BIOL 3506 Cat Sheet PDF

L1-2 Overview 8. Geography G*E: Differences how different individuals 9. Response to artificial selection (genotypes) respond to sunlight Why...

L1-2 Overview 8. Geography G*E: Differences how different individuals 9. Response to artificial selection (genotypes) respond to sunlight Why is Evolution Important ? 10. Antibiotic resistance 1. Health Sciences Type of mutation 2. Natural Products (eg. Penicillin) Main concept of Evolutionary Biology Germline (can pass by gametes (eggs and 3. Agriculture (eg. crop & animal breeding 1. Genes sperm)) & somatic (cannot pass) methods / artificial selection) - Genotype = genetic make-up of an mutations 4. Environmental Management organism ○ Type of germline mutations: 5. Understanding Ourselves - Phenotype = observable traits and Chromosomal Mutations & Gene characteristics of an organism made by Mutations History of Evolutionary Theory the interaction of its genotype ○ Gene Mutation include Point Pre-Darwinian Ideas - Mutations = copying errors Mutations (only single nucleotide 1. Georges Louis Leclerc, Comte de Buffon - Alleles = genes located at the same change) & Frameshift Mutations Buffon’s Law: different regions have position on a pair of homologous (Insertion or deletion of one or distinct fauna and flora 動植物 despite chromosomes that control different forms more nucleotides) similar environments of a certain trait Mutation rate (µ) is the frequency of new 2. Jean-Baptiste Lamarck 2. Natural Selection alleles in single gene, sequence or Species change to new species over time - Organisms that are more adapted to their genome over time (very low that mutations & Inheritance of acquired 後天 characters environment are more likely to survive and alone cannot account for the rapid Darwin’s theory pass on the genes evolution of populations) (Missense, Species descent from common ancestor - Genetic drift = Random changes in nonsense, and synonymous mutations) Only some species survive/reproduce population allele frequencies due to finite ○ mutation rate in males human is Favorable variants expected to survive = population size about 10x higher than females, ∵ Evolution by Natural Selection higher number of cell divisions Evidence of Darwin’s theory L3-4 Genetic Diversity & Mutation from zygote to gamete 1. All living thing have DNA & ATP Variation = Trait that differs slightly from another of ○ Inbreeding in small populations 2. Close related organisms will be genetically its type leads to accumulation of harmful more similar than distantly related mutations Calculation of different types of variation organisms L5-6 Selection & Drift 3. Anatomy 解剖學: Bilateral symmetry 雙邊 Phenotype = Genotype (G) + Environment (E) + 對稱 G*E interaction Evolution = A genetically based change in the 4. Homology 同源性: 2 or more species hv mean phenotype of a population over time eg. Skin color same ancestor - Change in the population mean phenotype G: Genetic differences among individuals within 5. Vestigial Structures (no longer use part) (P) does not mean evolution has taken population 6. Fossil Record place E: Tanning 曬黑 (phenotypic plasticity = changes in 7. Transitional fossils (show transition of a - If genotypes not randomly distributed in an organism's in response to unique environment) species) environments (Cov G*E), lack of change in  P does not mean that no evolution has 𝐻1 = [1 − 1 ] × 𝐻0 2𝑁 taken place Heterozygosity after t generations = Calculate response of Selection (Evolution) 1 𝑡 −𝑡/(2𝑁) 𝐻𝑡 = [1 − 2𝑁 ] × 𝐻0 = 𝐻0𝑒 2 𝑅 = 𝑆 ×ℎ Limitation of Ne - < actual population size (NC) where, Balancing selection (=) - Idealized population (1:1 sex ratio, random R = Expected response to selection (evolution) mating, no variance in offspring numbers, S = Strength directional selection (natural etc.) selection) [Some individuals are more successful at surviving and reproducing than others] L7-8 Populations & Gene flow h2 = heritability 遺傳力 of the trait (0 to 1) Genotype frequencies will stay the same if five Evolution will not take place if: conditions are met - There is no variation Natural selection become less efficient in later age 1. A very large population: no genetic drift - h2 = 0 and possible that alleles that have selective 2. No emigration or immigration: no gene - If there is no difference in survival or advantage in early life but reduce survival in late flow reproductive success between variants life when the alleles have not remove 3. No mutations 4. Random mating: no sexual selection Different types of natural selection Genetic drift 5. No natural selection: all alleles neutral Directional selection (-) (tend to select - Random changes in population allele benefit traits & reduce genetic variation) frequencies due to finite population size Hardy-Weinberg equilibrium states that in the - Caused by sampling error of zygotes from absence of disturbing干擾 factors, genetic variation the gene pool in a population will remain constant from one - results in allele frequencies in the offspring generation to the next. not matching those of the parents, (p2 = homozygous dominant, pq=heterozygosity, q2 especially in small populations = homozygous recessive) Disruptive selection (+) Calculation of effective population size 理論群體大 小 (Ne) over multiple generations harmonic mean 調和平均值 1 𝑁𝑒 = 1 𝑡 ( 1 𝑁0 + 1 𝑁1 +... + 1 𝑁𝑡−1 ) Stabilizing selection (-) Calculation of loss of heterozygosity in a random mating population  𝐹𝑆𝑇 = 1 with and are undiscriminating 不分青紅皂 (4𝑁𝑚+1) 白 with whom they will mate where Nm = the number of migrants successfully ○ mating opportunity limits male entering a population per generation reproductive success Types of non-random mating Two types of sexual selection Disassortative - mate with others who are Intrasexual selection: competition among genotypically or phenotypically different members of the same sex (usually males) Assortative - mate with others who are for access to mates similar to themselves genotypically or Intersexual selection: members of one sex phenotypically (usually females) choose to mate with Inbreeding depression 近親繁殖衰退: particular members of opposite usually caused by recessive deleterious 有 害 alleles The Benefit of Female Choice Gene flow = Introduce new alleles into a 1. Direct benefits population’s gene pool and change existing allele L9 Sexual Selection Direct ↑ immediate fecundity 生育力 frequencies (provide new genetic or maladaptive Sexual selection selects for traits that improve 2. Sensory exploitation 感官利用 variation) mating success (independent to natural selection) female prefer male traits that do not exist Natural selection favors large female size 3. Good genes Fixation index (FST) measures variation in allele when fecundity繁殖力 is size dependent Female choice increases genetic quality of frequencies among populations Niche divergence - males and females its offspring and pass her fitness 𝐹𝑆𝑇 = (𝐻𝑇−𝐻𝑆) 𝐻𝑇 =1− ( ) 𝐻𝑆 𝐻𝑇 (0≤FST≤1) evolve to fill different ecological niches only sexual selection could produce traits 4. Arbitrary(random) traits or runaway 失控 sexual model that compromise損害 survival Undermine破壞 natural selection when where, eg. Marine iguanas 海鬣蜥 (Amblyrhynchus female prefer for exaggerated H = 2pq cristatus) favour large size but easy to die when ornamentation誇張裝飾 (beatty) S = Average 2pq of individual subpopulations food scarce食物匱乏 (2𝑝𝑞1+2𝑝𝑞2+...+2𝑝𝑞𝑛) Mating strategy 𝑛 Sexual Differences in Reproductive Strategy T = Total 2pq when the subpopulations are Monogamy 1♂ vs 1♀ Female reproductive success affected by combined 2𝑝𝑎𝑣𝑒𝑟𝑎𝑔𝑒𝑞𝑎𝑣𝑒𝑟𝑎𝑔𝑒 Polygamy 1 vs ∞ mate quality ○ Polygyny: 1♂ vs ∞ ♀ ○ fecundity 生育力 limits female ○ Polyandry: 1♀ vs ∞♂ FST=0 (all hv same allele) reproductive success ○ eg. harem 後宮 polygamy, Lekking FST=1 (all hv diff. allele) (expensive eggs) polygamy (♂ aggregate聚合 in Males reproductive success ↑ by particular areas to display to ♀), Inferring 推斷 gene flow from FST increasing numbers of females they mate Territorial defense polygyny  Promiscuity ∞ vs ∞ Causes of speciation Ecological speciation L10 Specialion ○ Evolution reproductive evolution Biological species concept (BSC): a species is a as a side effect of adaptation to group of actually or potentially interbreeding different ecological circumstances natural populations which are reproductively Speciation by genetic conflict isolated from other such groups ○ Self-promoting elements (selfish - not apply to asexually reproducing species genes): promote their own spread, - hard to count allopatric異域 populations but sacrifice other genes within genome Phylogenetic species concept (PSC): the smallest Speciation by sexual selection set of organisms that share an ancestor and can Speciation by reinforcement加強 be distinguished from other such sets ○ Evolution of stronger reproductive isolation because of low-fitness Reproductive isolation mechanisms (RIMs) hybrids (selection unfavoured) Prezygotic (premating) RIMs Speciation by polyploidy ○ Ecological isolation: seasonal, Speciation by hybridization temporal, habitat isolation & Speciation by drift sexual (eg. diff. mating call) Geographic speciation Prezygotic (postmating) RIMs ○ Allopatric speciation (geographic ○ Mechanical isolation, Copulatory barrier) isolation, Gametic, ○ Sympatric同域 speciation Postzygotic RIMs ○ Parapatric speciation (between ○ Ecological (adaption), Behavioural, allopatric and sympatric Hybrid雜交 unviability不可行 & speciation) sterility不孕 L11-12 Phylogeography & Phylogenetics Phylogeny: A hypothesis of ancestor descendent relationships Phylogenetic tree: a graphical summary of a phylogeny (hypothesis) connecting related species Character and Distance Why Homoplasy occur? (same features evolved Some traits can remove by a species, but A phylogenetic tree can be based on: independently from diff. ancestor) keep by another → Hard to determine who 1. qualitative共同 aspects like common Parallel evolution divide first characters (to the history) ○ independent evolution from same 2. quantitative measures like the distance or ancestor Constructing Phylogenetic Trees similarity Convergent evolution ○ independent evolution from diff. Assumptions ancestor dichotomous branching 二分分支 Scondary loss Simple is the best ○ 返祖 Use homologous characters to construct but not homoplasious (same features evolved independently from diff. ancestor) Methods 3 main methods Monophyletic: group that includes ALL of the descendants後代 of a common ancestor. (as known as CLADES) Paraphyletic: group that includes some, but not all of the descendants of a common ancestor Polyphyletic: incorrect taxa分類單元 are formed by homogeneous (simliar) characters Plesiomorphy: Same ancestral character state for a particular clade. Species trees vs gene trees Character-based methods: use the aligned Apomorphy: a character state different than the In a species tree, each internal node 對齊 characters, such as DNA or protein ancestral state, or DERIVED STATE represents a speciation event. sequences (eg. maximum likelihood or Synapomorphy: a derived character state Genes may evolve before or after any Bayesian inference) (apomorphy) that is SHARED by two or more taxa given speciation event. due to inheritance遺傳 from a common Autapomorphy: a uniquely derived character state Gene trees problem Homoplasy: same features evolved independently Genes may evolve before or after any from diff. ancestor given speciation event.  Distance-based methods: Transform the Polygenic inheritance B: ground colour Black (recessive allele = Brown) sequence dissimilarities into pairwise Discontinuous variation → single genes affect C: expression of coat colour genes as a distances (eg. neighbour-joining) character whole (recessive allele = Albino白化症) Continuous variation → most characters such as height, mass or even eye colour ⇒ may be due to an environmental influence such as diet OR interaction of several genes. parsimony-based methods: the least evolutionary change (eg. maximum The interaction of two genes parsimony) Comb shape in chickens Parsimony-based methods θ = 𝑚𝑖𝑛 Σ𝑛 (𝑖, 𝑗| θ) Ratio of polygenic traits departs from Mendelian Given a family of trees T(θ) with minimum 9:3:3:1 substitutions n(i,j|θ) between branches i and j. ⇒ leads to a continuous distribution L13-14 Phenotypic evolution A polygenic (more gene) character typically shows: Peppered Moth (Biston betularia) continuous variation Observation: normal distribution Urban: ↑pepper color (white), ↓black several different genotypes may produce Rural: ↑black, ↓pepper color (white) same phenotype Hypothesis: bird predators were altering the What drives the evolution of polygenic traits? frequencies of the color morphs based on the moths’ contrast to their backgrounds The interaction of three or more genes Test: Correct, Coloration pattern of the Peppered In the coat colour of mice the are three genes (A, B moth has been under Natural Selection & C) interacting to produce a range of different (predation). coat colours Allele: black is caused by a dominant allele (DD, A: production of small yellow band near end of Dd); pepper color is recessive allele (dd) hair (agouti) (recessive allele = Non-agouti)  Black might be able to absorb sunlight. Higher Vd: dominance genetic variance (variance body temperatures may allow the lizards to move caused by epistatic deviations, i.e. faster and escape predators non-additive interactions between alleles at different loci) Statistical Methods Ve = Environmental variance μ = mean Vge = Genetic-Environmental Interaction σ = square root of the variance σ2 = variability of a group of measurements "reaction norm" = set of phenotypes produced by a given genotype across a range of environments Correlation coefficient (r): measures the strength of (phenotypic plasticity) their association [-1 (-ve) ~ 1 (+ve)] eg. diff. performance in the same gene in diff. Not follow Hardy-Weinberg equilibrium (p2+2pq+q2) environment Natural selection in choosing single-gene and Phenotypic variation Phenotypic variation → Heritability polygenic traits Heritability: The proportion of the total phenotypic Polygenic traits have a range of variation that is due to genetic difference phenotypes that often form a bell curve 2 Natural selection on polygenic traits can 𝐻 = 𝑉𝑔 / 𝑉𝑝 affect the distributions of phenotypes (shape of the curve) in three ways: If H2 = 0, then none of the phenotypic directional selection, stabilizing selection, variance is caused by genetic variance. or disruptive selection (L5-6 Different If H2 = 1, then the phenotypic variance is types of natural selection) 𝑉𝑝 = 𝑉𝑎 + 𝑉𝑑 + 𝑉𝑖 + 𝑉𝑒 + 𝑉𝑔×𝑒 100% caused by genetic variance. eg. lizard color Vp = Phenotypic variation Heritability response to population Vg = Genetic variance Breeder's equation Va: additive genetic variance (variance 2 caused by additive effects of alleles at all 𝑟 =ℎ 𝑠 relevant loci) Vi: genic interaction variance (variance r = response to selection (change in the phenotypic caused by dominance deviations, i.e. mean of a population from one generation to the non-additive interactions between alleles next) at a single locus) 2 Red lizards are more visible to predators, so they ℎ = 𝑉𝑎 / 𝑉𝑝 will be less likely to survive and reproduce. h2 = narrow-sense heritability (how much The development of advanced species passes phenotypic variation in a population is caused by through stages represented by adult organisms of genetic effects that can be passed on from parents more primitive species [development of an to their offspring) individual organism (ontogeny) follows same 𝑠 = μ 𝑎𝑓𝑡𝑒𝑟 − μ 𝑏𝑒𝑓𝑜𝑟𝑒 progression as evolutionary history of that s = directional selection differential (difference in organism's species (phylogeny)] mean phenotype between the original whole population before selection and the mean of the Hourglass-like metazoan phylotypic stage individuals who actually breed to produce the next generation) The transcriptome is dominated by highly conserved genes which involved in the patterning If we calculate h2 like this: of the metazoan後生動物 body plan 2 ℎ = 𝑟/𝑠 Early embryonic development shows a wide h2 = realized heritability (estimate the variety of forms (like the wide top of an hourglass), narrow-sense heritability by r & s) but as development progresses, the forms converge to a more similar structure (the narrow L15-16 Evolutionary developmental biology middle), before diverging again into (Evo-devo) species-specific forms. Compares the developmental processes of The two major hypotheses about how different organisms to infer how developmental developmental processes are conserved against processes evolved. Homeotic同源 genes and pattern formation evolutionary changes In animals, the key homeotic loci are These similar genetic/regulatory mechanisms may called Hox (for “homeobox”) genes – they explain similarities why some embryonic are a gene family created by gene developmental stages look similar in different taxa duplication events ○ Occur in groups (gene duplication events) – the number of genes in each group and the total number of groups varies among phyla ○ 3’ → 5’ ○ Hox genes specify anterior – posterior and dorso – ventral axes Recapitulation (Haeckel’s) concept of in bilateral animals (10 Hox loci), development (false proved) but homologues are present in  sponges and jellyfish, and plants and fungi (3-4 Hox loci) Retrotransposons: replicate through reverse ○ vertebrates have 4 Hox cluster transcription of an RNA copy and integrate the ○ loci are specific, fixed positions on product DNA into new sites in the host genome. a chromosome where a particular gene or genetic marker is located Relationship between genome & other factors //gene cluster is a group of ≥ 2 genes found within an organism's Genome size and organism complexity: positive DNA that encode similar linear relationship polypeptides or proteins which collectively share a generalized Genome size and body size: roughly positive linear function relationship In plants, the key homeotic genes are the MADS-box genes 1. Viruses, archaea, bacteria (typically