Download Evolution Quiz Week 9

1) If the father has hemophilia but the mother does not, how will the offspring be affected?
a. All daughters have hemophilia
b. All daughters are hemophilia carriers
c. All sons have hemophilia
d. All sons are hemophilia carriers
e. Offspring of both sex have hemophilia
2) Which is not a hypothesis proposed to explain the evolution of virulence?
a. Coincidental evolution hypothesis
b. Short-sighted evolution hypothesis
c. Palindrome hypothesis
d. Trade-off hypothesis
3) What is genomic sequencing not used for (pick one)?
a. Ancient DNA
b. Formalin DNA
c. eDNA
d. genetic hitchhiking
e. genomes
4) Which species concept defines species as reproductively isolated from one another?
a. Typological species concept
b. Biological species concept
c. Ecological species concept
d. Evolutionary Species concept
e. Phylogenetic species concept
5) List two questions you had on the paper this week
LECTURE 18 EVOLUTION AND HUMAN HEALTH
Genetic factors
 Many diseases are on sex chromosomes
o X, Hemophilia prevents blood clotting, carried through the Royal Family
o Sons have hemophilia & daughters are carriers (unless dad has hemophilia & mom is
carrier)
o If father has hemophilia, daughters
will be carriers but sons won’t have
(Fig 1)


Red headed birds: Males are homochromosome (ZZ), females heterochromosome (ZW)
o Red head dominant, black head
recessive
CRISPR: Clustered Regularly Interspaced
Short Palindromic Repeats
o Palindrome: sequence that reads
the same forwards & backwards
Figure 1: Hemophilia
Infectious diseases
 Viruses may have originated from our own
DNA, going out and becoming virus, coming back
 Antagonistic coevolution: evolution of viruses & their hosts
o Example of evolutionary arms race
o Influenza A virus is a retrovirus with 8 RNA strands (HIV only has 2)
 Originates in Asia
 Celliular coat is hemagglutinin (the main target of our
immune system)
 Antigenic sites: regions of protein that can be recognized by
our immune system
o Walter Fitch examined phylogenetic relationship among flu strains
over 20 years using hemagglutinin sites
o Hemagglutinin has evolved at a constant rate, constant selection
o Flu strains all arise from a single trunk, no branching (fig 2)
o Surviving lineage has more mutations at antigenic sites, keeps
challenging immune system
o Positive selection occurs when replacements exceed synonomous
Figure 2: Flu strains
o Influenza A, 18 codons exhibit higher rates of substitution
arise from single
o Human & bird strains recombine in swine host, reinfect humans
trunk
o Virulence is the affect a pathogen has on its host
 Rabbits & myxoma virus
o 1859, 12 rabbit brought to Oz. 6 years later there were 30,000
o 1950’s, myxoma virus brought to control rabbits & kill most of them
o Within 15 years, virus evolves to be less virulent & rabbits recover
 Coincidental evolution hypothesis: Different environment, different virulence


 Tetanus is bad pathogen for us, but directed at something else in dirt
Short-sighted evolution hypothesis: Increasing virulence are detrimental
Trade-off hypothesis: Virulence should evolve to balance transmission
LECTURE 19 EVOLUTIONARY GENOMICS
Genomics approaches
GC is heavier because it has water
molecules in it
Cot, melting, renaturation

When DNA denatured, common
sequences quickly come back together but
uncommon sequences do not come
backtogether (cannot find other strand)

Light passes differently through single vs
double strands

Meselson, Stahl, and the replication of
Figure 3: Minor
DNA: Used to calculate density of DNA, which is
groove is between
a number of water molecules in the minor
two strands, and
groove
major is large

Isochores cause chromosomal banding
space between
Figure 4: Top are quickly renatured, medium are less
paired strands

Sanger sequencing was popular for 20
common repetiive sequences, and slowest are singleyears, powerful technique
copy. X axis is time

Next generation sequencing (Pyrosequencing):
Everything is sequenced in parallel
o Plate with holes big enough for a molecule. Plate covered with one nucleotide which
attaches to molecule . Cheaper per molecule than other techniques
 RAD (Restriction site Associated DNA) sequencing
o Cut DNA with primer, sequence DNA next to cuts
o DNA sequenced with a barcode, can do up to 100 separate individuals with a single run
(cheap)
o SNP’s allow inference on population structure, gene flow
o Structure plot: you set order of individuals (populations) and program picks colors to
determine population structure
o Chance of restriction enzyme finding gene is very small, most of genome is introns
 Genetic hitchhiking: Detect genes by landing close with restriction site, see
genes that have gotten pulled along with gene being selected for
 RNA seq: reverse transcribe RNA to determine what genes are being expressed
 Genomic sequencing is used for:
o ancient DNA (Shapiro and her husband Ed Green)
o formalin DNA , which has been fixed in formalin
o eDNA
o genomes
LECTURE 20 SPECIES CONCEPTS
Speciation occurs when populations evolve reproductive isolating mechanisms
 Biological Species Concept (BSC)
 Prezygotic isolation prevents fertilization
 Postzygotic isolation creates inviable hybrids
Leaf density hypothesis: Leaves having veins allowed them to grow better, increased productivity of
land organisms, shifted biodiversity from marine ecosystem to terrestrial (Rich Grosberg & Geerat
Vermeji)
Cryptic species are visually indistinguishable but genetically unique
Species concepts
 Typological Species Concept: Species described by type specimen, voucher specimen
o Linnaeus is famous for binomial system (genus-species)
o Problems: polymorphisms within population, geographic variation among populations,
Sibling species (reproductively isolated groups that are morphologically
indistinguishable)
 Biological Species Concept: Reproductive isolation
o Ernst Mayr, Theodosios Dobzhansky are part of the New Synthesis (Integrating genetics
into Darwinian Evoution)
o Multidimensional is allopatric speciation &/or allochronous (reproduce at different
times)
o Nondimensional is sympatric speciation & synchronous (reproduce at same time)
o Problems: asexual species, reproductive isolation is often incomplete, multidimensional
concept difficult to verify (put species together and see If the reproduce?)
 Evolutionary Species Concept: (Simpson) lineage evolving separately
o Problems: arbitrary, does not provide mechanism
 Ecological species concept: Ecology plays role in shaping species into new ones
 Phylogenetic species concept: Smallest possible monophyletic group is species
o Problems: Which gene to use to make phylogeny
Pianka ER 1970 On r- and K-selection. American Society of Naturalists
 Dobzhansky (1950) stated that natural selection favors low fecundity & slower development in
the tropics to make individuals more competitive, and high fecundity & rapid development in
temperate regions to overcome environmental struggles
 MacArthur & Wilson (1967) coined r- & K-selection
 Perfectly r-selected species put as little energy into each offspring as possible, no densitydependent effects & no competition, leading to high productivity
 Perfectly K-selected species put lots of energy into a few extremely fit offspring in a highly
competitive environment. Efficient utilization of resources
 Exceptions:
o Aquatic organisms, especially fish, span the range of the r-K continuum, why?
o Turtles are k selected, but lay lots of eggs (r-selected)
o Sturgeon are long-lived (K), but lay lots of eggs & have no parental care (r-selected)
o Within gender: Males are r-selected, females are k-selected
o Trees produce lots of seeds (r), but live a long time (K)
 In ecological succession after big disturbance, primary colonizers are r-selected, followed by
increasing diversity of flora & fauna, then K-selected
 R-selected is good at new environments, environmental conditions, while k-selected is good at
species competition