Finished chapters 10 and 11. Skip to Chapter 16 to cover evolution

1. Finished chapters 10 and 11. Skip to Chapter 16 to cover evolution

2. Chapter 16: Population Genetics and Evolution Robert E. Ricklefs The Economy of Nature, Fifth Edition

3. Evolutionary responses to climate changes (drought: 1975-1978) (mortality+selection)

4. Background: Molecular Basis for Genetic Variation • Genetic information is encoded by DNA. • Genetic variation is caused by changes in the nucleotide sequence of DNA. • DNA serves as a template for the manufacturing of proteins and other nucleic acids: • each amino acid in a protein is encoded by a sequence of 3 nucleotides, called a codon • the genetic code contains redundancy because only 20 amino acids need be encoded from 64 possible codons

5. The source of genetic variation is mutation and recombination. • Mutations are errors in the nucleotide sequence of DNA: • substitutions (most common) • deletions, additions, and rearrangements also may occur • Causes of mutations: • random copying errors • highly reactive chemical agents • ionizing radiation

6. Can mutations be beneficial? • Most mutations are neither harmful nor beneficial: • the altered properties of proteins resulting from mutations are not likely to be beneficial • natural selection weeds out most deleterious genes, leaving only those that suit organisms to their environments • an example is the sickle-cell mutation, which alters the structure of the hemoglobin molecule with deleterious effects for its carriers

7. More on Mutation • Mutations are likely to be beneficial when the relationship of the organism to its environment changes: • selection for beneficial mutations is the basis for evolutionary change, enabling organisms to exploit new environmental conditions • Processes that cause mutations are blind to selective pressures -- mutation is a random force in evolution, producing genetic variation independently of its fitness consequences.

8. Mutation Rates • The rate of mutation for any nucleotide is low, 1 in 100 million per generation. • (Contextualize it and it changes ….) • Because a complex individual has a trillion or so nucleotides, each individual is likely to sustain one or more mutations. • Rates of expressed gene mutations average about 1 per 100,000 to 1 per million: • rates of expression of phenotypic effects are often higher because they are controlled by many genes.

9. Recombination • Variation is introduced during meiosis when parts of the genetic material inherited by an individual from its mother and father recombine with each other: • recombination is the exchange of homologous sections of maternal and paternal chromosomes • recombination produces new genetic variation rapidly  to know: ‘evolution of body size in Galapagos marine iguanas. Natural and sexual selection have opposing influences on the size of males. Read ‘more on the web’ (page 314 – go to the website of the textbook)

10. Sources of Genetic Variation • While mutation is the ultimate source of genetic variation: • recombination multiplies this variation • sexual reproduction produces further novel combinations of genetic material • the result is abundant variation upon which natural selection can operate

11. The genotypes of all individuals make up the gene pool. • The gene pool represents the total genetic variation within the population. (all the genes in all the individuals in a population) • Not all combinations of alleles for a given gene will be represented in the gene pool, especially those with low probability. • If a rare combination of alleles confers high fitness, individuals with this combination will produce more offspring, and these alleles will increase in frequency.

12. The Hardy-Weinberg Law • In 1908, Hardy and Weinberg independently described this fundamental law: the frequencies of both alleles and genotypes will remain constant from generation to generation in a population with: • a large number of individuals • random mating • no selection • no mutation • no migration between populations

13. Wait! Too many assumptions! • Natural populations rarely meet all of these conditions. • Large populations rarely occur in isolation • all populations experience some degree of random mutation • mating is seldom random, but rather is the result of careful selection of mates. • Most importantly, selective pressures favor individuals whose alleles give them the greatest fitness, so survival and reproductive success are never random. • Because of these factors inherent in natural selection, allelic frequencies do not remain constant and evolution occurs.

14. So – why study Hardy-Weinberg law? • (1) the law proves that natural selection is necessary for evolution to occur. Darwin's theory of evolution states that for evolution to occur, populations must be variable, there must be inheritance between generations, and natural selection must make survival and reproductive success non-random. The conditions set up by the Hardy-Weinberg Law allow for variability (the existence of different alleles) and inheritance, but they eliminate natural selection. The fact that no evolution occurs in a population meeting these conditions proves that evolution can only occur through natural selection. • (2) the Hardy-Weinberg Law allows us to estimate the effect of selection pressures by measuring the difference between actual and expected allelic frequencies or phenotypes.

15. Consequences of Hardy- Weinberg Law (what does it mean?) • No evolutionary change occurs through the process of sexual reproduction itself. • Changes in allele and genotype frequencies can result only from additional forces on the gene pool of a species. • Understanding the nature of these forces is one of the goals of evolutionary biology.

16. Deviations from Hardy-Weinberg Equilibrium 1 • For a gene with two alleles, A1 and A2, that occur in proportions p and q, the proportions of the 3 possible genotypes in the gene pool will be: • A1A1: p2 • A1A2: 2pq • A2A2: q2 • Deviations from these proportions are evidence for the presence of selection, nonrandom mating, or other factors that influence the genetic makeup of a population.

17. Deviations from Hardy-Weinberg Equilibrium 2 • Most natural populations deviate from Hardy-Weinberg equilibrium. • We thus consider some of the forces responsible for such deviations (setting aside mutation and selection): • effects of small population size • nonrandom mating • migration

18. Want more? • http://bcs.whfreeman.com/ricklefs6e/content/cat_010/hw01.html • After completing this module you will understand how the Hardy-Weinberg equilibrium provides a foundation for studying changes in gene frequencies over time. In addition, you will understand how to statistically test whether populations are or are not in equilibrium.

19. Genetic Drift • Genetic drift is a change in allele frequencies due to random variations in fecundity and mortality in a a population: • genetic drift has its greatest effects in small populations • when all but one allele for a particular gene disappears from a population because of genetic drift, the remaining allele is said to be fixed

20. Founder Events • When a small number of individuals found a new population, they carry only a partial sample of the gene pool of the parent population: • this phenomenon is called a founder event • founding of a population by ten or fewer individuals results in a substantially reduced sample of the total genetic variation

21. Population Bottlenecks • Continued existence at low population size of a recently founded population results in further loss of genetic variation by genetic drift, referred to as a population bottleneck: • such a situation may have occurred in the recent past for the population of cheetahs in East Africa • fragmentation of populations into small subpopulations may eventually reduce their genetic responsiveness to selective pressures of changing environments

22. Saharan Cheetah, Algeria Estimates put the numbers of the animal, also known as the Northwest African cheetah (Acinonyx jubatus hecki) as low as 250, but, says Sarah Durant of the Zoological Society of London, this is guesswork. "Virtually nothing is known about the population," she says.

23. The Cheetah “The cheetah is unusual among felids in exhibiting near genetic uniformity at a variety of loci previously screened to measure population genetic diversity. It has been hypothesized that a demographic crash or population bottleneck in the recent history of the species is causal to the observed monomorphic profiles for nuclear coding loci. The timing of a bottleneck is difficult to assess, but certain aspects of the cheetah's natural history suggest it may have occurred near the end of the last ice age (late Pleistocene, approximately 10,000 years ago), when a remarkable extinction of large vertebrates occurred on several continents. To further define the timing of such a bottleneck, the character of genetic diversity for two rapidly evolving DNA sequences, mitochondrial DNA and hypervariable minisatellite loci, was examined” (Dating the genetic bottleneck of the African cheetah, 1993)

25. Effective Population Size: The bottleneck effect “Alleles” in original population “Alleles” remaining after bottleneck

26. The Founder effect • Outlying populations founded by a small number of individuals from source population • Analogous to bottleneck • Expect higher drift, lower diversity in outlying populations

27. The significance… • … of founder events and bottlenecks for natural populations is that the fragmentation of populations into small subpopulations may eventually restrict the evolutionary responsiveness of those subpopulations to the selective pressures of changing environments, making them MORE vulnerable to extinction

28. Assortative Mating • Assortative mating occurs when individuals select mates nonrandomly with respect to their own genotypes: • positive assortative mating pairs like with like • negative assortative mating pairs mates that differ genetically (opposites attract) • assortative mating does not change allele frequencies but does affect frequencies of genotypes

29. Positive assortative mating leads to inbreeding. • Positive assortative mating can lead to an overabundance of homozygotes: • one result is the unmasking of deleterious recessive alleles not expressed in heterozygous condition (inbreeding depression) • most species have mechanisms that assist them in avoiding matings with close relatives: • dispersal, recognition of close relatives, negative assortative mating, genetic self-incompatibility

30. Is inbreeding always undesirable? • Inbreeding creates genetic problems, particularly loss of heterozygosity. • But - In some cases inbreeding may be beneficial: • plants that can self-pollinate are capable of sexual reproduction even when suitable pollinators are absent • when organisms are adapted to local conditions, matings with distant individuals may reduce fitness of progeny

31. Inbreeding: Can you marry your first-cousin?

32. To marry or not to marry your 1st cousin? (illegal in 24 US states) a team of scientists led by Robin L. Bennett, a genetic counselor at the University of Washington and the president of the National Society of Genetic Counselors, announced that cousin marriages are not significantly riskier than any other marriage. The study, published in the Journal of Genetic Counseling in 2002, determined that children of first cousins face about a 2 to 3 percent higher risk of birth defects than the population at large first-cousin marriages entail roughly the same increased risk of abnormality that a woman undertakes when she gives birth at 41 rather than at 30. Banning cousin marriages makes about as much sense, critics argue, as trying to ban childbearing by older women. A closer look reveals that moderate inbreeding has always been the rule, not the exception, for humans. Inbreeding is also commonplace in the natural world, and contrary to our expectations, this can be a very good thing. It depends in part on the degree of inbreeding.

33. Global inbreeding Researchers who study inbreeding track consanguineous marriages—those between second cousins or closer. In green countries, at least 20 percent and, in some cases, more than 50 percent of marriages fall into this category. Pink countries report 1 to 10 percent consanguinity; peach-colored countries, less than 1 percent. Data is unavailable for white countries.

34. Optimal Outcrossing Distance • Mating with individuals located at intermediate distances (optimal outcrossing distance) may be desirable: • nearby individuals are likely to be close relatives, resulting in inbreeding • distant individuals may be adapted to different conditions: • in controlled matings in larkspur plants, crosses between individuals 10 m apart enhanced seed set and seedling survival, compared to selfing and mating with distant individuals

35. Optimal outcrossing distance balances the risks of inbreeding and of mating with individuals adapted to different conditions

36. Inbreeding / outbreeding • The consequences of inbreeding are unpredictable and depend largely on what biologists call the founder effect • Field biologists have often observed that animals reared together from an early age become imprinted on one another and lack mutual sexual interest as adults; they have an innate aversion to homegrown romance – to avoid incest • normal patterns of dispersal actually encourage inbreeding. When young birds leave the nest, for instance, they typically move four or five home ranges away, not 10 or 100; that is, they stay within breeding distance of their cousins. Intense loyalty to a home territory helps keep a population healthy because it encourages "optimal inbreeding." This elusive ideal is the point at which a population gets the benefit of adaptations to local habitat—the coadapted gene complexes—without the hazardous unmasking of recessive disorders.

37. Inbreeding / outbreeding • In some cases, outbreeding can be the real hazard. A study conducted by E. L. Brannon, an ecologist at the University of Idaho, looked at two separate populations of sockeye salmon, one breeding where a river entered a lake, the other where it exited. Salmon fry at the inlet evolved to swim downstream to the lake. The ones at the outlet evolved to swim upstream. When researchers crossed the populations, they ended up with salmon young too confused to know which way to go. In the wild, such a hybrid population might lose half or more of its fry and soon vanish. • What about humans?

38. Humans vs salmon? • Patrick Bateson, a professor of ethology at Cambridge University, argues that outbreeding has at times been hazardous for humans too. For instance, the size and shape of our teeth is a strongly inherited trait. So is jaw size and shape. But the two traits aren't inherited together. If a woman with small jaws and small teeth marries a man with big jaws and big teeth, their grandchildren may end up with a mouthful of gnashers in a Tinkertoy jaw. Before dentistry was commonplace, Bateson adds, "ill-fitting teeth were probably a serious cause of mortality because it increased the likelihood of abscesses in the mouth." Marrying a cousin was one way to avoid a potentially lethal mismatch. • Studies have shown that people overwhelmingly choose spouses similar to themselves (assortative mating). The similarities are social, psychological, and physical, even down to traits like earlobe length. Cousins, Bateson says, perfectly fit this human preference for "slight novelty."

39. Migration and Deviations from Hardy-Weinberg Equilibrium • Mixing individuals from populations with different allele frequencies can result in deviations from genotypic frequencies under the Hardy-Weinberg equilibrium: • such movement of genes is called gene flow • mixing results in under-representation of heterozygotes • this phenomenon is called the Wahlund effect

40. Genotypes vary geographically. • Differences in allelic frequencies between populations can result from: • random changes (genetic drift, founder events) • differences in selective factors • Such differences are particularly evident when there are substantial geographic barriers to gene flow.

41. Ecotypes • The Swedish botanist Göte Turreson used a common garden experiment to show that differences among plants from different localities had a genetic basis: • under identical conditions (in the common garden) plants retained different forms seen in their original habitats • Turreson called these different forms ecotypes

42. Ecotypes may be close to one another or distant. • Although ecotypes may be geographically isolated and found some distance apart, this is not always the case: • if selective pressures between nearby localities are strong relative to the rate of gene flow, ecotypic differences may arise: • plants on mine tailings and uncontaminated soils nearby may differ greatly in their tolerance to toxic metals (copper, lead, zinc, arsenic)

44. Clines and Other Geographic Patterns • Some traits may exhibit patterns of gradual change over distance: • such patterns are referred to as clines • clinal variation usually represents adaptation to gradually changing conditions of the environment • Other genetic patterns may be found: • geographic variation related to random founder effects • differentiation related to abrupt geographic barriers and spatial/temporal variation

45. Clinal variation may occur over distance with variations in the environment: duration of nymphal development and width of the adult head in males of the field cricket show a cline from north to south; genetic basis…

46. No genetic basis for these variations (the differences geographically bear no relationship to habitat or locality) These traits (for the land snail) vary over distance independently of variations in the environment

47. Geographic isolation: 2 pop. -> genetically distinct

48. Natural Selection • Natural selection occurs when genetic factors influence survival and fecundity: • individuals with the highest reproductive rate are said to be selected, and the proportion of their genotypes increases over time • Natural selection can take various forms depending on the heterogeneity of, and rate of change in, the environment.

49. Stabilizing Selection • Stabilizing selection occurs when individuals with intermediate, or average, phenotypes have higher reproductive success than those with extreme phenotypes: • favors an optimum or intermediate phenotype, counteracting tendency of phenotypic variation to increase from mutation and gene flow • this is the prevailing mode of selection in unchanging environments

50. Directional Selection • Under directional selection, the fittest individuals have more extreme phenotypes than the average for the population: • individuals producing the most progeny are to one extreme of the population’s distribution of phenotypes • the distribution of phenotypes in succeeding generations shifts toward a new optimum • runaway sexual selection is an excellent example of this phenomenon