Exam 1 Flashcards
How many people infected by HIV worldwide?
~76 Million
How does HIV spread?
Through bodily fluids
What is HIV?
Intracellular parasite
Cells vulnerable to HIV?
Macrophage cells, effector helper T cells, memory helper T cells
What does HIV latch on to on the outside of the cells?
CD4 and CCR5 Receptors
Why is HIV difficult to treat?
Hard to find drugs that interrupt the viral life cycle but not the host cell’s life cycle
How does the body respond to HIV infection?
Destroys virion in bloodstream, kills infected T cells and macrophages
What is AIDS?
Acquired Immune Deficiency Syndrome
When does AIDS occur after infection?
~10 years
How does HIV cause AIDS?
The immune system begins to collapse and can no longer fend off a number of opportunistic viruses, bacteria, and fungi
What is AZT?
Reverse transcriptase inhibitor that prevents HIV from reproducing
How does AZT work?
It inserts itself (azidothymidine) in thymidine’s place in growing DNA strand, stops transcription
Why doesn’t AZT effect our own transcriptase?
Our cells are more selective and will not choose the AZT in place of T
Why does AZT fail in the long run?
Natural mutations in HIV that are more selective (don’t pick AZT over T) will increase in abundance as all of the ones that AZT worked on die out
Coreceptor Inhibitors
Block HIV from attaching to cells
Entry/Fusion Inhibitors
Bar entry into host cell
RT Inhibitors
Inhibit reverse transcriptase by mimicking normal building blocks of DNA or interfere with bonding site
Integrase Inhibitors
Block viral DNA incorporation into host DNA
Protease Inhibitors
Block the enzyme that cleaves precursor proteins to allow maturation of virions
HAART Cocktails
Highly Active Anti-Retroviral Therapy (mix of many drugs)
What did HIV evolve from?
SIV (simian Immunodeficiency Virus)
HIV-1
The most prevalent and pathogenic type of HIV virus, came from chimps
HIV-2
Found primarily in West Africa and less virulent, came from sooty mangabeys
HIV-1 Group M
Major/Main
9 Subtypes
Global (95%)
HIV-1 Group N
Non-M, Non-O
< 20 cases
Cameroon only
HIV-1 Group O
Outlier
High diversity
West-Central Africa
HIV-1 Group P
Pending
One case
Found in gorillas
Virulence
Severity or harmfulness of a disease
Caused by reproduction rate of a virus
Transmission Rate Hypothesis
If transmission of sexually transmitted diseases is frequent, virulent viruses are naturally selected. If transmission is low, less virulent strains are selected. Cost/benefit ratio for the virus
Relationship between HIV virulence and sexual practices
Increase in safe sex decreases virulence, no change in practices keep virulence the same
Delta32 Mutation
Has 32-base pair deletion so CCR5 coreceptor does not present itself on surface of host T-cells
Special Creation
Earth 6,000-10,000 years old
Species independently created
Species do not change
Descent with Modification
Species change over time
New life forms derive from old life forms
Earth 4.5 billion years old
Microevolution
Species change over time
Speciation
Lineages split and diverge
Macroevolution
New life forms derive from older forms
Common Ancestry
All life forms are related
Discovery of Charles Darwin
Natural selection, the mechanism of evolution (NOT evolution itself)
Hutton Hypothesis
Proposed geological change because of Earth’s hot core
Lamarck Hypothesis
Species evolve through use and disuse, and those change are heritable
Paul Kammerer Experiment
Inheritance of acquired traits in midwife toads when forced back into water
Darwin’s Biogeographic Discoveries
Plants and animals more similar based on location rather than biome type
Darwin’s Geology Discoveries
Fossils of seashells in mountains
More recent the fossils, more similar to extant organisms
Uniformitarianism
Earth has been undergoing the same natural processes since the beginning
Most important observations made in the Galapagos Islands
Animals on island most similar to those on mainland South America
Islands have different environment, organisms also differed
Works by Darwin
Origin of Species
Descent of Man
Evidence for Evolution
Selective breeding (species not immutable)
Vestigial structures
Homology
Fossil record
Vestigial Structures
Structure in an organism that has lost all or most of its original function in the course of evolution
Homologous Structures
Structures that are inherited from a common ancestor but may have different functions (ex. forelimb of mammals)
Analogous Structures (Homoplasy)
Structures similar in appearance and function but details of structure differ and not derived from common ancestor
Convergent Evolution
When. two or more unrelated lineages. acquire the same biological trait because of selection for a shared ecological niche
Functional Genes
Exons
Introns
Promoters
Processed Pseudogenes
Missing introns and promoters (non-functional)
What causes processed pseudogenes?
Reverse transcription of mRNA into DNA and put randomly at another locus
Law of Succession
States that extinct specie are ancestors of living species
Transitional Forms
Organisms that usually show a blend of traits that you would expect at intermediate stages of evolution (can be alive or in fossil record)
Example of living transitional form
Amphibious Mudskipper compared to aquatic and terrestrial relatives
Example of fossil transitional form
Archaeopteryx (Dino with modern flight feathers)
What does the universal genetic code support?
Evidence we all descend from a common ancestor
Universal Genetic Code
With only minor exceptions, all organisms studied to date use the same nucleotide triplicates or codons to specify the same amino acids
Who first proposed continental drift?
Alfred Wegener
Said the continental shelves fit together like a puzzle (plate tectonics)
How was Earth concluded to be very old?
Early geologists measured rates of erosion, then also used relative dating
Marie Tharp
Combined datât from ship surroundings and undersea earthquakes to make map of seafloor (confirmed plate tectonics)
Marie Curie
Discovered radioactivity
Lead to radiometric dating
Radiometric Dating
Absolute dating of rocks measuring decay of radioactive isotopes into its daughter isotopes using known half-life rates
Half-life
Length of time for 50% of an isotope to decay
Age of Earth
4.54 ± 0.05 billion years
Age of Life
~3.7 billion years
Darwin’s Four Postulates
Variation between individuals within a population
Some variation is passed on to offspring
More young are born than can survive
Survival and reproduction are not random
Who else independently developed a theory of natural selection?
Alfred Russel Wallace
fw2.2 gene
Protein made during early fruit development to repress cell division (ex. tomatoes)
Darwinian Fitness
The ability of an individual to survive and reproduce in its environment
Darwinian Fitness Example
Beach mice of Alabama/Florida
Where did Peter and Rosemary Grant study finches?
Galapagos Islands, isla Daphne Major
Most isolated island because of distance from other islands
How did the Grants test for postulate 1?
Was beak depth variable? Yes
How did the Grants test for postulate 2?
Is the variation in be beak depth heritable? Yes
Why is measuring heritability difficult?
Misidentified paternity
Nest parasitism (birds)
Maternal effects
Shared environments
BMP4
Bone morphogenic protein 4
Associated with deep beaks
How did the Grants test for postulate 3?
Testing for excess offspring
89% die before reproduction
How did the Grants test for postulate 4?
Was survival nonrandom (due to beak depth)? Finches with deepest beaks survived more during drought
Why were deep finch beaks favorable after drought?
Only birds with deep, narrow beaks could crack the fruit of one of the one plant that could produce fruit
What does natural selection act on?
Individuals and EXISTING phenotypes (can’t make new ones)
Where does evolution occur?
Populations and allele frequencies
Where is the evidence of natural selection seen?
The NEXT generation, its a backwards looking process (not predicting for the future)
Artificial Selection Experiment
Selection for highest oil content in corn, over 60 years went from 4-6% to 20% oil
How did pandas get as “thumb” if natural selection can’t make new structures?
Elongated wrist bone grew to serve as a sort of thumb (natural selection used what was already there)
Is natural selection perfect?
No, it makes organisms good enough for survival
Darwin’s 3 Problems
- Did not know how variability was created (mutations)
- Did not know how traits were inherited (alleles)
- Earth thought to be 15-20 million years old and two young for mutation (radioactive isotopes proved older)
How did Darwin understand variability?
Thought there was set variability and it would all eventually be used up
How did Darwin understand traits?
Thought individual traits would be lost eventually by merging with other traits
The Modern Synthesis
The fusion of genetics with evolutionary biology
Modern Synthesis Postulate 1
Individuals within a population are variable because of mutations making new alleles and recombination of those alleles
Modern Synthesis Postulate 2
Individuals pass their alleles onto their offspring
Modern Synthesis Postulate 3
In most generations, more offspring produced than can survive
Modern Synthesis Postulate 4
Individuals that survive and reproduce the most are those with alleles and allelic combinations that best adapt them to their environment
Is natural selection the only cause of evolution?
No, just means of adaptive evolution
Scopes Monkey Trial
Tennessee schoolteacher John Scopes was arrested for teaching the theory of evolution despite a state law banning it
When did the US protest teaching evolution by law?
1967
When was “Creation Science” (creationism) banned being taught in public schools?
1987
Why was creationism given the title creation science?
So it would look less religious and be taught alongside evolution
What did creationism morph into?
Intelligent Design Theory
Argument by William Paley
Like a watch, which you would assume was made by an intelligent organisms, the vertebrate eye must be the same
Darwin rebuttal to Paley
Vertebrate eyes must have arisen from simpler eye
Proof of simpler eyes in living organisms
How does science differ from creationism?
Creationism does not use evidence to test its claims, does not allow evidence to alter beliefs, and does not grow in capacity to explain the natural world
Hypothesis
A proposition
Scientific Fact
A hypothesis that has become so well supported by evidence that we feel safe in acting as if it were true
Scientific Theory
A mature, interconnected body of statements, based on reasoning and evidence, that explains a wide variety of observations
Is evolution untestable?
No, you can test the 4 postulates of evolution
Can test predictions based on evolution
How has entropy been compared to evolution?
Since organisms evolve to be more complex, they are going against the idea of entropy
Why does evolution NOT break the second law of thermodynamics?
Entropy only applies to CLOSED systems which Earth is not, also organisms don’t always evolve to be more complex
Example of organisms evolving to be less complex
Snakes losing their legs
Entropy
A measure of disorder or randomness
Significance of butterfly. species in genus Hedylepta?
Genus to native Hawaii, but 2 species have mouthparts which only allow them to eat bananas (which were only introduced to Hawaii 1000 years ago) -> proof of species evolution
How old was Earth originally thought to be based on combustion?
15-20 million years old
Is the sun combustion or nuclear fusion?
Nuclear fusion
Epigenetics
The environment can influence the way genes are expressed
Examples of observed evolution
HIV
Daphne Major finches
London Underground vs Above Ground mosquitoes
Systematics
Study of biological diversity and evolutionary relationship of organisms
The two field of Systematics
Study of biological diversity and evolutionary relationship of organisms
Taxonomy
The science of naming taxa and placing them into groups
Taxon
Species, genus, or kingdom, etc
Is taxonomy absolute?
No, taxonomy is always changing as new data is discovered
Where do the formal rules of taxonomy come from?
International Union of Zoological Nomenclature
Who was the father of modern classification system (binomial nomenclature)?
Carolus Linnaeus
Taxonomic levels from highest to lowest
Kingdom, Phylum, Class, Order, Family, Genus, Species
What levels of classification are in binomial nomenclature?
Genus species
How are taxonomic groups formed?
Based on evolutionary history regardless of outwards similarity
How did scientists used to form taxonomic groups?
Based on similarity of appearance
What makes grouping organisms into taxonomic groups difficult?
Convergence/Homoplasies
Phylogeny
Hypothesis of evolutionary relationships
Phylogenetic Tree
Graphical summary of evolutionary history
Is phylogeny absolute?
No, it is only an estimate
Law of Parsimony
The simplest explanation is most likely to be true
Occam’s Razor
Law of Parsimony
Trying to minimize homoplasy in a data set
Who came up with Occam’s Razor?
William of Ockham
Homology
Evolutionary relationships should only be reconstructed from traits that are similar because they are derived from a common ancestor
Synapomorphy
Shared derived characters of all members of a group
What is used to decide where branches should be on a phylogeny?
Synapomorphies
Can common ancestors ever be living?
NO! Even the most ancient-like animals that are typically the outgrip are still not technically the same species as the ancestor placed at where that branch splits
Autapomorphy
Unique derived trait
Can autapomorphies be used for estimating relatedness?
No, they are basically useless
Pleisiomorphy
Any ancestral or primitive character
Shared among members of a clade, but significantly older than that group’s common ancestor
What is a pleisiomorphy also know as?
Sympleisiomorphy
Homoplasy
A similar (analogous) structure or molecular sequence that has evolved independently in two species
What creates homoplasies?
Convergent evolution
Does homoplasy come from common ancestry?
No
What traits are uninformative?
Autapomorphies
Uniformative
Not very useful or helpful info
What kind of characters does homoplasy choose?
Characters that evolve slowly relative to the age of taxa
Maximum parsimony method
Minimizes total amount of evolutionary change in a tree
Evolutionary Reversal
When a lineage evolves toward one of its ancestral traits, effectively losing a more recently evolved trait
What are the most common types of traits?
Synapomorphies
Assumptions of characters for phylogenetic analysis
Homology
Character states have genetic basis
Characters are independent
Characters evolution reflects organismal phylogeny
Examples of phylogenetic characters
DNA sequence
Presence/Absence of skeletal elements
Mode of embryonic development
Pros of grouping taxon with morphological traits
Well established characters
Loss of material
Less expensive
Examine many “genes” at once
Can use fossils
Can look at more individuals more often
Pros of grouping taxon with molecular traits
Huge number of characters
Closer to real genetic basis
Better models of how characters evolve
More amenable to certain analyses
3 Principles of Cladistics
- Any group of organisms is related by descent from a common ancestor
- There is a bifurcating pattern of cladogenesis
- Change in characteristics occurs in lineage over time
Cladistic methods of phylogenetic
Techniques that identify monophyletic groups based on synapomorphies and direction of change through time
Most commonly used cladistic method
Outgroup method
Outgroup
A closely related taxon that is used to represent the ancestor
What does the outgrip in a phylogenetic tree tell ups?
Which characters are derived and which are ancestral
Clade
Monophyletic group (they mean the exact same thing)
When are all synapomorphies congruent?
When no convergence or reversal occurs
Node (on a genetic tree)
Represent EXTINCT taxa and bifurcating branching points
What does it means when you rotate a branch about the node of a tree?
As long as it does not change the relationships, it will still represent the same tree
Cladogram vs Phylogram
Cladogram- branch lengths have no meaning
Phylogram- branch lengths are proportional to change
What does cladogram branch length mean?
Represent the amount of changes that have been undergone
Polytomy
A branch point form which more than two descendant groups emerge
Why is there polygamy in some trees?
It occurs when the evolutionary relationship between 3 or more species is not fully understood and so is left unresolved
Monophyletic Group
All members are believed to stem from a single common ancestor, and the group includes this common ancestor
Paraphyletic Group
Group that is monophyletic except that some descendants of the common ancestor have been left out
Polyphyletic Group
Consisting of unrelated lineages, each more closely related to other lineages not placed in the taxon
What is more common, paraphyly or polyphyly?
Paraphyly
What is more troublesome, paraphyly or polyphyly?
Polyphyly (again, complicates finding monophyletic groups to classify species)
Order of whales and dolphins
Cetacea
Synapomorphy of Cetacea
loss of posterior limbs
What order are whales closely related to?
Artiodactyla (even toed ungulates) which includes pigs, camels, cattle, and hippos
What does new molecular research suggest about where hippos belong in phylogenetic trees?
Hippos more mostly related to Cetacea than previously thought (based on genetics)
Clade of cetaceans with hippos more likely than clade with all artiodactyls and cetaceans
Why are homoplasies hard to identify in molecular phylogeny?
Only 4 bases (ATCG)
Why were hippos previously believed to not be as closely related to whales?
Whales lack the astragalus, which all artiodactyls have
Astragalus
Ankle joint bone
What morphological data suggested that whales may be artiodactyls?
While modern whales don’t have an astragalus, extinct whales with legs had features of astragalus similar o artiodactyls
How do scientists evaluate the statistical confidence in a tree?
Bootstrapping
Bootstrap values
Percentages of the number of times the same branch arose after repeated sampling
When percent of bootstrap support is needed to indicate the correct relationship in a tree?
Over 70%
Reconstruction methods for trees besides parsimony
UPGMA
Neighbor Joining
Maximum Likelihood
Bayesian Analysis
UPGMA
Unweighted pair-group method using arithmetic averages
Neighbor Joining
A distance method for reconstructing phylogenies; identifies the tree topology with the shortest possible branch lengths using ALL characters (homoplasy, synapomorphies, autapomorphies, etc)
Maximum Likelihood
Assumes a particular probabilistic model of sequence evolution and then calculates for each tree the probability of the data given the tree P(data|tree)
What characters does the maximum likelihood method use?
Synapomoprhies
Autapomorphies
Invariant Sites
ALL DATA
What does the maximum likelihood calculate?
The likelihood statistic, which helps estimate the topology of the tree
Distance reconstruction methods for trees
Uses differences (distances) among genetic character states to group taxa
NOT a cladistic method
Typically very fast and easy to estimate trees
Why aren’t distance methods considered cladistic?
They do not look for synapomorphies, just overall similarity
Prone to error when many homoplasies present
Topology
Shape of phylogenetic trees
How accurate are maximum likelihood methods?/
VERY accurate, among the most accurate methods
Is maximum likelihood a quick process or a long process?
Very computationally intensive
A tree with 100 species may take several months
Bayesian Markov Chain Monte Carlo
Combine Bayesian statistics with Marcov Chain Monte Carlo algorithms
P(tree|data)
Characteristics of ancient fossils related to whales and artiodactyls
Whale like ear bones
Artiodactyls like astragalus
SINE/LINE
Non-coding DNA inserted into genomes (retrotransposons)
Molecular Clock
Model that uses DNA comparisons to estimate the length of time that two species have been evolving independently
What does the molecular clock hypothesize?
Molecular change happens at a steady rate
Use known dates to calibrate the molecular clock
What is used to calibrate a molecular clock?
Fossils or geological events
What rate do most taxa progress on molecular clocks?
2% sequence divergence per million
What genes do molecular clocks use?
Mitochondrial genes (because other gene evolve at different rates)
Difficulties with molecular clocks
Many estimates/assumptions are likely to have a high degree of uncertainty
Many irregularities caused by natural selection and/or evolutionary fluctuations
What kind of group is artiodactyla?
Not monophyletic
Order Cetacea should be sunk to family level
How is phylogeny mapping done?
Optimizing all characters on a phylogeny
Sources of Variation
Genetic
Environmental
Genotype-by-environment interaction
Examples of genetic variation in humans
Whether phenythiocarbamide (PTC) tastes bitter or not (and overall ability to detect toxins)
Gene responsible for bitter flavors in humans
TAS2R38
What chromosome is TAS2R38 on?
7
What alleles are involved in the TAS2R38 gene?
PAV (encodes proper PTC taste receptor)
AVI (encodes deformed PTC taste receptor)
Environmental Variation
Traits that are not genetically controlled (not heritable)
Phenotypic Plasticity
The ability of an organism to change its phenotype in response to changes in the environment
Phenotypic plasticity is a form of what kind of variation?
Environmental
Inducible Defenses
Defensive traits produced only in response to the presence of a predator
Inducible defenses are considered what kind of variation?
Environmental
Example of genotype-by-environment interaction in humans
Hating cilantro
Reaction Norm
Phenotypic expression of a single genotype across a range of environments
How is genotype-by-environment interaction tested?
Testing a phenotype across a range of environments (if there’s no interaction, the phenotype should be the same in all environments)
Reaction Norm Graph
Steepness of slope indicates amount of plasticity
Example of environmental sex determination
Sex determination in leopard geckos
Genotype and temperature influence sex (G-by-E interaction)
What is the raw material of evolution?
Mutations
What creates new alleles?
Mutations
Components of DNA
Deoxyribose sugar
Phosphate group
Nitrogenous base
How many rings in purines?
2
How many rings in pyrimidines?
1
What enzyme helps with DNA replication?
DNA polymerase
DNA Polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule
Point Mutation
Gene mutation in which a single base pair in DNA has been changed
Order of pathway in protein synthesis
DNA -> mRNA -> protein
Why don’t all point mutations result in a change of protein?
Multiple codons can code for the same amino acid
Transition Mutation
Change from purine to purine or pyrimidine to pyrimidine
Transversion Mutations
Change between purine and pyrimidine or vice versa
What kind of point mutations are most common?
Transition mutations (2x as common as transversions)
Exons
Expressed sequence of DNA; codes for a protein
Introns
Noncoding segments of DNA that lie between coding sequences
Synonymous Mutation
“Silent”
Does not change amino acid sequence
Nonsynonomous Mutation
“Replacement”
Changes amino acid sequence
Frameshift Mutations
Mutation that shifts the reading frame of the genetic message by inserting/deleting a nucleotide
Nonsense Mutation
(Point Mutation) changes a normal codon into a stop codon
What causes gene duplications?
Unequal crossing over during meiosis
Where do new genes come from?
Gene duplication
Retroposition
Retroposition
Processed mRNA inserted back into genome
Gene duplication relating to mutations
Creates an extra copy that is free from natural selection and able to accumulate mutations
Example of gene duplication in humans
Different global gene families
Produced by past gene duplication events that allowed the gene to take on new functions over time
Paralogous Genes
Genes that duplicated and diverge in a species (like globin in humans) _> may have different functions
Orthologous Genes
Genes that are homologous and evolved from a common ancestral gene by speciation (like the original globin gene that can also be found in mice)
Inversions
Segment of DNA is cleaved in two places, the excited segment flips, and re-anneals in the opposite direction
Problem with inversions
Can disrupt gene linkage
Cannot align properly with homologs (makes dysfunctional gametes)
Example of Inversions
Fruit flies
5/6 chromosomes are polymorphic for inversions
Inversion frequencies vary along cline
Polyploidy
Entire extra sets of chromosomes
what species most commonly have polyploidy?
Plants and rare in animals
Hermaphroditic species that can self-fertilize
How can polyploidy lead to speciation?
Meiosis error creates diploid gametes
If two diploids fuse, they make tetraploid
If two tetraploids can mate, a new species is created
How does triploidy occur?
If diploidy gamete fuses with a haploid one
How fertile are triploids?
Low fertility unless parthenogenetic
Why are polyploids so prone to speciation?
They have entire chromosomes of genes that are free from natural selection and can undergo mutation
Kleptogenesis
Female “steals” sperm from the male, used for energy or to stimulate parthenogenesis, but not fertilization, then eject the sperm nucleus
Example of triploid species
Ambystoma Salamanders
Use reproductive mode of kleptogenesis
What causes sickle cell anemia?
Single transversion in hemoglobin gene
Where is the best data on mutation rates from?
Loss-of-function mutations
Loss-of-function Mutations
Mutation deactivates gene and causes protein not to be made
What are loss of function mutations caused by?
Point mutations
Insertions
Deletions
Transposable genetic elements
What percentage of human gametes carry a phenotypically detectible mutation?
10%
Why are mutation rates variable?
DNA polymerase vary in error rates
Mismatch repair systems vary in effectiveness
Some species have varying mutation rates overall
Examples of species with high mutation rate vs low mutation rate
High: Viruses
Low: Fruit flies
What regions of DNA have more mutations, coding, or noncoding?
Noncoding DNA regions (natural selection allows for less errors)
What was traditionally believed about allelic variation?
Was low within populations
Variation from wild type was rare
How do we known that genetic variation within populations is actually very high?
Huge advances in methods for directly measuring genetic and genomic diversity
How are genotypes determined?
For ome loci, examining phenotype
Others, looking directly at proteins or DNA sequences
Gel Electrophoresis
Applying electric current to samples of DNA and proteins so they migrate to oppositely charged poles, they migrate according to size and mass (different sized alleles go different distances)
HIV Infections and CC-CKR-5 gene
Encodes for CCr5 surface protein receptor
If homo, dom (+/+) can be infected
If homo rec. (Delta32/Delat32) cannot be infected
If het. (+/Delta32) infected but progress to AIDS slower
Mean Heterozygosity
Average frequency of heterozygotes across loci in the genotype of the average individual
Percent of polymorphic loci
Fraction of loci in a population that have multiple alleles
Selectionist Theory
Natural selection favors allelic diversity
Neutral Theory
Polymorphic alleles are functionally equivalent so they are not selected against
What factors can influence rate of mutation?
Environmental:
UV Radiation
Carcinogens
