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