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89 Cards in this Set
- Front
- Back
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Which of the following is the most correct explanation of why more antibiotics become ineffective in the treatment of bacterial infection?
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Mutations on bacterial genes that cause bacteria’s resistance to drug become positively selected.
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Which of the following does not support the hypothesis that teosinte is the progenitor of maize?
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More sequence polymorphism is observed in maize population than teosinte population.
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Which of the following correctly describes a selective sweep caused by a recent positive selection?
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Immediately after the fixation of an advantageous mutation, the amount of genetic variation around the mutation is greatly reduced.
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about when did chimpanzees and humans diverge?
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5-7mya
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“hominin” =
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hominids (human-like species in the past) that are sister group of the chimpanzees
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Homo erectus
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appeared ~1.6 Mya
before 1 Mya, spread from Africa into Asia (to China and Java) |
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Archaic Homo sapiens
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appeared ~300 Kya in Africa, Asia and Europe
differs from “anatomically modern sapiens” in minor respects best-known population: Neanderthals (Homo neanderthalensis?) |
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Modern sapiens
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appeared ~170 Kya in Africa
Anatomically indistinguishable from today’s humans overlapped with Neanderthals but abruptly replaced them (in Europe about 40,000 years ago) |
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when did the first mitochondrial dna appear? (according to records)
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~140,000 years ago “mitochondrial Eve”
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Why phylogenetic trees?
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Helps conceptually distinguish between evolution (pattern) and mechanisms of evolution (process)
Provides an organizational tool for thinking about biodiversity and evolution |
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What do Phylogeny, Evolutionary tree, Cladogram, Dendrogram, Phylogram all have in common?
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They are all alternative Phylogenetic tree names
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taxon/ taxa
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the ends of the trees- species/ genes
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nodes
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the splitting points on the trees- extinct common ancestors
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root
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the node at the end of the tree- the common ancestor of all taxa
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internal branch
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node to node
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external branch
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node to tip
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bifurcating tree
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each branch leads to a pair of species
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polytomy
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more than two branches leading from a node
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branch numbers
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Indicate level of support or confidence
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Bootstrap percentage
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Ranges from 100 (high confidence/support) to 0 (no confidence/support).
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Monophyletic Group
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Single origin
The given set of taxa forms a group that contains their most recent common ancestor and all its descendants |
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Paraphyletic Group
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– Single origin, but with exceptions
– The given set of taxa forms a group whose founding ancestor produced some descendants that are not in the group |
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Polyphyletic Group
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– Multiple independent origins.
– The given set of taxa forms multiple groups each of which is either monophyletic or paraphyletic |
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Homology
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characters which are
similar due to common descent – They are inherited from a common ancestor Ex: 8 Vertebrate in mammalian necks |
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Analogy:
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characters which are similar
due to convergence or parallel evolution Ex: bird and bat wings – They are NOT inherited from a common ancestor |
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So which tree most likely represents the evolutionary history?
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the most parsimonious
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evolutionary distance
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the number of substitutions that have occurred in two sequences since their divergence from a common ancestor
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How can you transform p distance (which tapers off) into true distance?
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Jukes Cantor distance
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Assumptions of Jukes Cantor
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Each nucleotide (A, C, G, & T) occurs with
equal frequency (i.e., 25% each) – All sites in a sequence have the same mutation rate – The rate of all types of substitution are identical (e.g., A → C = A → G = A → T) – Reversibility: C → G = G → C |
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How to correct p distance into true distance?
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Poisson Distance
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Max protien p-distance?
Max nucleotide distance? |
0.95 (1/20)
0.75 (3/4) |
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how to calculate p distance
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#of differences/#of common sites (meaning total sites)
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Lets say there are 7 nucleotide differences between sequences of DNA from a cow and a human- what would that tell you?
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Each branch accumulated 3.5 nucleotide differences for a total of 7
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UPGMA method
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“Unweighted Pair-Group Method with Arithmetic mean”
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UPGMA assumes constant rate
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average rate r=distance/2t
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quantitative traits
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phenotypes that show continuous variation rather than simple Mendelian descrete variation the most phenotype variation we observe
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Fitness=viability x fertility
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quantitative trait
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early investigator of evolution
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believed that characteristics from both parents blended together to make offspring
Did not accept Mendel's theory, particulate inheritance cannot explain phenotypic variation |
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P=Xm + Xp + E
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The phenotype value
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Xm
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mating is done at random
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Xp
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Phenotypic variance
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E
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environmental variance
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Xmi or Xpi
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is what determines the allele or alleles this individual receives from the corresponding parent
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All Xmi and Xpi are equal when
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there is no genetic variation in the population the variances become zero
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Va
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variance of genetic variation
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Ve
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variation due to environmental variation
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Va>0
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individuals in the population carry different sets of alleles that produce different phenotypes
Va increases with genetic variation (polymorphism) in the population |
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polymorphism
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when multiple alleles of a gene within a population express different phenotypes
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additive genetic variation
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Genetic variance associated with the average effects of substituting one allele for another
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polygenic variation
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having different sources of an orgin
ex: pigmentation in mice on the beach and mainland of Florida are different variations of fur coat color brown, white, dark, etc. |
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what happens if phenotypic effects of alleles are not additive?
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non-additive effects increase phenotypic variance beyond Va
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h2=Va/Vp
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Narrow sense heritability
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H2=Vg/Vp
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Broad sense heritability
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heritability
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proportion of phenotypic variance that can be explained by genetic variation
determines the correlation between relatives determine the response to directional selection on phenotype |
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h2
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is equal to the slope of regression of offspring values on mean of two parents
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h2=1---> Vp=Va
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phenotype differences are entirely due to genetic differences
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h2=0 --> Va=0
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phenotype difference are entirely due to environmental differences
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corr {Pa, Pb} = r2
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correlation of phenotypic values in pairs of individuals A and B
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R is
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the coefficient of relationship: the probability that one allele chosen from individual A is found in individual B (proportion of shared alleles)
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phenotypic variance and heritability depends on...
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allele frequency
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Charles Darwin and finches
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noticed a great diversity of bill morphology in closely related finches--rapid evolution upon colonization
ex: Peter Grants surveyed during drought on finches. Drought lead to shortage of small soft seeds selection for finches with large beaks. Birds with large beaks are expressed more in pop. |
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Genetic variation in a quantitative trait is
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raw material for natural selection
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what maintains genetic variation in a quantitative trait
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New mutations
Variable selection Intra-species competition |
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New mutation
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new mutations compensate for loss of variation due to selection
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variable selection
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optimum phenotype change in space and time
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Intra-species competition
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avoidance of competition may promote genetic diversity
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Pleiotrophy
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one genetic change affects multiple phenotypes
mutation for smaller size may produce low fertility environmental change may favor to increase both size and fertility |
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An extreme directional change in one phenotype
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is accompanied by fitness-lowering changes in other phenotypes
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P element
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an element that replicates by inserting its copy at random positions in genome
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what's in a good "species" definition
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classify organisms systematically, discrete groups, clusters, products of evolution, variety of organisms
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biological species concept
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reproductive isolation genetic differences between population prevents the exchange of genes- no mating
Problems: restricted to sexual outcrossing organisms. Reproductive isolation cannot be known. borderline cases. hybrid zone. |
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hybrid zone
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practice mating with other individuals- inbreeding- speciation
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outcrossing
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practice mating with other individuals- inbreeding
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phylogenetic species concept
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luster of organisms different from other groups where there is a parental pattern of ancestry
applies to asexual organisms may lead too many species, occur whenever a population undergoes fixation of genetic differences in related pop. gaining acceptance among systematics |
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genealogical species concept
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species are exclusive groups of organisms which one or more are closely related to one another than outside the group
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recognition species concept
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a species is the most inclusive population of individual biparental organisms that share common fertilization system
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Cohesion species concept
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a species is the most inclusive having potential for phenotypic cohesion through intistic cohesion mechanism
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zygote
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a single celled individual formed by union of gametes
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prezygotic isolation
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premating barriers ecological isolation- breeding at different seasons, diff. habitat
incompatibility of sperm and egg |
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In a simple model of infectious disease, the number of new infections produced by an infected host is given by R0. Which of the following factor is positively correlated to R0?
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number of uninfected hosts
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Which of the following is an important reason that vector-borne diseases are generally more lethal than directly transmitted diseases?
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Pathogens transmitted directly are under evolutionary pressure not to decrease the host’s mobility
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Loss of function in a gene
Degeneration |
pseudogene
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Neofunctionalization
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One copy acquires adaptive mutations and gains a new function. The other copy maintains the original function
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Subfunctionalization
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Two copies lose partial functions complementarily
- Ex) Original gene was expressed in both brain and liver. One duplicate copy loses expression in brain. The other copy loses expression in liver. |
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Which fates of the new duplicates result in new genes?
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subfunctionalization and neofunctionalization
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Have diverged from a common ancestral gene by phylogenetic splitting
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Orthologous genes
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paralogous genes
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evolve parallel (think of orthologous as perpendicular)
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Trans-acting factors
Different cell types express different sets of genes (by tissue/cell-specific trans-acting factors) |
diffusible regulatory proteins (transcription factors produced by other genes) that bind to DNA and switch transcription on and off.
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Cis-acting factors:
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segments of DNA that do not encode proteins, but interact with trans-acting factors to regulate the expression of nearby genes. Usually located at 5’ upstream of protein-coding sequence
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