exam 1 Flashcards
cuvier
paleontology - study of fossils
lyell and hutton
described natural geologic processes like erosion,sedimentation, uplift (gradual changes, big impacts)
louis pasteur
fall of spontaneous generation, living organisms come from other living organisms
stages before Darwin
earth is old, extinction, fossils similar to extra forms, lamarcks principle of adaptation, a principle of evolution
Darwins timeline
1831-1836 voyage of the beagle darwins only field trip
1844 wrote his first manuscript on natural selection - not published
1858 alfred wallace sent to darwin a manuscript that described natural section
1859 encouraged by Lyell and hooker - darwin published the origin of species in 1859
adaptation (darwins proposal)
evolutionary modifications that improve the chances of survival and reproductive success
natural selection (darwins proposal)
the mechanism by which better adapted organisms are more likely to survive and become the parents of the next generation
modern synthesis of evolution
population genetics and natural selection combine to explain micro and macro evolution
genetics and origin of species by TG D in 1937
impact of darwins work
many separate observations supported by a single explanation
provided a dynamic view of species
man no longer at the pinnacle of life
classification of organisms along evolutionary lines (still working on it)
central unifying theme of biology
all existing organisms are modified descendants of other organisms - common ancestry
natural selection - differential survivorship and reproduction is the main mechanism of evolutionary change
fossils - evidence of evolution
extinction is common
intermediate stages - the discovery of transitional forms has filled in some of the most talked about gaps in fossil record
stratigraphic columns - ancestral on bottom
radiometric dating - decay of isotopes at a constant rate
morphology
vestigial structure - reduced or useless body parts are evidence of both micro and macro evolution
limbs in snakes, tiny use less wings in borwn kiwi
tailbone in humans pelvis in whale and dolphin
homologous as what
homology - similar due to shared common ancestor
bat wings and bird wings
homologous?
as wings? no common ancestor did not have wings
as modified forearms? yes
evidence of homology
homology is descended from a common ancestor
as compared to the analogy - functional similarity but evolved independently
developmental homologies
embryos from different vertebrates are very similar early in development
gil pouches and postnatal tail in human embryos are also found in embryos of other vertebrates
molecular homology - the genetic code
the same nucleotide triplets or codons specify the same amino acid across almost all organisms
processed pseudogenes - test hypothesis of common ancestry
biogeography
similar species are clustered geographically
island faunas similar to adjacent continents
fossil forms on islands more similar to mainland form
suboptimal design
accidents of evolutionary history explain many features that no intelligent engineer would be expected to design
food and air crosses in the pharynx of terrestrial vertebrates
human eye has a “blind spot”
watching evolution happen
some of the most dramatic examples result from pressures human are imposing on the planet
postulates that lead to evolution by natural selection
individuals within the populations vary
variation is passed on from parents to offspring
in every generation, some individuals are more successful at surviving and reproducing than others
survival and reproduction are not random but tied to variation
characteristics of natural selection
main “unit” of selection is the individual but its consequences occur and are measured in populations
natural selection act on phenotypes but evolution consists of changes in allele frequencies
not forward looking - can only respond to what has occured
new traits evolve even though natural selection acts on existing variation
types of reasoning
inductive reasoning - summary of a series of specific observations that lead to a general explanation
deductive reasoning - using general explanations to make specific statements
scientific method - classical vs increased precision model
classical -
scientists observe, record without preconceptions, universal truths eventually emerge
increased precision model -
1.add refinement to induction (deduce, test, revise, deduce)
correlation does not equal causation
ex : lung cancer vs tobacco
what would be “good” evidence that smoking causes cancer?
ruling out the alternatives
C naive falsification model
falsification and corroboration
null hypothesis falsified = corroboration for alternative
can “prove” things “beyond a reasonable doubt” again uncertainty only at the limits
problems with it -
falsification can fail
data is theory laden
it is the theory that decides what we can observe
hypothetico deductive
science is a complex enterprise consisting of two interdependent episodes
1. imagination and creativity (invention)
2. validation and confirmation (critical examination and empirical testing)
E paradigms model of science
paradigm = a scientific frame of reference defined by a set of value choices (science as a social activity)
- science is invention or discovery followed by validation or confirmation
dealing with uncertainty basic decision theory
a. applicable to all sorts of decisions
b. steps formalized
1. state probable hypothesis
2. assess two ways of being wrong
- state consequences if accept and is false
-state consequences reject and true
3. where to place burden of proof?
better to be too credulous? (accept and false)
better to be too skeptical? (reject and true)
- level of evidence needed
phylogeny
an hypothesis about the evolutionary relationships among organisms
systematics
constructing phylogenetic hypotheses
taxonomy
identification and naming species
1. sort out closely related taxa
2. arrange species into higher taxonomic groups
taxa - taxanomic units
synapomorphies
shared (due to ancestry) and derived traits
shared - homologous traits in closely related groups
derived - need to know direction of change (polarity of change)
all synapomorphies are homologies, but not all homologies are synapomorphies
problem with homoplasy
convergence and reversal both are classified as homoplasy
noise in the data
methods - maximum parsimony and maximum likelihood
maximum parsimony - preferred tree is the one that minimizes the total amount of evolutionary change
assumes that synapomorphies are more common than homoplasy
maximum likelihood - given a math formula describing the probability that different types of nucleotide substitutions will occur
given a particular tree
how likely am i to obtain this set of DNA sequences
boot strapping
creates a new data set from existing one by resampling
uses new data set to estimate phylogeny
determines how often each branch can be found in the trees estimated from the resampled data
coevolution
when interactions between species produce adaptations in both
cospeciation
speciation occurs in two interacting species simultaneously
three kinds of variations
genetic variation, environmental variation, genotype X environment interaction
the importance of mutations
any change to the genomic sequence of an organism
raw material for evolution
ultimate source of genetic variation
types of mutations
point (transition, transversion)
replacement (nonsynonymous) versus silent (synonymous)
insertions and deletions
duplication and inversions
where do new genes come from
gene duplication due to unequal cross over
retain original function
gain new function through mutation and selection (as in hemoglobin)
can also become functionless pseudogenes
promiscuous proteins
capable of carrying out two functions; are espeically likely to take on new functions if duplicated
paralog
a homologous gene that arises by gene duplication
gene recruitment
the co option of a particular gene or network for a totally different function as a result of a mutation; the reorganization of a preexisting regulatory network can be a major evolutionary event
gene duplication due to retroposition
processed mRNA (introns spliced out) reverse transcribed to form a double stranded segment of DNA
integrated into one of the main chromosomes (copies not next to one another)
often functionless psuedogene (not transcribed)
can become functional (next to regulatory sequence or acquires via transposable element insertion)
inversions (lock alleles into supergenes)
1 radiation causes two double strand breaks in chromosome
2. segment detaches, flips and is reannelaed
3. locked = not separated by crossing over
how do complex adaptations evolve
made up of coexpressed traits that experience selection for a common, often novel, function
gene expression
the expression of a gene is influenced by a network of regulatory elements and interactions with RNA and other gene products - important building blocks for complex adaptations
novel traits can arise when existing genes are expressed in developmental context.
a mutation that occurs in the coding region of a gene
may be beneficial in one context but hugely detrimental in another
less common - as experience strong purifying selection
mutations in a cis acting element
regions of non coding DNA which regulate the transcription of neighboring genes) by contrast, affect gene expression only in a single developmental context
more common - less catastrophic effects on the resulting phenotype
convergent evolution
independant evolution leading to similar traits in two different lineages - result of similar selection pressures
