the frequency of genes will be different. In some cases, it may lead to speciation. “For example, the Afrikaner population of Dutch settlers in South Africa is descended mainly from a few colonists. Today, the Afrikaner population has an unusually high frequency of the gene that causes Huntington’s disease, because those original Dutch colonists just happened to carry that gene with unusually high frequency. This effect is easy to recognize in genetic diseases, but of course, the frequencies of all sorts of genes are affected by founder events.” http://evolution.berkeley.edu/evosite/evo101/IIID3Bottlenecks.shtml GENETIC DRIFT IN REAL POPULATIONS Laboratory populations Experiment by Peter Buri (1956) Started 107 experimental populations of Drosophila melanogaster with 8 males and 8 females. Followed the allele bw and bw^75 for eye color by which all three genotypes are recognized. Propagated each population for 19 generations. By generation 19, 30 populations had lost the bw^75 allele, and 28 had become fixed for it. Among the unfixed populations, intermediate allele frequencies were quite evenly distributed. The results matched those expected by the genetic drift theory. Other experiments conducted by McCommas and Bryant (1990) with house flies also supports the mathematical predictions of the genetic drift theory. Four populations of houseflies were established at each three bottleneck sizes: 1, 4 and 16 pairs. Each population rapidly increased to 1000 individuals, after which the populations were reduced to same bottleneck size. The procedure was repeated five times. The average heterozygosity decline steadily after each bottleneck. The smaller the bottlenecks were, the more rapidly it declined. Natural populations Theories tell us what patterns to expect in the genetic features of natural populations. We infer the causes of evolution by interpreting these patterns. Patterns of molecular genetic variation in natural populations often correspond to what we would expect if the loci were affected by genetic drift. Fixation of deleterious alleles can reduce survival and reproduction, increasing the risk of extinction.
THE NEUTRAL THEORY OF MOLECULAR EVOLUTION
Neutral alleles are not subject to natural selection because they do not affect or have very little effect on fitness. “The neutral theory of molecular evolution is that most evolutionary change at the molecular level is driven by random drift rather than natural selection. The neutral theory does not suggest that random drift explains all evolutionary change: natural selection is still needed to explain adaptation. However, the neutral theory states that evolution at the level of the DNA and proteins, but not of morphology, is dominated by random processes; most evolution at the molecular level would then be non-adaptive. The neutral theory can be contrasted with the idea that almost all molecular evolution has been driven by natural selection.” Source: http://www.blackwellpublishing.com/ridley/tutorials/Molecular_evolution_and_neutral_theory2.asp Proposed by Motoo Kimura in the late 1960s and early 1970s. Small minority of mutations in DNA or protein sequences is advantageous and become fixed by natural selection. Many mutations are disadvantageous and become eliminated by natural selection. The great majority of mutations that are fixed do not affect fitness – they are neutral. Silent or synonymous mutations. Neutral mutations are fixed by genetic drift because natural selection does not act on it. Additional explanations: http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution http://darwin.eeb.uconn.edu/eeb348/lecture-notes/molevol-neutral.pdf The neutral theory of molecular evolution also proposes that: Evolutionary substitutions at the molecular level proceed at a roughly constant rate, So that the degree of sequence difference between species can serve as a molecular clock It is possible to determine the divergence time of species. “…large parts of non-protein-coding DNA sequences are highly conserved under strong purifying selection and thus do not vary much from individual to individual, indicating that mutations in these regions have deleterious consequences.[19][20]^ When genetic variation does not result in differences in fitness, selection cannot directly affect the frequency of such variation. As a result, the genetic variation at those sites will be higher than at sites where variation does influence fitness.[7]” (^7) Rice SH. (2004). Evolutionary Theory: Mathematical and Conceptual Foundations. Sinauer Associates: Sunderland, Massachusetts, USA. ISBN 0-87893-702-1 See ch. 1. (^19) Kryukov GV, Schmidt S & Sunyaev S (2005) Small fitness effect of mutations in highly conserved non-coding regions. Human Molecular Genetics 14:2221- (^20) Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS & Haussler D (2004) Ultraconserved elements in the human genome. Science 304:1321- Source: http://en.wikipedia.org/wiki/Natural_selection PRINCIPLES OF THE NEUTRAL THEORY Only a fraction of the mutations that occur is effectively neutral. The neutral mutation rate , μ 0 , will be less than the total mutation rate , μT. Effectively neutral means that the mutant allele is so similar to the original one that in its effect on survival and reproduction that changes in its frequency are governed by genetic drift alone, not by natural selection.
The neutral theory should be the preferred explanation only if natural selection cannot explain the data. What percentage of the alleles is “neutral” versus those that are “non-neutral”? VARIATION WITHIN AND AMONG SPECIES. The fraction of mutations that are neutral is higher for synonymous than for non-synonymous (amino acid-replacing) nucleotide substitutions. A study by McDonald and Kreitman (1991) showed that 5% of the polymorphisms, but fully 29% of the substitutions that distinguish species, are replacement changes. They concluded that amino acid replacing substitutions is an adaptive process governed by natural selection. If most replacement substitutions are advantageous rather than neutral, they will increase in frequency and be fixed more rapidly than by genetic drift alone. Replacement substitutions will spend less time in the polymorphic state than selectively neutral synonymous substitutions do. They will contribute less to polymorphic variation within species. “PROTEINS often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations.” Adaptive protein evolution at the Adh locus in Drosophila by John H. McDonald & Martin Kreitman. Nature 351: 652-654, 20 June 1991. “…data from Drosophila simulans and D. yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species.” Adaptive protein evolution in Drosophila by Nick G. C. Smith and Adam Eyre-Walker. Nature 415, 1022-1024, 28 Feb. 2002 DO COMPARISONS AMONG SPECIES SUPPORT THE NEUTRAL THEORY? Sequencing DNA has provided data on the rate of molecular evolution Most DNA sequence evolution has been neutral.
- Rate of synonymous substitutions is generally greater than the rate of replacement substitutions, e. g. various genes of humans versus rodents.
- Substitution occurs most frequently at third-base position in codons and least frequently in second- base positions.
- Rates of substitutions are higher in introns than in coding regions of the same gene, and even higher in pseudogenes. Pseudogenes are non-functional genes related in sequence to functional genes.
- Some genes evolve more slowly than other, e. g. histone genes.
Genes that evolve most slowly are those thought to be most strongly constrained by their precise function. The rate of evolution is greatest at DNA positions that, when altered, are least likely to affect function, and therefore least likely to alter the organism’s fitness. Support for the neutral theory’s prediction that the rate of evolution should be constant is equivocal. Some rates have been constant and others not. Mitochondrial DNA sequences have evolved more slowly in turtles than in other vertebrates.
GENE FLOW AND GENETIC DRIFT
Gene flow or gene migration is the transfer of alleles from one population to another. The rate at which populations drift toward fixation of one allele or another is inversely proportional to the effective population size. Gene flow counteracts gene fixation. The mathematical model (page 241) shows that a little gene flow keeps all the demes fairly similar in allele frequency and heterozygosity remains high. Genetic drift and gene flow affect all loci the same way, whereas natural selection affects different loci more or less independently. If each of a number of polymorphic loci yields about the same value of gene frequency, it is likely that selection is not strong. GENE TREES AND POPULATION HISTORY The genealogical history of genes in populations is the basis of Coalescent Theory. Because gene lineages within a population become extinct by chance over the course of time, all gene copies in a population today are descended from one gene copy that existed at some time in the past. The smaller the effective size of a population, the more rapidly genetic drift transpires. The existing gene copies in a small population must stem from a more recent common ancestor than the gene copies in a large population. It takes longer for the present genes in the larger population to coalesce to their common ancestor. In a diploid population, the common ancestor of a random pair of gene copies occurred 2Ne generations ago, where Ne is the size of the effective population. THE ORIGIN OF MODERN HOMO SAPIENS REVISITED Homo erectus migrated from Africa to Europe and Asia about 1.8 million years ago.
