ZOO611 Exam 1
Peramorphosis
Evolution of a more extreme character state by prolongation of development in the descendant, compared to the ancestor. we grow our legs for a longer amount of developmental time than chimps some sharks grow their teeth for longer
Macroevolution
Evolutionary change above the species level.
ATP synthase structure
F0 domain: water insoluble protein, it rotates F1 domain: hydrophillic end protrudes into mitochondrial matrix catalyses ADP + P -> ATP production
Fitness landscape is constant
False; it is constantly changing due to the world
Speciation
Formation of new species
Mutations used to be all considered
Harmful; focused on point mutations that had dramatic impacts on the organism
Most mutations have
Minor impacts on phenotype ; some are really bad (but weeded out almost immediately which is why they're rare)
Gould believed that speciation is mostly adaptive/nonadaptive
non adaptive! (due to founder effects that caused large punctuated change)
two most basic types of heterochrony
paedomorphosis: Retention of ancestrally "juvenile" traits into adulthood peramorphosis: Emphasis or elaboration of ancestrally "adult" traits in adulthood
Axle
the rotational motor subunit of f1, changes conformation as its spun by f0, catalyzing ATP synthesis
Chemically driven droplet growth
chemically active droplets; drops have active chemistry and grow until they reach the size of an average prokaryotic cell. then divide and grow again. could be a form of selection present favoring more efficient droplets
ADP -> ATP reaction is powered through
chemiosmosis
what molecule helps maintain proper membrane fluidity?
cholesterol
Did Gould believe in anagenesis or cladogenesis?
cladogenesis
allopatric speciation is always a form of
cladogenesis
horizontal gene transfer is more common among
close relatives (the genes are more likely to function)
Van der Waals interactions break under what membrane tail formations? what temperature is this good for?
unsaturated (double bond) -- low temperature
heterochrony
an evolutionary change in the rate or timing of developmental events
the long tail of a skewed distribution always points ____ from where directional selection is pushing a population
away
Prokaryotes vs. Eukaryotes
- Prokaryotes have no nucleus or membrane bound organelles (single cell) - Eukaryotes have a nucleus and membrane bound organelles (one to many cells) - Both can reproduce and respond to the environment
Tempo of Speciation
- event rate or time between events. - evidence from the fossil record.
how many std covers 95% of population in normal dist?
2
most scientists doubted darwin's natural selection theory from ______ to _______
1860s ; 1910s
how many std covers 99% of population in normal dist?
3
what percent of population is 1 std of normal distribution?
68%
genetic drift
A change in the allele frequency of a population as a result of chance events rather than natural selection.
Aneuploidy
Abnormal number of chromosomes.
Cladogenesis vs Anagenesis
Anagenesis = evolutionary change within a lineage Cladogenesis = splitting of one lineage into 2 lineages
Anagenesis vs. Cladogenesis
Cladogenesis: splitting into a new clade; divergence (when organisms are physically separated and undergo unique changes) Anagenesis: change within a lineage (change in gene frequency)(entire population is different from its ancestoral population) Both account for the major long term features of evolution
What concepts form the basis of natural selection?
Competition/death before reproduction of organisms Variation
Darwin's sketches of evolution tree imply that
Darwin agrees with the idea of species sorting! (species competition for survival as much as populations competing), but still included anagenesis
Punctuated Equilibrium problem in article 1
Does not really grasp the concept perfectly, rapid evolution does not require punctuated equilibrium model
which theory, Gould or Modern Synthesis, would argue that evolution is more random
Gould
DNA as a baking recipe
Gould suggests that DNA is like "how" ingredients are combined and results in vast difference in phenotypes. EPIGENETIC factors
hot springs
Hot springs occur when groundwater circulates near magma chambers and is heated.
example of paedomorphosis
Humans; we are alike to our ancestral juvenile monkeys in head size and shape (big head compared to body, unlike older monkeys) Canids; retain more juvenile head proportions compared to wolves and coyotes (read slides more)
Darwin used who's equations to form what hypothesis?
Malthus' economics calculations to show that far more animals are born than can survive to reproductive age. individuals vary and that those variations seemed to help with reproduction/survival
Differences between bacteria, archaea, and eukarya is super simple!
NOPE! lots of similarities and differences, regardless of ancestry
punctuated equilibrium
Pattern of evolution in which long stable periods are interrupted by brief periods of more rapid change
____ selection can help further natural selection when hybrids are present in sympathetic speciation
Sexual ; non random
Who created the punctuated equilibrium model?
Stephen Jay Gould
allopatric speciation
The formation of new species in populations that are geographically isolated from one another.
sympatric speciation
The formation of new species in populations that live in the same geographic area
Hopeful monster hypothesis
The idea that a single mutation could lead to a rapid transition from one form to another, called macromutations (Goldschmidt) turns out there are genes that can result in massive changes (not adaptive reasons)
Vicariance
The physical splitting of a population into smaller, isolated populations by a geographic barrier.
oxidative phosphorylation
The production of ATP using energy derived from the redox reactions of an electron transport chain;
horizontal gene transfer (3 mechanisms -learn for exam)
The transfer of genes from one genome to another through non-mating mechanisms. Transformation: incorporating ingested genetic material into your own DNA Transduction: genetic material brought by bacteriophages Conjugation: transfer of DNA in plasmids during cell-to-cell contact
disadvantages of hot spring models
While high temperatures drive some forms of reactions, most hot springs lack really strong chemical/temperature gradients UV light also breaks certain kinds of organic bonds, so shallow springs may run into a limit of organic complexity While geothermal activity was more widespread on the early Earth, it's hard to quantify how common hot springs were
is there room for some error in DNA replication that doesn't affect protein function?
YES!
fitness landscape
a heuristic representation of fitness as a function of genotype or phenotype; fitness peaks at the top
Red Queen Effect
a phenomenon seen in coevolving populations- to maintain relative fitness, each population must constantly adapt to the other / evolve to constantly shifting adaptive landscapes
What is Mendelian inheritance?
a set of primary princples relating to the transmission of hereditary characteristics from parent organisms to their offspring
genetic bottleneck
a sudden reduction in the number of alleles in a population
quantum evolution
adaptive evolutionary change within a lineage characterized by long periods of little change that are suddenly interrupted by short bursts of rapid change ALL about major environmental events creating strong selective peaks similar result to Gould, differ in mechanism!
Mode of speciation
allopatric and sympatric; cladogenesis and anagenesis
researchers physically modeled black smokers in ancient oceans!
an ongoing study, have already seen amino acids and other formations results already remove a lot of the advantages of the hot springs model
dogs evolve via
anagenesis
What isn't true about reading 1 about macro/microevolution regarding anagenesis?
anagenesis isn't always gradual but the author implies it is a slow process
North american dinosaurs at the end of the age of dinos mainly seem to evolve _____
anagenically!
non-adaptive evolution
any change in allele frequency that does not by itself lead a population to become more adapted to its environment (even sexual selection, epigenetic changes)
horizontal gene transfer happens repeatedly within
bacteria and archaea, and between those domains, even 40 or so human genes that have MAYBE been acquired this way
Cryptic speciation
biological process that results in a group of species (which, by definition, cannot interbreed) that contain individuals that are morphologically identical to each other but belong to different species. major problem of punctuated equilibrium because it suggests that cladogenesis is not necessarily coupled with phenotypic change!!!!
from the 1910s to 1940s, what scientific change occured?
biology pushed towards quantifying results, such as statistical approaches and population genetics, demonstrating that mendelian genetics and natural selection are compatible. Modern Synthesis was super successful
black smoker or hot springs more so found on other planets
black smoker
simple metabolism may have come first under which model?
black smokers
Is evolution a theory or a fact?
both; scientists consider the evidence for shared ancestry to be very established (fact) while theories are frameworks for explaining how and why evolution occured as it did
reading 2 takeaways:
cancer cells mutate rapidly, more than predicted by "Darwinian gradualism". Hopeful monsters and punctuated equilibrium are promoted! yeast/cancer non exactly 1:1 (cancer has its own support system)
sickle-cell anemia is not weeded out by natural selection because
carries are resistant to malaria
species sorting
competition between rapidly evolving species; SPECIES by chance are more fit than others = won't go extinct a different hierarchy of evolution, species vs populations
Transcription factors diffuse out of cells, and create
concentration gradients that affect timing of development
Chemiosmosis
creating and maintaining electrochem gradients to drive chem requires active trans ATP synthase is a double-motor "machine"!
reducing phenotypic diversity usually reduces genetic diversity, which
decreases the chances of surviving short-term threats (which is a problem for selective breeding and even stabilizing selection) can even decrease a population's ability to evolve when faces with sustained directional selection
biological evolution
descent with modification
the large jumps that macromutations cause would be usually
detrimental due to need of a mate with similar mutation
Epigenetic factors for Gould act on the
development of an organism so much that natural selection isn't always acting directly on genes oversimplified
embryologists and geneticists together created
developmental genetics
cladogenesis creates more species via what selection mechanism?
disruptive selection (and subsequent directional selection afterwards to push the species apart)
Cladogenesis: allopatric speciation . Does it explain everything?
does not explain all! weak point of punctuated equilibrium argument
what are a few examples of microevolution?
dog breeds and chicken breeds are all one species even cabbage, kale, broccoli, and cauliflower!
if the short tail of a skewed distribution gets really sharp in the drop-off, it indicates that
either directional selection is outpacing mutation or that it's running into a hard developmental limit
Eukaryote organelles were acquired from horizontal gene transfer via
endosymbiosis!!
Taxonomy implications and modes of measuring
establishing new species can have large social and economic impacts testing directional selection (if one has it and one doesn't) testing hybrid zones (fusion? stability? reinforcement of pushing apart/destructive selection?) Conservation concerns! (we are starting to see polar-bear-grizzly hybrids which means that polar bears will become more extinct)
Darwin's actual main accomplishment was his
evidence for evolution, he ALSO predicted a viable mechanism which was later discovered by the framers of the Modern Synthesis
Gould on spandrels
evolution as spandrel: side consequence of building arches (developmental constraint), subsequently co-opted for a spandrel (adaptations in organisms) sometimes, an organism literally cannot evolve in a particular direction, so if it adapts it will go the other way
evolutionary theory and biology today
evolution discovery caused huge advancements for biological science
Microevolution
evolution within a species
name a fact, law, and theory of gravity.
fact: gravity does x law: newtonian gravitation 9.8 theory: Einstein's relativity model
Darwin did invent the idea of evolution.
false
Macroevolution requires large phenotypic changes
false
cladogenesis is tied to phenotypic change
false
horizontal gene transfer is rare
false
oxidant loses electrons
false
reductant gains electrons
false
There is an inadequate amount of fossils available to support punctuated equilibrium
false. we have plenty of fossils, just not show stasis and rapid change definitively.
the hopeful monster hypothesis is widely accepted today
false; unnecessary to explain some evolution can never even test in the fossil record due to complications
stabilizing selection is a form of adaptation
false; it is not adaptation, it is optimization
many evolutionary biologists agree that punctuated equilibrium plays a significant role in determining macroevolutionary trends
false; most biologists probably agree that adaptive changes are more to come by
benefits of hot spring models
focused on raw organic molecules necessary for life and where they came from Being at the surface allows for UV & lightning to interact with chemicals dissolved in the pools, and experiments show a wide range of organic chemicals can be produced this way This model is often linked to origin of life models that put self-reproducing molecules (usually RNA/ribozyme based) ahead of metabolism or cellular containment
disruptive selection
form of natural selection in which a single curve splits into two; occurs when individuals at the upper and lower ends of a distribution curve have higher fitness than individuals near the middle
Darwin was not very impressed with
fossils; paleontology didn't have enough fossils to have a good record in 1850s
non-adaptive change can occur from
genetic drift and founder effects.... accidental change in alleles with nothing to do with survival (not adapting to environment) (founder effect is opposite of adaptive lol)
Gould thought that almost all speciation occurred due to
geographic isolation (allopatric speciation) (founder effects even!) ----> leads to punctuated change
an environmental model for the origin of life must satisfy several conditions...
had to actually exist on earth Production (or abundance) of organic chemicals Method to drive production of larger chemicals (some form of ion gradient)
How did life appear?
hard question, several ways it could have happened. maybe it hadn't started on Earth! Panspermia (simple life can come from other planets on asteroids or even cosmic dust) is definitely "in play"
Plants and speciation
hard to measure/track macroevolution not many major extinctions of trees and plants during the recent ice ages due to large spread same genome can = different phenotypes depending on environment (phenotypic plasticity)
thale cress genes/mutations
has parts of its genome which has less error-correction mechanisms = more mutation rate, may give larger amount of genetic "raw material" for natural selection to work on overall good? if certain parts evolve faster than others (hypermutation model = one mutation that takes away error-correction = more rapid rate of mutations later)
Rotifers
have around 8 percent of their genome acquired from non-ancestors
What did Gould do to contradict modern synthesis?
he looked at the history of fossil record, where there was punctuated periods of change and periods of non change!
variations in the timing of developmental events can create
heterochrony effects (via evo-devo lol)
black smoker model advantages
high energy to drive organic chemistry reactions (and high differentials) strong chemical gradients for electron exchange it turns out that the most primitive form of metabolic pathway today uses iron to produce ATPs METABOLISM-FIRST mindset
Darwin was very impressed with
homology; the sharing of parts inherited from ancestors (even if the parts are used differently)
the success of heterochrony shoots down what theories?
hopeful monsters and spandrels Because hopeless monsters theory relies and hangs on the idea that a single mutation can have massive phenotypic and evolutionary effects whereas heterochrony focuses on the network as a whole via transcription factors and rates of diffusion of gene/protein regulation. Natural selection then acts on these conglomerative changes rather than a single mutation with a huge effect.
electron receptors of life:
iron oxidizers chemotrophs (oxidize sulfur or ammonia) methanogens acetogens (produce acetate and fix co2 to produce biomass) phototrophs (not producing oxygen as a byproduct) LEARN THESE
what role did natural selection play for Gould?
it still drove some changes such as driving some towards a fitness peak. But did not account for the driving pattern of macroevolution seen in the fossil record.
Gould inspired other scientists in embryology and other developmental fields to
jump into the debate about Modern Synthesis theory
unsaturated tails create a ___
kink, misaligning the tails and creating more fluidity (good at low temp)
summarizing macroevolutionary patterns
land vertebrate evolution is driven more by adaptive anagenesis marine invertebrates MAY rely more on punctuated cladogenic speciation plants????
in peripheral isolate models, smaller numbers are involved and therefore smaller/larger change is experienced.
larger!
if an anagenesis event is pushing a population vector to the right, which side is the skew?
left!
longer membrane tails are
less fluid (good at high temp)
disadvantages of black smoker model
less obvious source of initial raw organic chemicals no uv or lightning exposure in deep waters
competition between niches of two different species =
maladaptive, it will reinforce disruptive selection and push the overlapping populations further apart. Even happens with hybridizing populations
which two values are not the same in a skewed distribution?
mean and median
Scientists doubted that Darwin's theory _____ was powerful enough for evolution
mechanism! They WERE impressed with his evidence for evolution
Modern Synthesis approach claims that (in article 1)
microevolution accounts for macroevolution over time
shorter membrane tails are
more fluid (good at low temp)
what concept forms both genetic variation and mendelian inheritance?
mutation
What is a mechanism for timing of development?
mutation in transcription factor proteins can cause gene expression sooner or later = developmental effects
what three concepts from to create modern synthesis?
natural selection, genetic variation, and mendelian inheritance
Can theories become laws?
never
over time, directional selection causes adaptation across generations and creates
new morphospecies (via anagenesis)
microevolution creates macroevolution to gould
nope
is heterochrony a mechanism?
nope! just a way of describing how ontogenies evolve
if there is stabilizing selection in a population, what distribution would we expect to see?
normal
what role does species sorting in phenotypic evolution?
not very clear. large body size is actively selected against by species sorting(metabolically?) yet body size has evolved to be large in some species today! Non-adaptive species sorting is real!
peripheral isolate model
offshoots of the population (partial allopatric) enter a new niche peripatric -> small pop gets temporarily cut off from the rest of the pop (close to allopatric) parapatric -> similar, but instead of fully cut off there is a filter (biggest and heartiest can mix?)
spandrels are hard to
operationalize, often can't tell whether a developmental constraint is real, or if it evolved to be constrained after the fact. Did it evolve as a cause of constraint or did it cause the constraint after the fact? As a result, exaptation is a favored idea today
stabilizing selection results in a mean value that is the _____ measure of a trait.
optimal; helps survival and reproduction the most
Many genes covary, meaning
optimizing one genetic pathway necessarily hurts another (if some 'good' is selected for, 'bad' comes along for the ride)
predictive conservation
population modeling, evolutionary modeling, and thermodynamic modeling we can change reactive conservation to predictive === saving more species!
Bacteria and Archaea are
prokaryotes; NOT A BIOLOGICAL group because archaea are closer to eukaryotes!!! so prokaryotes is pretty much "all life that isn't a eukaryote"
transcription factors create anatomy via which two mechanisms?
proliferation (cell growth) and apoptosis (cell death) apoptosis can help separate fingers webbed feet genes delay apoptosis!
the rock record sucks for determining truth of ______
punctuated equilibrium; rocks are not deposited at a constant rate = false impression of time
Gould argues that ecosystems create a "____" pattern of evolution and do not lead to a major change (speciation)
random walk
founder effect (form of genetic drift)
rare allele occur in a higher frequency in a new SMALL population than they do in the old general population due to accident
nearly all of the reactions that drive your physiology are
redox reactions; mostly aq solution
What happened in the 1960s related to evolution?
researchers showed that not everything in an organism is adaptive, so evolution must have other, more complex mechanisms in addition. aka: the modern synthesis went too far.
what's the problem with loss of heterozygosity ?
same genes on both sides of chromosome = bad genes will show its phenotype
Eastern Emerald Elysia
sea slug that appears to have permanently incorporated some algal DNA in order to "operate" chloroplasts that it co-opts from the algae
hybrid species can help disruptive selection since their "medium" features are
selected AGAINST. ex-> white and black finches are final product. hybrid brown finch does not reproduce while white and black reproduce more rapidly! === sympatric speciation
Anagenesis visualized
selection to a certain extent in which a species will not "readily" reproduce with itself anymore and therefore changes enough to become a new species (replacement)
Darwin realized that extreme modification of organisms was possible through what main two processes/features?
selective breeding and island biogeography
what are two forces that push and pull the normal distribution 's standard deviation?
selective pressure pushes in the distribution (small sd) while mutation pulls the distribution wider (large sd)
what are the necessary conditions to be alive?
self-reproducing offspring inherit your characters consume energy locally oppose entropy (open systems can and frequently do decrease local entropy, allowing more complexity) (closed systems where no more energy goes in = death) the universe is a closed system, so it eventually will die
almost all protein function is ____ dependent
shape
Anagenesis
species formation without branching of the evolutionary line of descent.
punctuated equilibrium's main mechanism for macroevolution is
species sorting (non adaptive, luck) ; decoupled from adaptive evolution
Stator
stiff f1 subunit that binds f0 and f1 together
criticisms of reading 2
straw-manning of modern synthesis --- gradualism is still under debate!!!! not easy to just shut it down so easily oversimplified punctuated equilibrium --- only related to tempo, an assumption is made that rapid evolution must = punctuated equilibrium can their results be applied to other organisms? (plants/animals? not really buying it) ------> useful addition to debate over tempo in evolution, however, they self-inflate the importance of their work and the conclusions seem misleading.
rapid evolution and extinction are linked because
strong stabilizing selection that occurs with rapid evolution may not be in line with a changing ecosystem = species more susceptible to extinction
the finches on the galapagos underwent
sympatric speciation via disruptive selection
Fossil problem in article 1
the author claims that the fossil record almost always shows rapid change and stasis, but this is heavily debated in paleontology "Living fossils" are a problematic concept
Cladogenesis
the formation of a new group of organisms or higher taxon by evolutionary divergence from an ancestral form.
heterochrony (definition)
the intersection of ontogeny (how an organism develops) and phylogeny (whom you are related to/evolved from) === how developmental sequences change over evolutionary time
exaptation
the likely most lasting idea of Gould when a spandrel (or previous adaptation) is adapted to a new role that it was not originally intended for broadly accepted idea! fingers and toes are like bones we find in fish which support fins, bird feathers and wings were found in non-bird dinosaurs before flight occurred, horns on rhinoceros beetle
Archaea
thought of extremophiles, lived where no bacteria could live. But are not JUST extremophiles, found in all environments
as embryos get larger they take up more space, thus ... (relating to transcription)
transcription factors impact relatively smaller segments (proportion) of the organism as the signal becomes more diffuse as it spreads.
Earth life may have already infected much of the galaxy (possibly) via asteroids
true
Most researchers today agree that modern synthesis 1930s-50s went too far
true
Theories cannot be proven
true
active chemical droplets may have formed the first cell-like containment
true
cell membranes are fluid
true
dogs have lots of phenotypic change but no cladogenesis
true
founder effect is a form of genetic drift
true
in Anagenesis, the old species goes completely extinct
true
interacting networks of genes give variations in phenotype which natural selection can act on
true
macroevolution means speciation
true
oxidant gains electrons
true
phospholipid bilayers are easy to make
true
phospholipid tail length and tail saturation must be modified for a particular thermal environment
true
reductant loses electrons
true
archaeans are closer to eukaryotes than to bacteria
true!
punctuated equilibrium suggests that cladogenesis is coupled with phenotypic change
true, cryptic speciation conflicts with this theory
Goulds data was partially wrong
true, new stats methods have shown that his data is equally consistent with gradual evolution, quantum evolution, and punctuated equilibrium
ATP synthase can also run backwards, acting as a proton pump
true; pump may have evolved first
Integrative Science
uses lots of perspectives and methods to investigate questions about ______ tend to be particularly productive due to combining of perspectives and strategies
black smokers
vents on the sea floor that form as hot mineral-rich water rushes from the hot rock at mid-ocean ridges and mixes with surrounding cold ocean water
maybe both hot springs and black smokers models have a role to play??
water runoff from hot-springs into oceans? Asteroids providing earth with amino acids
A scientific law has what to do with facts?
while a fact is well verified descriptive data, a law is a (mostly) permanent relationship between facts. Laws are often discovered empirically
Can laws become theories?
yes, laws can help form theories
what is genetic variation?
● Variations in the genotypes of organisms of the same species due to the presence of different alleles ● Creates differences in phenotypes CONTINUOUS
