test 2 Flashcards
phylogeny
history of evolutionary relationships
taxon (plural: taxa)
group of related organisms, species, genus, family, order, class; never populations
what does someone mean when they ask how closely related are they?
how much of their genomes do they share
the more nodes you and some species shares….
the more related you are
what strategy doesn’t work for reading evolutionary trees
counting nodes
(evolutionary trees) branches
lead to animals/other branches
(evolutionary trees) nodes
where branches connect
(evolutionary trees) animal species that was at a _____ is __________ of branches beyond them
node; ancestor
(evolutionary trees) T or F: flipping the order of branches doesn’t matter
true
(evolutionary trees) how can you tell how closely related two groups are?
by finding the closest (most recent) common ancestor
counting what the closest _____ is between 2 species while comparing 3 different ones can help figure out which 2 out of 3 are ____ _______ compared to the other one
node; “more related”
(evolutionary trees) zoonitic pathogen
one that has (+/- recently) jumped from animal to human
how many non-human species did HIV colonize humans from?
2
what do different branch lengths represent?
degree of differences (usually genetic)
genetic drift
evolution by luck
genetic drift states that change is still possible, why?
lucky (or unlucky) differences in individual reproductive success
even ______ alleles can change allele _________ unpredictably
neutral; frequencies
(neutral alleles) example of bad luck
accidental deaths, etc
(neutral alleles) example of good luck
extra offspring survive, etc
natural selection criterion (changed by genetic drift)
1) individuals are different 2) some variants have more offspring than others because of luck 3) individuals inherit their differences
what stays the same in neutral alleles?
same fitness and reproductive success; none better than others
if an allele is lost, what’s its frequency?
0
if an allele is fixed, what’s its frequency?
1
by genetic drift, ________ populations evolve more slowly than _________ ones
bigger; smaller
what does genetic drift lead to, whether in big/small populations?
loos/fixation of neutral alleles; new, neutral mutations arise (many exist at the same time)
diploids
2 chromosomes per individual –> 2 copies per parent –> double number of allele copies in population
what makes alleles not neutral?
they have different fitnesses
the most ____ allele is more likely to become fixed, but it’s not ____________
fit; guaranteed
advantageous allele
has higher fitness than other alleles
deleterious allele
has lower fitness than other alleles (s > 0)
neutral allele
same fitness as other alleles
selection coefficient
strength of selection against a trait/allele
selection coefficient formula
s= 1- fitness
what does someone mean when they say, “selection tips the scales”
even a deleterious allele can get lucky
what does selection depend on?
only on relative fitness
what does genetic drift depend on?
only on population size
when is natural selection “more efficient”?
in larger populations
what is implied when someone says “more efficient”?
more likely to produce the outcome predicted by fitness differences
T or F: drift has less effect in larger populations
true
it becomes harder to distinguish between selection and drift as…
selection gets weaker and population size stays the same AND when population size increases and selection rate stays the same
conservation biology
biological principles used for managing: species threathened with extinction, and habitats threatened with loss
population bottleneck
the rapid shrinking of a population
(population bottleneck) recovery
when populations grow to larger size again
what happens the longer it takes a population to recover from a bottleneck?
faster genetic variation is lost
population will less likely be able to adapt to environmental changes
fixed alleles have to wait for ______ ________ to form in order to adapt to new environments
new mutation
evolutionary trap
population gets smaller –> deleterious alleles fixed faster –> population gets even smaller –> deleterious alleles fixed even faster
genetic rescue
escape the evolutionary trap
genetic drift _____ and natural selection _____ tend to reduce genetic variation
always; often
mutation
changes alleles
recombination
shuffles different loci
meiosis
gamete formation
meiosis process
single cell: 2 copies of each chromosome –> DNA replication –> single cell: 4 copies of each chromosome –> cell divides –> 2 cells: 2 copies of each chromosome per cell –> cell divides again without DNA replication –> egg or sperm cells: 1 copy per cell
why is there variation in each row of a chromosome?
because each column is from a different individual
why are DNA sequences different?
because neutral polymorphism has accumulated in the population
two gene-shuffling step
1) crossover; 2) different chromosomes randomly mixed
(two gene-shuffling step) crossover
pieces of chromosomes switch places
how many pairs of chromosomes does a human have?
23
chunks of chromosomes inherited from grandparents will become _______ into smaller and smaller ____ AND those chunks will be in (approximately) ________ sizes because crossing over is (approximately) ________
fragmented; pieces; random; random
SNP
single-nucleotide polymorphism
SNP map
locations of SNPs on chromosomes
(genetic drift w neutral mutations/one locus) T or F: most new, neutral mutations are quickly lost
true
(genetic drift w neutral mutations/one locus) T or F: no loci are mutating
false; many loci arr always mutating
(genetic drift w neutral mutations/one locus) T or F: two is the maximum number of alleles that can exist at a time at a locus; one must become fixed before a new one can arise
false; mutations don’t care if there’s variation and can happen anywhere/any time
(genetic drift w neutral mutations/one locus) after a sufficiently long time, the fraction of ________ ________ on the DNA that are polymorphic will __________
neutral sites; stabilize
(purifying selection on a beneficial mutation) what does it mean for deleterious alleles when new beneficial mutations are fixed?
they become lost
(purifying selection on a beneficial mutation) when the beneficial alleles increase, _____________ ______ increase too
neutral alleles
(purifying selection on a beneficial mutation) selective sweep
whole chunk of chromosome is fixed; other nearby chunks retain their polymorphism
what probably occurred if an area has low polymorphism?
natural selection must’ve swept through –> “signature of selection”
how can anybody “read” the DNA to find gene experiencing natural selection?
areas that have lost their polymorphism must have undergone recent selection
human skin color is:
continuous
rickets
calcium deficiency in bones
what causes rickets?
vitamin D2 and D3 deficiency AND low calcium
what does rickets lead to?
broken bones and malnutrition
what does calcium do for the body?
mechanisms moving things in/out of cells and contracting muscles rely on calcium
calcium deficiency
taking supply out of the bone and moving into the rest of the body –> rickety bones
what is the cure for rickets?
increasing vitamins D2 and D3
sources of vitamin D
diet: fish and meats
make our own: photosynthesis, hunter-gatherer cultures (high vitamin D), shift to agriculture (low vitamin D)
UV light
a mutagen
mutagen
cause of mutation
when is a mutation formed?
when something is incorrectly repaired
what can UV lights change?
base on DNA
calcitriol
hormone controlling calcium flow in/out of cells
where is UV light lowest at?
high latitudes
where is UV light highest at?
near equator and in high mountains (low latitudes)
where are the chances of getting skin cancer higher at?
low latitudes
melanins
pigments that protect against UV light
2 types of melanin
eumelanin and pheomelanin
pigment cell
type of skin cell that contains melanin
T or F: most cells don’t have melanin in them
true
T or F: all cells are the same color
false
melanosome
“ball of melanin” in a pigment cell
what helps contribute to what color a person is/how much melanin they have in their body?
pigment cells and melanosomes
what are the major genes with the biggest effects on skin pigmentation?
TYR (tyrosinase): starts melanin synthesis
IRF4 and TYRP1: control TYR activity
MC1R: controls pheomelanin branch
DCT: controls eumelanin branch
2 major genes that help with melanosome formation and provisioning
OCA2 and TCNP2
(melanosome formation and provisioning) OCA2
moves molecules (that are used to make melanin) into melanosomes; controls how many melanosomes a person makes
(melanosome formation and provisioning) TCPN2
controls melanin synthesis through how many molecules (that make melanin) are made
if pale skin evolved more than once, the _______ ________ in major pigmentation genes should be ________ in those populations (at least for neutral mutations)
point mutations; different
what 6 major pigment genes have point mutations for indigenous East Asian and Europeans
TYR, DCT, TYRP1, MC1R, OCA2, KITLG
what evolved independently in East Asia and Europe?
pale skin color
when did pale skin evolve in Europe?
in Middle East ~14k years ago
in Europe ~4-5k years ago
speciation
the origin of species; origin of new branches on evolutionary trees
how to distinguish species in practice
look for distinct phenotypes/genotypes without intermediates
why can phenotypes make distinguishing species hard?
cryptic species have very similar, easily confused phenotypes; not very ambiguous if you’re looking at the right thing
how many different definitions are there of “species”?
72+ different species concepts; 3 or 4 major categories
things “not different” enough to be species
subspecies, varieties, strains, ‘races’
subspecies (animals)
population of the same species that look/is different in some way
varieties
different habitats, different “looks”
‘races’ (some insects)
not used by biologists; doesn’t have biological meaning in humans
biological species concept
species are populations (or groups of populations) whose members are reproductively isolated from other such groups
(animals and many plants) reproductively isolated
cannot (or won’t) share genes successfully; no gene exchange between them because no mating or hybrids are infertile/dead
gene pools
alleles shared among individuals that can only interbreed among themselves –> they evolve independently
(animals and many plants) speciation (BSC rephrased)
evolution of reproductive isolation (separate species evolve independently)
(animals and many plants) hybridization
interbreeding between differentiated populations –> hybrids
(animals and many plants) introgression
the spread of genes into another species
(bacteria and archaeans) broad-sense “sex”
individuals steal or trade DNA from same and other bacterial strains; environmental DNA incorporated into chromosomes
(bacteria and archaeans) horizontal gene transfer
genes passing between species
(bacteria and archaeans) core genome
genes unique to each species
(bacteria and archaeans) accessory gene
more readily shared, often define strains
(bacteria and archaeans) what does horizontal gene transfer cause?
introgression
(bacteria and archaeans) what are evolutionary trees more likely to do?
more likely to net (not clear branches)
(bacteria and archaeans) what are evolutionary trees more likely to do?
more likely to net (not clear branches)
(bacteria and archaeans) T or F: species evolve only partly independently
true
separate species have different ecological roles, therefore…
occupy different niches
(many plants and some animals) what do related species sometimes share?
genes
(many plants and some animals) what do separate species have?
different ecological roles
(many plants and some animals) species evolve ________ ______________
(partly) independently
(many plants and some animals) speciation
evolution of new ecological role
(how species evolve) ecological context
side-effect of adaptation to different conditions
(how species evolve) geographic context
where populations are as speciation proceeds
(how species evolve) evolution of reproductive isolation
many ways it can happen
(how species evolve –> animals and many plants) what happens to hybrid species before they reach maturity?
they die or are infertile (even if offspring of “pure species” crosses are normal)
(how species evolve –> animals and many plants) why do hybrids not make it long?
genes from the different species don’t interact properly
(how species evolve –> animals and many plants) what do parents only “care” about?
their own reproductive success, not about the purity of their species (purity is a consequence of choosing high-quality mates)
zygote
fertilized egg
breakdown of life cycle
fertilization –> birth/hatching –> grow to maturity – egg/sperm reproduce –> egg and sperm find each other –> fertilization
(breakdown of life cycle) postzygotic
between fertilization and egg/sperm reproducing
(breakdown of life cycle) prezygotic
between egg/sperm production and fertilization
(breakdown of life cycle) postzygotic reproductive isolation
hybrid dies/is sterile
(breakdown of life cycle) postzygotic incomplete
hybrid has lower fitness
Dobzhansky-Muller interactions
negative genetic interactions in hybrids
(breakdown of life cycle) prezygotic reproductive isolation
egg and sperm never combine
(breakdown of life cycle) prezygotic incomplete
sometimes combine
Phylogenetic analysis of immunodeficiency virus strains in humans (HIV), apes (specifically, chimps and gorillas) and monkeys (SIV) indicates that:
HIV evolved from SIV when people were infected with SIV; Several SIV strains from different monkey and ape species independently
infected humans and evolved to become HIV
Which is always true of ‘nodes’ on evolutionary trees, regardless of any other information that’s included in (or left out of) the tree?
Each node represents a single species (or strain) that gave rise to all the organisms on the branches that radiate from it
Bats have a high diversity of coronaviruses. They also roost in colonies every night in close contact with one another. From an evolutionary perspective, based on this behavior of bats, what properties do you expect those coronavirus strains to have evolved in their native bat hosts?
a: In bats, the viruses are not likely to be very virulent – i.e., the symptoms should be mild or even asymptomatic.
b: In bats, the viruses are likely to be able to evade the immune system for a long time (or equivalently, they are likely to be able to re-infect bats that have built up immunity, just like SARS-CoV-2 can occasionally re-infect people who are vaccinated).
c: Both of the above.
d: Just the opposite of the above! In bats, the viruses should be especially highly
virulent just like it is in humans, and the bats that do survive will become permanently immune. Therefore, most bats in the wild should be well protected by their immune systems, and the viruses should be rare.
c
T or F: Each of our 23 chromosomes is made up of a single, giant DNA molecule
true
Every cell has the same DNA, so every time a cell divides, all of its DNA first has to be copied. In mammals (for example), what are the chances for a given base pair that copying introduces an error (a mutation)? (Genes typically have tens up to thousands of base pairs, so (if indeed there were errors) the rate would be higher for whole genes. This question is about base pairs.)
a: It doesn’t – DNA is copied pretty much perfectly every time. Every one of our cells has identical DNA.
b: Errors are very rare; on the order of 1 or 2 in a billion base pairs is mis-copied every time a cell divides.
c: Errors are unfortunately quite common, on the order of 1 in 1000 base pairs mis-copied, so each cell has thousands of mutations.
b
For a virus to be able to attack a cell, that cell has to have a specific protein on its surface that the virus can attach to.
a: True, otherwise that cell can’t become infected. (Actually, some viruses attach to specific molecules that aren’t proteins.)
b: False; the virus does have to encounter a protein (or other molecule) on the cell surface, but cells have many kinds of surface proteins and the vast majority of them are vulnerable.
a
Natural selection favors virus strains that can attach to cell-surface molecules (proteins, commonly) that are essential to the host organism.
True – the host can’t easily alter those molecules via mutation because they’re essential.
The process of making proteins from information in mRNA molecules is called…
translation
Which of these statements about the genetic code is TRUE? (Choose the best answer)
All organisms use the same code.
LUCA used the same genetic code that we do. Both the above are true.
None of the above is true.
both are true
T or F: For natural selection to act on a protein, the mutation has to result in a change in its amino acid sequence
true
T or F: All organisms have 61 different tRNA genes, each corresponding to a codon in the genetic code.
true
The so-called “central dogma” of biology is that proteins are made using information from RNA, and in turn, RNA is made using information from DNA; copies of the DNA are made whenever cells divide.
Which of these statements is FALSE?
Copying DNA from DNA requires proteins.
Making RNA from information stored in DNA requires proteins.
Making proteins from information stored in RNA does not require proteins.
Trick question! They’re all true!
Making proteins from information stored in RNA does not require proteins.
Can RNA act as an enzyme by catalyzing (promoting) chemical reactions?
Yes, but only some forms of RNA can do it.
What seems likely to have been the cause of (or at least, a major contributor to) the Permian-Triassic extinction 250 million years ago, the largest of the mass extinctions?
global warming and volcanoes erupting
Melanin is a molecule that arose early in the history of life, and a great many organisms can produce it. It plays many roles, including camouflage (animals matching their color to dark or light backgrounds), immune response (but only in insects), and of course
protection from mutation, because it absorbs ultraviolet light before it can cause damage to DNA
Now that people can obtain Vitamin D through dietary supplements, alleles that produce light-colored skin have become …
deleterious
neutral
beneficial
deleterious
So far, there isn’t enough DNA data to figure out how different shades of dark skin have evolved, though at this early stage, it appears likely that natural selection in the not-too-distant past (say, within the last 15,000 years) has led to an increase in average skin pigmentation in more than one region on earth. But we do know that within that same 15,000 year period, lighter colored skin has evolved?
twice for sure
