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Hardy-Weinberg equilibrium (HWE) One locus with 2 alleles at HWE: p2 + 2pq + q2 = 1 HWE illustrates an important principle: random mating of individuals is usually equivalent to random union of gametes (alleles) Assumptions of HWE •Random Mating •large population size (no drifting) •no selection •no migration •no mutation Implicit assumptions: •sexual reproduction • nonoverlapping generations •normal mendelian segregation of alleles • equal fertility of parent genotypes • equal fertilizing capacity of gametes • equal survival of all genotypes Is this realistic? Probably not. Linkage equilibrium •Alleles at separate loci are expected to segregate independently during meiosis. They show linkage equilibrium. Example: • 2 loci with alleles A1 and A2; B1 and B2 their frequencies will be p1 and p2 and q1 and q2. •Possible gametes A1B1; A1B2; A2B1; A2B2 • Genotype frequencies will be the product of constituent allele frequencies Linkage disequilibrium Linkage disequilibrium = a deviation from random associations of alleles at different loci • Linkage disequilibrium can be caused by : - chance events - population bottlenecks - recent mixing of different populations - selection • Linkage disequilibrium is important because: - It is common in threatened species with small populations - evolutionary processes are altered - functionally important genes may exhibit linkage disequilibrium - can be a signal of recent admixture of populations LECTURE THREE: EVOLUTION IN LARGE POPULATIONS: SELECTION Influences upon genetic diversity and the evolution of populations Genetic Drift Mutation Natural Selection Migration The need to evolve • environmental change is ubiquitous – Pests, parasites, novel competitors, anthropogenic change, global warming, new diseases • Species must adapt and evolve to avoid extinction Ecological responses to recent climate change (Walther et al. (2002) Nature 416: 389-395) Ecological responses to recent climate change (Walther et al. (2002) Nature 416: 389-395) Ecological responses to recent climate change (Walther et al. (2002) Nature 416: 389-395) The need to evolve • environmental change is ubiquitous – Pests, parasites, novel competitors, anthropogenic change, global warming, new diseases • Species must adapt and evolve to avoid extinction The “Red Queen Hypothesis” (Van Valen, 1973) • species must continually evolve in order to avoid falling behind competitors Adaptation • 3 forms of adaptation: Physiological, behavioural and genetic Physiological adaptation: change in metabolism or biochemistry to deal with an environmental problem Example: High-altitude adaptations in vertebrate haemoglobins • Increased blood O2 affinities at altitude • Linked to structural changes in haemoglobin molecules Weber (2007) Respiratory Physiology & Neurobiology vol 158 132–142 Adaptation Behavioural adaptation: the things organisms do to survive Example: feeding specialisations in bottlenose dolphins in Shark Bay, WA • Subset of population uses sponges to probe substrate for fish • Recent co-ancestry • Vertical social transmission among females • Cultural transmission of tool use? Krützen et al. (2005) PNAS vol 102 8939-8943 Adaptive evolution Adaptive evolution: long term evolutionary changes in response to natural selection upon superior genetic variants • Adaptive evolutionary changes in animals have been documented in: - morphology, behaviour, colour, prey size, body size, life history, disease tolerance and resistance, biocide resistance, tolerance to pollutants. • Plants evolve in response to: - soil conditions, light regimes, water stress, flooding, air pollution and herbicides. Plant populations adapted to diverse ecological conditions are so common that they have their own term, called ecotypes. Rapid adaptive evolution in Darwin’s finches Case study: evolution of Darwin’s finches caused by a rare climatic event (Grant and Grant, 1993 Proc. R. Soc. Lond. B 251 111-117) • Darwin’s finches studied continuously on Galapagos Is. Daphne Major since 1973 • Major El Nino 1982-83 causing 8 months rain • Plant and seed communities changing introducing new selection pressures • Directional selection for longer, slender beaks better adapted for eating smaller seeds Unpredictable Evolution in a 30-Year Study of Darwin’s Finches (Grant and Grant, 1993 Science 296: 707) Adaptive evolution and explosive speciation in cichlid fish Kocher, T (2004) Nature Reviews Genetics 5: 288-29 • Genetic adaptation and adaptive evolution is ubiquitous in species that have genetic diversity Adaptive evolution • Take home message: Adaptive evolution is ubiquitous in plants and animals that have genetic variation • Adaptive evolution is important in the following conservation contexts: - Preserving evolutionary potential - Adaptation to marginal environments - Genetic adaptation to captivity - Adaptation of invasive species - Outbreeding depression Natural Selection Natural Selection • Differential survival and reproduction in nature that favors individuals that are better adapted to their environment • eliminates of less fit organisms and genetic variants • Moulds the variation made available by mutation, drift and migration • Adaptive changes occur only by natural selection. During the process of adaptation, natural selection can enhance, retain or eliminate variants Evolving populations are complex systems • Evolving populations are complex systems influenced by mutation, migration, selection and chance operating within the context of the breeding system Competition Climate Disease Loss of genetic diversity Zygotes SELECTION CHANCE SAMPLING deaths Adults Mating MIGRATION Gametes Selection of mates MUTATION Introduction to Conservation Genetics 2 Fig 6.1 Evolving pop as complex systems.ppt Selection • Alleles whose carriers produce fertile offspring that survive to reproductive age increase in frequency • Alleles whose carriers produce fewer offspring decrease in frequency • Selection operates at all stages of the life cycle: - Acquisition of mates - Mating success - Fertlization success - Number and survival of offspring - Longevity - Pollen production - Pollination success - Zygote viability - Dispersal ability Selection decreases the frequency of deleterious alleles • Consider selection against a recessive lethal, Chondrodystrophic dwarfism in California condors • Recessive homozygotes die but heterozygotes have normal survival Modelling the impact of selection against chondrodystrophy: refer to table 6.1 and Example 6.1 Selection increases the frequency of advantageous alleles • Consider adaptive evolutionary change, industrial melanism in the peppered moth • Melanic moths first recorded in 1848 • By 1900 99% of population melanic • Frequency of M (melanic) allele increases until eventually fixed • Rate of change depends on the strength of Selection against the non melanic form or the selection coefficient, s. Modelling adaptive evolutionary change, refer to Figure 6.4, Box 6.2 Selection models • The impact of selection depends on: - Strength of selection (selection coefficient, s) - Mode of inheritance - Allele frequencies Selection is stronger on some loci and characters than others… Selection is stronger on some loci than others… For equivalent circumstances, selection has a greater impact on haploid loci than on autosomal diploid loci. Sex-linked loci are intermediate (refer to table 6.2) Selection is stronger on some characters than others… – introns / microsatellites – proteins ~ weak ~ moderate – MHC ~ stronger • All still relatively weak compared to selection on morphological or quantitative characters • Eg. selection coefficient at MHC typically ≤ 1% Selection on quantitative characters • Variation is determined by several loci and environmental effects • Selection affects phenotypic means and variances 3 forms of selection on quantitative characters: Directional selection: favours phenotypes toward one end of the distribution and shifts mean towards that extreme Stabilizing selection: favours phenotypic intermediates and reduces variation about the mean Disruptive Selection: favours both phenotypic extremes and increases variation about the mean Case study: directional selection Undesirable evolutionary consequences of trophy hunting in Bighorn sheep Coltman et al. (2003) Nature 426, 655-658 Directional selection: favours phenotypes toward one end of the distribution and shifts mean towards that extreme Case study: stabilizing selection Stabilizing selection for birth weight in humans after Mather, 1973 Stabilizing selection: favours phenotypic intermediates and reduces variation about the mean Case study: disruptive selection Disruptive Selection: favours both phenotypic extremes and increases variation about the mean Disruptive selection and then what? Rueffler et al. (2006) TREE 21, 238-245; Schulter and McPhail (1992) The American Naturalist 140: 85-108 B e n t h i c P l a n k f e e d EVOLUTION IN LARGE POPULATIONS: INTERACTIONS OF MUTATION, MIGRATION AND SELECTION Mutation • Sudden genetic change in an allele or chromosome • ALL GENETIC DIVERSITY ORIGINATES FROM MUTATION • Single locus mutations are generated by base substitutions, additions and deletions, gene duplication events and by insertion and excision of mobile elements • Mutations that affect fitness traits are most important to conservation biology • Silent or neutral mutations are still important as molecular markers Mutation rates vary across loci and characters • Generally speaking, mutation rates are low and can often be ignored as an evolutionary force Mutation is a recurrent process • Mutations continue to arise over time. • Modelling the impact of mutation on a population: A1 p0 u Frequency of A1 in the next generation: A2 q0 p1 = p0 (1-u) Change in frequency of the A1 allele: ∆p = p1 – p0 Substitute for p1: ∆p = p0 (1-u) – p0 ∆p = -up0 • Genetic diversity takes hundreds to millions of generations to be regenerated by mutation (refer to box 7.1) Mutation occurs in both directions • The balance between forward and reverse mutations (up = vq) results in an equilibrium A1 p u v A2 q u q̂ = u+ v Example: What is the equilibrium frequency of the A2 allele in a case where the forward mutation rate (u) is 10-5 and the reverse mutation rate (v) is 3x10-6 u q̂ = u+ v -5 10 q̂ = = 10/13 = 0.77 -5 -6 10 + 3x10 Equilibrium frequency of A2 (q) = 77% . Equilibrium A1(p) = 1 - 0.77 = 0.23 Mutation-Selection balance • Most mutations are deleterious and their removal by selection is slow, thus they accumulate within the genome. This is referred to as the ‘mutation load’ •High cumulative rate of deleterious mutations is kept in check by selection mutation-selection balance Autosomal recessive u q̂ = √ s Refer to Pg 149 of text derivation and table 7.4 for expressions for other modes of inheritance. Migration • Population differentiation through selection and genetic drift is slowed by migration (gene flow) ∆q = q1 - q0 = q0 + m (qm – q0) – q0 = m (qm – q0) Importance of mutation, migration and their interactions with selection to conservation • genetic diversity lost by chance and selection is regenerated by mutation • forced migration through translocation can be used as a management tool to recover lost genetic diversity in small threatened populations • migration can reverse inbreeding depression • inbreeding results in exposure of rare deleterious alleles in the mutation load leading to reduced reproduction and survival • understanding these interactions allow us to tease apart the effects of the various forces upon natural populations, leading to improved understanding of the study system 3 Founders NEXT LECTURE: GENETIC CONSQUENCES OF SMALL POPULATION SIZE, MAINTAINING GENETIC DIVERSITY G1 G2 G3 Genetic Drift /chance events Mutation Relevance of Mutations in Populations • Mutations are the source of variation, but the process of mutation does not itself drive genetic change in populations • Mutation rates (probability that one allele changes to another allelic form in one generation) are too slow Relevance of Mutations in Populations •Mutation works best in larger populations •In large populations, nearly every conceivable mutation will occur, which gives natural selection the chance to “try them out” and retain the few beneficial ones • For species that have lost substantial proportions of their genetic variation, regeneration by mutation may take a million or more generations (unlikely to occur during the lifespan of the species) • Mutation is almost entirely ineffective in generating useful variation in small populations and probably too slow to help species of conservation concern Migration Migration • Genetically effective migration from another population will replace lost, or introduce new, variation to a population • Migration reduces differences among populations generated by mutation, selection or chance • reduced migration limiting geneflow leads to random differentiation among sub-populations With gene flow – panmixia, or one population Without gene flow – population fragmentation and subdivision Migration • Migration increases genetic diversity within a population according to: - the proportion of migrants in the “new” population (i.e. the postmigration population) - the difference of allele frequencies in the migrants compared to those of the “old” pop. Old popn Migrant popn New popn Original population plus migrants and their new alleles or different frequencies. Therefore, Diversity increases. Migration • Increased loss of alleles by drift in small populations is counterbalanced by the greater impact of an individual migrant • Very few migrants are needed to prevent differentiation of subpopulations by drift at neutral loci Fst = measure of population differentiation Nm = no. of individuals in the pop X no. of migrants per generation