Exam 2 Flashcards
what is a phylogenetic tree?
shows history of divergence and evolutionary change from a single ancestral lineage to a group of descendants
what is a phylogenetic tree based on?
DNA
what is a polytomy?
simultaneous divergence of taxa
-shows uncertainty (3-way split)
when drawing a phylogeny tree in a different way, what is one thing you must keep in mind?
the branch order must stay the same
what is a synapomorphy?
shared derived traits/characteristics
-must be present in 2+ species
what is the outgroup?
relatives of the ingroup but less closely related
what is an apomorphy?
‘separate from’
-new derived character
-only in one species
-EX: absence of legs in snakes
what is a plesiomorphy?
‘near from’
-pre-existing ancestral character
-tell us nothing about relationships within the group
-EX: legs in reptiles
what is a monophyletic clade?
ancestor and all its descendants
-identified by synapomorphies
what is paraphyletic?
-ancestor and some (not all) its descendants
what is polyphyletic?
-some (not all) of the ancestors descendants, excluding the ancestor
what do paraphyletic and polyphyletic have in common?
groups that contain some but not all of an ancestor’s descendants
-artificial group based on plesiomorphies
what two analysis methods can we use to help determine if novel traits were evolved and lost?
-outgroup analysis
-parsimony analysis
what is parsimony analysis?
-picking the hypothesis with fewest number of change (gains or losses)
-Ockham’s Razor
what is homoplasy?
similar traits due to convergence and reversal
-they seem similar but are NOT
-comparing apples to oranges
what is convergence?
independent appearance in difference lineages
what is reversal?
loss of derived traits in a lineage that results in a return to ancestral conditions
what is more prone to convergence and homoplasy?
genetic info (DNA sequencing)
what is homology?
shared traits due to common ancestor descents
what is the group of whales called that was studied heavily to determine its placement on a phylogeny tree and what was the ancestor it was eventually discovered to arose from?
whale group: cetaca
ancestor group: artiodatyls
-determined after molecular analysis when fossils were found
-found synapomorphies in the skull and ankle bones
-clear transition from land to sea
what is the initial and most important step when using molecular sequences for phylogeny testing?
ALIGNMENT
-must account for insertions and deletions when aligning
-sequences must be homologous
what is maximum likelihood analysis?
compares probability of all tree possibilities and selects the highest likelihood value
-accounts for a specific model of sequence evolution, branch lengths, and probability of a tree given our data
what is neighbor joining?
-less preferred
-Calculates genetic distances between samples and groups those with the fewest differences together
-fast and reasonably accurate, but oversimplified
what is bootstrapping? (BS)
generation of artificial datasets by random sampling
-gives an idea of uncertainty
in bootstrapping, below what percentage is considered unresolved?
below 70%
what is posterior probability? (PP)
probability of the data
what is Bayesian inference
allows scientists to assign posterior probabilities (PP) of trees
-set to equal proportions
which values are higher, PS or BS?
PS
in PS, what percentage is considered a strong statement?
90%
how is can phylogeny be used as a tool and what was the conclusion made in the example?
can help trace tumors in dogs
-determined that the tumors were related to other tumors
-not related to the dog species
what is the molecular clock?
answering questions about the timing of major events that impacted life through molecular traits that change at a steady state
what do mutations change?
DNA sequence, not phenoypes
what are neutral changes?
changes not affected by natural selection
-change through genetic drift
the number of neutral molecular difference b/w two taxa should be proportional to… (given that mutation rate is constant)
the age of the MRCA
what is phylogeography?
overlaying of genetic diversity on geographic space
-Chameleon on a deserted island example
what were the two hypothesis that arose with the Chameleon on a deserted island example and which one was correct?
Vicariance Hypothesis
Dispersal Hypothesis (CORRECT)
what was the vicariance hypothesis?
the Seychellean island broke off from Gondwana and they stayed put on the island
-would be closely related to species from India and Madagascar
what was the dispersal hypothesis?
they rode through vegetation from Africa to the island
-was found to be closely related to species from Africa
____ is the raw material for evolution
Heritable Variation
what are the two basketball players and what are their heights? what was determined from them?
Tracy McGrady (6’8) and Muggsy Bogues (5’3)
-humans stay relative to the same size, animals vary widely in size for their species
what is coefficient of variation?
allows us to compare variability in different species
what are cells distinguished by?
by the proteins they make
what is a gene?
located on a chromosome and are stretches of nucleotides that code for a protein
what is genetic variation?
differences due to genes
-individual genotypes produce phenotypic variation
how was genetic variation tested?
-chemical PTC was digested
-some found the taste bitter (PAV allele), others couldn’t taste it (AVI allele)
-chemical could bind to the receptor if they didn’t have the mutation in the allele
what comes from mom and dad?
a chromosome from each
-same gene
-different alleles
what is environmental variation?
differences due to external factors (where you live)
-different expression of genes can be triggered by environment
-even identical twins show this difference
how does the Daphnia pulex water flea show environmental variation?
when it was present in an area with predators it developed special defenses
-when it grew up in a safe area, it was smooth
are expression changes due to environmental variation heritable?
NO, not heritable
-organisms alter identity or quantity of proteins but isn’t passed to offspring
-they only alter the phenotype
what are epigenetic markers?
enzymes that can alter phenotypes by changing gene expression
-non-genetic inheritance
what is a chemical modification that is an example of epigenetic markers?
methyl group attachment of cytosine nucleotides that can attach/detach when exposed to certain environments
are epigenetic markers heritable?
YES heritable
what is genotype-by-environment interaction?
differences in encoded DNA of individuals that make them differ in their sensitivity to environmental factors
how do leopard gecko’s show genotype-by-environment interaction?
-sex is determined by the temperature of the egg incubation
-extremes: female, middle temps: male
-there was variation among fathers in the effect of temperature on the sex ratio of their offspring
what is reaction norm?
pattern of phenotypes an individual may develop upon exposure to different environments
how were humans tested to show genotype-by-environment interaction?
-ll gene for serotonin had no difference w/ maltreatment
-ss gene for serotonin were more depressed w/ maltreatment (due to less amount of the serotonin transporter)
what is phenotypic plasticity?
when an organism develops different phenotypes in different environments
-has a range of responses
-has genetic variation for environmental sensitivity
how were hornworms tested to show phenotypic plasticity?
normal color: green
w/ heat shock: black
when do mutations occur?
when DNA is altered and missed by the repair mechanisms
what is cytosine deamination?
-methyl cytosine can spontaneously lose an amine group when exposed to water
-it turns into a thymine
-causes a mismatch pair if not repaired before translation
when is misalignment common and what is it?
in repeats
-comes from insertion or deletion of nucleotides
what are premutations?
alterations to DNA due to chemical degradation and must be corrected
how common do mutations happen on a daily basis? how about per division?
20,000 daily
100,000 per division
what do you call it when the code has so many ways to make the same amino acid?
the code is redundant
what are point mutations?
substitution of one base
transition mutation
purine to purine (A-G)
OR
pyrimidine to pyrimidine (C-T)
transversion mutation
pyrimidine to purine (A-T, G-C, A-C, G-T)
which mutation is easier and more common? (transversion or transition)
Transition
what are synonymous (silent) mutations?
change nucleotide but AA is the same
what are nonsynonymous (noisy) mutations?
change nucleotide and changes AA
what are nonsense mutations?
change nucleotide and AA is a STOP codon
what are introns?
non-coding regions of DNA
-contains promoters
what can insertions and deletions (indels) cause?
frameshift mutations
-it shifts the reading frame and causes changes all AA codons downstream
what are two mechanisms to create new genes?
unequal crossing over
retroposition
what is unequal crossing over?
recombination error in meiosis
-one chromatid has an insertion and the other one has a deletion
how does the Douc langur monkey show unequal crossing over?
it only eats leaves due to two RNase1B enzymes
-RNase breaks down nitrogen in RNA
-RNase1B mutated from RNase1
what are paralogous genes?
genes that duplicated w/in a genome and later diverged in function
-EX: monkey that only eats leaves
what are orthologous genes and what is an example of it?
genes derived from a common ancestral sequence and separated by a speciation event
-RNase1 in Douc monkey and RNase1 in humans
what is retroposition?
reverse transcribed DNA that integrates into chromosome
how are corgis an example of retroposition?
they have a condition called Chondrodysplasia that gives them short legs
-duplicate copy of the gene for fibroblast growth
-it lacks introns but got a promoter inserted into the middle of a transposable element
___ and then ____ _ ____ generates new genes
duplication, divergence of function
how do inversions happen?
radiation causes 2 double strand breaks in the DNA
what happens in inversions?
the chunk can detach, flip, and reanneal
-creates new positions for the genes
what do inversions effect besides the location of the genes themselves?
linkage of genes
what is linkage?
tendency for alleles to go together at meiosis
what reduces linkage?
crossing-over
how are drosophila an example of linkage?
it has 6 chromosomes, 5 of them can contain inversions
-inversions can be more likely depending on climate and latitude
what is a cline?
a regular change over a geographic area
-EX: climate and latitude
how does genome duplication occur?
when chromosomes fail to segregate in meiosis 1 or 2 and result in double the number of chromosomes
how do plants show genome duplication?
the germ line is not segregated and duplication can occur in mitotic divisions
-results in a tetraploidy (4n)
-this can create a new species of plants
what is a polyploid and how does this create a new species?
2+ chromosome sets (4n, 6n, 8n, etc.)
-can lead to new species because it allows them to get new phenotypes that better adapt them to their environment
what is a polyploid common in and why?
common in plants due to self-fertilization
what is significant about mutation rates in different species?
mutation rates are diverse, evolve, and have several orders of magnitude dependent on the species
what are the outcomes of most mutations that affect fitness?
the are lethal or neutral, not beneficial
what will happen to a population not under natural selection?
it will decrease in average fitness over time
what happens to a population under natural selection conditions?
the bad mutations ‘weed’ out and the fitness doesn’t decrease
