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Genes, genetics and natural selection • Darwin’s theory of natural selection explained macroevolutionary patterns in terms of population-level processes • The birth of modern genetics led initially to a battle between the Mendelians and the Darwinians • The neo-synthesis saw the coming together of genetics and evolutionary thought. The selfish gene is just a (very elegant) restatement of this fact. • Patterns of molecular evolution have generated many more controversies, notably over the neutral theory. • The processes of speciation and extinction are still very little understood, however important progress has been made in understanding what types of genetic differences can lead to reproductive isolation What Darwin said Organisms produce too many offspring Heritable differences exist in traits influencing the adaptation of an organism to its environment Organisms that are better adapted have a higher chance of survival 1 Galton’s law of regression to the mean 2 Mendel’s peas x x AA x aa Aa x Aa AA/Aa & • Characters are correlated between relatives 3 – height, hereditary genius • But over time, deviations from the mean tend to be diluted • Natural selection cannot produce persistent change aa 1 – Great men have less great sons! Rediscovered c. 1901 by de Vries, Correns and Tschermak von Seysenegg 3 4 Mendelians versus biometricians • Mendelians – – – – – • Nilsson Ehle’s wheat (1909) Adherents of Galton’s conclusion that natural selection is ineffective Evolution proceeds in large steps (saltational) Mutations of discrete nature Natural selection cannot work because of regression towards mean Bateson, de Vries Genotype AA Aa aa BB Biometricians – – – – Bb Adherents of gradualist, Darwinian view Variation is truly continuous Large mutations happen, but are not very important Pearson, Weldon bb 5 Fisher’s results on genetic variation Morgan and the fly-room (Sturtevant, Muller and Bridges) • • • 6 • • First widely read mathematical treatment of selection Three types of quantitative trait – Continuous (weight, height, milk yield) – Meristic (bristle number in Drosophila) – Discrete with continuous liability (disease susceptibility) Discovered crossing-over (cM) Proved chromosomes carried hereditary factors Showed heritability of bristle number in Drosophila Frequency Phenotypic variance = σ2P Trait value 2 P Phenotypic Additive genetic = 2 A + 2 D + Dominance 2 I + 2 E Epistatic Environmental Genetic 7 8 The neo-synthesis (1920s-1930s) Estimating the genetic component of quantitative traits Offspring value (y) y=a+bx X X X X X X X X X b= X X Cov(x, y) = h2 = Var(x) • Contributions to a coherent Darwinian view of evolution by natural selection from geology, palaentology, natural history, cytology, genetics, and populations genetics • Variation in natural populations 2 A 2 P X – – – – – – – Mid-parent value (x) µ µS ∆µ = h2 (µS - µ) Selection response Trait value Mimicry in butterflies Industrial melanism in moths Pin and thrum flower forms in Primula Darwin’s finches Sickle-cell anaemia Birth weight Disease Trait value 9 The selfish gene • • Mimicry? considers whether a new mutation will spread through a population NOT what is best for the population • However, natural selection acts on the set of genes it finds in an individual • The correlation of relatedness over evolutionary time will determine whether of nor the fitness interactions between genes are important in shaping evolution – – – 10 Can natural selection explain The evolutionary theory of Haldane, Fisher and Wright is a gene-centred view – – All maintained by natural selection The photo shows unpalatable swallowtail model species (left) and palatable mimetic forms of female Papilio memnon (right). At bottom is the Papilio memnon male. This polymorphic, female-limited Batesian mimicry was first described by Alfred Russel Wallace (1865). Y chromosome genes Green-beard genes and kin recognition Selfish genetic elements (segregation distorters, cytoplasmic male sterility, sex-ratio distorters) 11 12 Kin selection • Social insects? A Camponotus japonicus ant sharing honey with another ant • Work by Hamilton, Price and others showed the importance of interactions between relatives in explaining biological patterns • JBS Haldane – “I would be willing to lay down my life for 2 brothers or 8 cousins.” rb − c > 0 Mother Sister Daughter Father brother son Niece or Nephew female 0.5 0.75 0.5 0.5 0.25 0.5 0.375 male 1 0.5 1 0 0.5 0 0.25 Cost to actor Relatedness Benefit to receiver of action Haplodiploid Relatedness in haplodiploid insects 13 • 14 Two or three theories of sexual selection Sex-related characteristics? • Fisherian runaway process – – – – • Good-genes – – • Stalk-eyed fly Females have an asymmetric preference for a male trait which varies in the population Males with the favoured trait are more successful in mating irrespective of whether they are better adapted to their environment The population will shift towards the new trait Requires covariance between trait and female preference Sexually selected traits are indicators of good genes (Hamilton and Zuk) E.g. the wattle on a rooster indicates parasite load Costly traits and the handicap principle – – Costly traits can evolve as honest signals of quality as females will always benefit from being choosy (Doesn’t have to be a good genes argument) Irish elk 15 16 Species-level selection? (Stanley 1975) • • The number of differences between genes at the molecular level correlates with the time separating the species (Zuckerkandl and Pauling 1962) • The rate of substitution is constant over time • Sarich and Wilson (1967) used the molecular clock to estimate the human-chimp split as 5MY – previously thought to be 14MY Higher-level selection leading to long-term changes in clade morphology can occur if… – – – • The molecular clock Speciation rates are correlated with parameters of life-history/ecology OR extinction is selective AND rates of speciation and extinction are uncoupled from what natural selection favours within populations Evidence? – – – Major extinctions were highly selective Planktotrophic gastropod molluscs have lower extinction rates than those with direct development BUT the fossil record shows a relative increase in the number with direct development (higher speciation rates?) Completely asexual lineages (e.g. some rotifers, fish, lizards) usually at tips of trees, suggesting they are short-lived Doolittle et al. (1996) 17 18 Kimura’s neutral theory Does natural selection explain molecular evolution? Kimura (1968); King and Jukes (1969) • • Constancy of rate of molecular evolution (the molecular clock) • • More important regions of proteins evolve at a slower rate than less important domains • • High levels of protein polymorphism • High rates of molecular evolution (about 1.5x10-9 changes per amino acid per year – even in living fossils!) The majority of changes in proteins and at the level DNA which are fixed between species, or segregate within species, are of no selective importance The rate of substitution is equal to the rate of neutral mutation k = f neutral The level of polymorphism in a population is a function of the effective population size and the neutral mutation rate • = 4Ne Polymorphisms are transient rather than balanced Frequency NOW Balanced NOW Transient Time 19 20 Detecting natural selection at the gene level • Speciation and extinction Bursts of amino acid substitution in lineages • How do new species arise? – Gradual accumulation of differences between geographically separated populations exposed to different selective pressures - allopatric – Rapid event associated with change in lifestyle (e.g. host-plant preference, mating song, chromosome number, hybridisation) – sympatric • • Amino acid changes concentrated at sites within proteins • Specific footprints in patterns of genetic variation How can we study the process of speciation? – Hybrid zones – Genetic footprints – Analysis of reproductive isolation • Why do species go extinct? – Major extinctions in evolutionary history – Anthropogenic extinction – Genetic hitchhiking 21 The biological species concept • Allopatric speciation A species is a population whose members are able to interbreed freely under natural conditions • • • – Gene trees versus species trees Incongruent Peripatric – Populations at periphery of species range get separated and diverge – May be associated with ‘founder’ events – E.g. island species Phylogenetic - Individuals within a species are more closely related to each other than to any other organisms Congruent Vicariance events – Mountain, river, marsh, forest arises and separates populations – E.g. numerous species boundaries at Pyrenees – Many species can hybridise when brought together (e.g. ligers & tions) – Where do primarily asexual species fit in? (e.g. bacteria) – Many species complexes (particularly plants, e.g. elms) • 22 Centrifugal – Contraction of species range leads to differentiation among refugial populations, which overwhelm peripheral populations (like Wright’s shifting balance) E.g. Only 52% human genes closest to chimps. Rest are (H,(C,G)) or ((H,G),C) Satta et al. (2000) 23 24 Islands – extreme allopatry New and unusual species often form on islands associated with reduced competition and broadening of potential ecological niches Gigantism Vertebrate species richness • Geographical patterns in species richness Flightlessness Energy (evapotranspiration) Occupation of Unusal niches Species richness in the US 25 Sympatric speciation • 26 Studying speciation – ring species Speciation over over-lapping populations due to change in Greenish warblers in Asia – Host-plant preference (Rhagoletis) – Local adaptation in association with the evolution of pre-mating isolation (Chiclid fishes in lake Victoria) – Changes in courtship song (crickets) • Maybe driven by sexual selection? – Birds of paradise – Leipdoptera The two overlapping Siberian forms have different song patterns Elsewhere, the pattern varies more or less continuously with an EW axis of increasing complexity Irwin (2000) 27 28 Studying speciation - hybrid zones The genetics of speciation • Gradients in allele frequency across hybrid zones indicate that some genes can cross the genetic barrier • Variation in gradient indicates some genes are linked to factors generating hybrid incompatibility • Studies on Drosophila show some variation is shared between species while others are only in one Pyrenean hybrid zone in Corthippus parallelus 29 Haldane’s rule • 30 Chromosomal speciation In crosses between two species, if one sex is missing or sterile it is the heterogametic (XY) sex • New plant species can form when species hybridise – E.g. Wheat, Helianthus petiolaris and H. annuus x X Y Mammals Bird Butterflies • Male Female Female X X natural selection Female Male Male Natural experiment Similar set of chromosomal segments retained Interactions between genes on the X and autosomes are ‘imbalanced in the heterogametic hybrid Artifical selection x • Years of ‘Speciation genes’ can be mapped in Drosophila between related species For viability – Only one putative speciation gene has been found (but it is very interesting) Lab experiment 31 32 Taxonomic survivorship curves Van Valen’s Red Queen hypothesis • Deterioration in the environment of a species caused by continual adaptation of competitors leads to a constant per unit time risk of extinction, so a geometric distribution of species survivorship times • Based around idea that ecology is a zero-sum game 33 The Permian extinction • • • • 34 The K/T mass extinction Largest extinction in the history of life – 251 MY ago 80% marine species went extinct in 1MY 9 orders of insect and therapsid reptiles lost Associated with massive volcanic activity, large increase in CO2 and global warming • • • 35 65 MY ago 15% marine invertebrate families and 45% genera lost Extinction of the dinosaurs 36 Evidence for the asteroid theory (Alvarez et al. 1980) • Historical anthropogenic extinctions Iridium spike at K/T boundary • – High concentrations in extraterrestrial objects – BUT • • • Soot in same layer Shocked quartz crystals Putative crater off Yucatan peninsula • BUT all can also be produced by volcanoes? Worldwide, there is no evidence of Indigenous hunter-gatherers hunting nor over-killing megafauna. The largest regularly hunted animal was bison in North America and Eurasia, yet it survived for about 10,000 years until the early 20th century. For social, religious and economic reasons, Indigenous hunters harvested game in a sustainable manner. http://www.amonline.net.au/factsheets/megafauna.htm • 37 Factors endangering species • • • • • Habitat loss Exotics Pollution Over-harvesting Disease 88% 46% 20% 14% 2% (43 % UK plant species exotics) (Wilcove et al 1998) Number of species in group Vertebrates Mammals Birds Reptiles Amphibians Fishes Subtotal Wave of extinction of large animals in Australia around time of appearance of first humans (c. 50,000 YA) Number of Number of Number of % of total in % of total threatened threatened threatened group assessed species in species in species in threatened in threatened in 2002 2002* 4,763 9,946 7,970 4,950 1996 1,096 1,107 253 124 2000 1,130 1,183 296 146 2002 1,137 1,192 293 157 25,000 52,629 734 3,314 752 3,507 742 3,521 24% 12% 4% 3% 24% 12% 25% 21% 3% 7% 30% 18% IUCN Red list 2002 39 However, in the last 300 years there have been 27 extinctions of large mammals on continents and 55 on islands (including Australia) 38