Biology Exam 1: Evolution Flashcards
Lectures 1-4
Cardia bifida example for why knowledge of evolution is important in medicine
Humans are bilateral symmetric organisms (mirrored development on both sides of the body). The hearth results from the fusion of two proto-hearts thus explaining WHY cardia bifida exists.
Hernia example for why knowledge of evolution is important
Hernias are 25x more common in men than women because the descent of the testes through the abdominal wall causing an area of weakness, making men susceptible to hernias
What is the unifying theme in biology?
evolution
Untrained assumption: disease causing organisms will change over time to become more benign. Reality:
disease causing organisms are constantly evolving to become more fit, thus becoming more dangerous to their hosts
Untrained assumption: Humans will eventually evolve to be resistant to disease causing organisms
Disease causing organisms can evolve much faster than humans because of their low generation time, meaning that over time humans will become less resistant due to more dangerous bacteria
When did antibiotics first start losing their effectiveness?
1950’s
Factors that lead to antibiotic resistance: (5)
- over prescribing
- inaccurate prescribing
- early discontinuation of use
- high density low sanitary living conditions
- extreme overuse in livestock industry
Give two examples of Evolutionary anatomy
- Wisdom teeth impaction because of the shrinking of human jaws
- the complexity of the cranial nerves because as the muscles and bones of the skull shifted, the nerves attached to these structures shifted as well (cranial nerve XI is associated with shoulder shrugging because your collarbone was part of your gill covering millions of years ago
What organism is used as a model for Alzheimer’s research? What portion of our genome is identical to this organism?
yeast. 2/3
Assumption of population biology: biological populations will evolve to restrain their own reproduction so as to benefit the species.
Reality: every organism for him/herself: the evolutionary goal is to pass on one’s genes
With what two scientists and when did our modern understanding of evolution begin?
Buffon and his protege Lamarck in the 1700’s
Why were the groundbreaking ideas of Buffon and Lamarck quickly rejected during their time and by whom were they rejected best?
Couvier:
- tinkering with a complex and fantastic machine suck as the human hand can only do more harm than good
- Fossils=the aftermath of the biblical flood. (Couvier was the first person to understand extinction in Western culture)
- Egyptian cat v. modern cat (~5000 years): found no change
- People accepted biblical creation
Who created a date of creation based on theology and what was it? Who changes this idea?
James Usher: Oct 23, 4004 BC at 9:00 am.
James Hutton
Hadrian’s wall
Hutton’s wall had been there for 1500 years and was relatively perfect. If 1500 years didn’t change a wall, how long would it take to carve a canyon? Thus he realized the earth had to be incredibly old.
Hutton’s unconformity
many layers, some vertical and some horizontal. Layers showed how old earth must be and the different orientations ____________.
Darwin was not the first to hypothesize evolution. What did he do?
He came up with the mechanism for evolutionary change: natural selection
In what year did Darwin publish the Origin of Species?
1859
Law of fossil succession (+example)
If two species are evolutionarily related, we should be able to find a pattern where the extant (living) and extinct (dead) forms live. Example: Glyptodont and armadillo
Two v important questions Darwin had to be able to answer if people were going to believe him
- HOW do species change?
2. WHY do species change?
________ keeps population size in check
competition
What happens to species that allows them to better compete for limited resources?
They change (WHY?)
The first evolutionist who confidently and publicly stated his ideas about the processes leading to biological change
Lamarck, Buffon’s protege. Buffon was one of the first scientists to postulate that life was not fixed.
When did the idea of evolution first begin?
1700’s
Who was responsible for the dismantling of early evolution?
Couvier. He was the first comparative anatomist and the fist person to dismantle evolution with something other than the Bible
James Usher
Put a date on creation. He used the bible, started at Christ, and moved backwards to get October 23, 4004 BC at 9am
James Hutton
Hadrian’s wall and hutton’s unconformity: Hutton first states that the earth is way older than we thought it was
Catastrophism:
How scientists married the Bible with logic and an old Earth.
Charles Lyell
Picks up on age of the earth work where Hutton left off. Writes Principals of Geology, the first geology textbook and a book that would be given to Darwin right before he boarded the HMS Beagle. Lyell was the man to refute catastrophism in favor of uniformitarianism: the earth doesn’t just look old, it IS old
Charles Darwin
Darwin did not start as an evo. thinker or much of a thinker at all but after he returns from his trip on the HMS Beagle he is obsessed. Darwin was not the first person to hypothesize evolution but he WAS the first to come up with a mechanism for it.
Darwin’s three ideas on evolution
- 2.
3.
Thomas Mathus
Political economist of the late 1700’s- warned about uncontrolled population growth. Darwin picks up his book and has an Ah-hah moment (?)
What did pre-darwinian evolutionary theorists stress?
Perfection, hierarchy, and increasing complexity
Darwinian evolution showed that evolution is about:
competition for limited resources and reproduction. He showed that evolution has no direction and that there is no real hierarchy of beings (no higher/lower)
The superior competitors are always more/less complex?
Either could have the advantage. Example: cave fish evolving to lack eyes or surface pigment
Darwin’s main problem in his theory of evolution published in “On The Origin of Species” in 1859 was that… (2)
- He didn’t know HOW traits were passed down from parent to child (this information was found with Mendel in Darwin’s lifetime but no one actually read it)
- How do you get new traits to arise?
When was DNA discovered?
1953
Though Darwin’s theory on evolution was published in ______, the theory remained unaccepted and highly controversial until ______ in the ______ community
1859
1950’s
Academic
What are 5 pieces of evidence in favor of evolution?
- Transitional Forms
- Vestigial Traits
- Homology in Development
- DNA Analysis
- Chromosomal Analysis
Radiometric dating
a technique used to date materials such as rocks or carbon, in which trace radioactive impurities were selectively incorporated when they were formed. The method compares the abundance of a naturally occurring radioactive isotope within the material to the abundance of its decay products, which form at a known constant rate of decay
Example of transitional forms
Lucy
Example of vestigial traits
what is left of limbs on a snake butt, whale pelvis
Example of homogeny in development (3)
- embryos of vertebrates showing extremely similar structures during development
- The circulatory system of a human at 29 days of development is almost the same as that of a fish.
- forelimbs of mammals (one bone, two bones, wrist bones, fingers)
Examples of DNA Analysis
Percent similarities:
- Chimp 99%
- Gorilla 98%
- Mouse 93%
Examples of chromosomal evidence
Chromosome 23 in humans which appears to be a merge of the 2 chromosomes that make up chromosome 23 in chimps
Name the 5 tenants of modern evolutionary recursion
- New DNA mutations occur in every generation
- These mutations produce individuals that are genetically and physically different from each other (ie population variation)
- Individuals within a population compete with each other for limited resources
- The outcome of competition is non-random: these traits make some individuals more successful than others and
- These successfully competing organisms are more likely to contribute more genes to the next generation than unsuccessful individuals are.
If the 5 tenants of modern evolutionary recursion are true, what must also be true?
The gene pool will change over time- evolution is genetic change over time
Intelligent Design
William Paley: pocket watch on an island: Humans and animals and plants are too complex to have been made naturally, we need an “intelligent designer” AKA God. Even the pope rejects this shit. (PPJII)
Father John Zahm
One of the first Catholic leaders to stand up for evolution
Theory v Hypothesis
When people use the word theory, they typically mean hypothesis or guess.
Hypothesis: a suggested explanation for an observable phenomenon.
Theory: is a tested, well-substantiated, unifying explanation for a set of verified, proven factors.
Individuals (do/do not) evolve.
do not. populations evolve but selection acts on the individual
Artificial selection and what we can learn from examples of artificial selection (2)
accelerates evolution
Examples: wild mustard plant and bristle number on drosophila
1. Natural populations have significant heritable variety
2. Heritable variety is easily acted in by a selective agent to cause evolutionary change
Natural selection
differential survival and reproduction of individuals in a population based on heritable (genetic) variation. Natural selection is the mechanism by which evolution occurs.
Evolution
change in genetic frequencies (composition) of a population
Hardy-Weinberg Equilibrium
Why is it useful?
What does it assume?
p2+2pq+q2=1 with 1=100% frequency
p2=AA // 2pq=Aa // q2=aa
The utility of the HW equation is that it teaches us the various forces that causes changes in gene frequencies
HW assumes no mutations.
What conditions must be met in order for population gene frequencies to stay constant?
- Mating is random (does not always occur in nature)
- Population size in large
- No flow of genes in or out of the population
- No new mutations occuring
- No natural selection
genetic drift
When population size is small, gene frequencies can change randomly. This can cause the the loss of advantageous alleles or perpetuation of deleterious alleles.
Founder effect
when a large population has a section isolated and a new population is started from just those few individuals
Population bottleneck
a population in reduced in size
All new heritable features of organisms ultimately arise from _________.
mutation
How often do mutations occur?
every new generation will have mutations their parents did not. In Eukaryotes, the rate of mutation is 10^-8 bp/gen. This number is very small but with 3x10^9 bp, mutations are quite common. For point mutations, some RNA viruses have a mutation rate as high as 10^-3
Genetic mutation is good/bad/neutral and why?
Neutral is the most common effect because most of eukaryotic DNA is non-coding. Negative gene mutations are more common than positive ones because it is more probable that a change in bp and aa’s will be harmful because they are changing at random
_____ is random but _____ is not. Natural selection eliminates the unfit
mutation
evolutionary change
DNA with this type of sequence are far more susceptible to mutations
triplet repeats (cgg cgg cgg cgg)
repeat expansion
an increase in the number of mutations in a region that causes a trinucleotide expansion disease
stabilizing selection with example
preserves the average characteristics of a population by favoring average individuals. Decreases variation while maintaining the mean. Example: mean human birth weight
Directional Selection
changes the characteristics of a population by favoring individuals that vary in one direction from the mean of the population. Occurs when an optimal phenotype is reached or when trade-offs oppose further change. Example: Texas Longhorns
disruptive selection
changes the characteristics of a population by favoring individuals that vary in both directions from the mean of the population. Example: West African finches beak size
Frequency dependent selection
Neither one is good or bad- the one that is least common is the better one (L handed or R handed scale eating fish)
Sexual Selection
can be for male-male competition or in order to attract the opposite sex. Sexy offspring (sexy sons) and good genes (good sense) Example: tail length in African widow bird
__________ allows a population to respond to change and prevent inbreeding effects.
Genetic variation
which population has the greatest genetic complexity?
African populations
The major route of gene flow in human populations:
Out of Africa
Most antibiotics are derived from ________
bacteria
Is selection stronger at the level of the individual or the population?
The individual
What two kinds of explanation do all biological traits need?
proximate and evolutionary. Proximate describes what is wrong in the bodily mechanism of the individual (why people are different) and the evolutionary explanation explains why people are all the same in ways that leave us susceptible to disease
The six reasons selection has left us vulnerable
- Pathogens evolve faster than we do
- We do not evolve fast enough to keep up with changing environments
- constraints (impossibility of maintaining uncorrupted DNA, path dependence such as the way our vision works that leaves us with a blind spot, once a gene has a job it must maintain that job. If it changed, the loss of the original function would be detrimental)
- Tradeoffs (thicker bones = stronger = less mobility, antibiotic resistance, antlers, TTX toxin)
- Traits that increase reproduction even though they decrease health
- Defenses (pain, fever, vomiting)
Smoke detector principle
Defenses, such as flight, cough, stress, and anxiety, should theoretically be expressed to a degree that is near the optimum needed to protect against a given threat. Many defenses seem, however, to be expressed too readily or too intensely.
Alexander Phlemming
Discovered penicillin in 1945
How many people a year do the CDC estimate are infected with a “super bug”
2 mill/yr
23,000/yr die (more than AIDS)
________ can restore genetic variation in a population that other evolutionary mechanisms have removed.
mutation
Positive selection
selection for beneficial changes
Purifying Selection
selection against deleterious changes
Heterozygotic advantage
the advantage of a heterozygotic genotype over a homozygous genotype. Example: Colias butterfly in the Rocky Mountains and flying temperature
Clinal variation:
gradual change in phenotype across a geographic gradient. Example: white clover and its production of cyanide or homo or hetero genotype for pines in CO
Evolution is highly constrained- in what ways is it constrained?
- Evolution must work on existing structures- there is no denovo trait generation.
- Mutations are random: there is no way for a geen to know what “needs” to be changed foe increased survival and reproduction
- Short term v Long term success can sometimes be in opposition within organisms (ie resources and reproduction // ST(indiv.)–LT(population) Ex: Locusts and rats
- Trade-offs
What does it mean when two populations have the same gene pool?
the two populations have the same gene frequencies for A and a
Allele frequencies measure…
the amount of genetic variation in a populations
Genotype frequencies show…
how a population’s genetic variation is distributed among its members
When looking at different animals, what two assumptions did evolutionary biologists make only 50 years ago? How were these assumptions disproven?
- Their genes must have all arisen independently because they are all so different
- There are a huge number of developmental genes required for producing these animals
These assumptions were disproven by the discovery of HOX genes (linear construction, modularity of bodies)
W. Ghering performed the transgenic eyeless muntant experiment with a mouse and drosophila. What does this experiment tell us about how bodies are formed?
Both organisms (the mouse and the fruit fly) share the genetic mechanism for body formation. Why? Because they share a common ancestor where this evolved.
Where do HOX genes exist?
In every part of the body. The only reason we don’t have a hand on our forehead is because the gene was not expressed.
If you wanted to make a big change quickly in an individual, what genes should you change?
Developmental genes (HOX)
Plasticity or developmental plasticity:
Changes in gene expression as the result of environmental signals such as crowding, stress, pollution, violence, diet, etc.
Example: Vegetarian v canibal tadpole
Systematics or taxonomy:
the origin of naming and classifying organisms.
Linnaean Classification stresses…
classifying species and groups of species into higher level organization. Kingdom, phylum, class, order, family, genus, species. Linnaeus did not believe organisms were evolutionarily related and thus focused on classifying them based on their physical similarity.
Phylogeny or phylogenetics
Organizing organisms based on their evolutionary similarities based on their genetic data. This is the goal of modern classification
What are the uses for phylogenetic analysis other than classification? (6)
- Tracking the spread of disease
- Understanding how pathogens evolve and change
- Knowledge of ideal medications
- Criminology and identification
- Knowledge of models for medical research
6 (Best). All life on earth comes from a common ancestor so it is the study of our shared family history
How is evolutionary relatedness determined between organisms? (4)
- fossil record
- morphological comparison
- genetic comparison
- developmental patterns
NOTE: 3 and 4 can only be used in analysis of living organisms. If extinct species, the fossil record is the only line of direct evidence
Speciation (cladogenesis): what is it, example
the divergence of biological lineages and the emergence of reproductive isolation between those lineages. Example: Lake Malawi
What allowed the immense speciation at Lake Malawi to occur in only 2 million years? (3)
- Diverse habitats of the lake (sandy v rocky)
- Diet speciation within the habitats
- Sexual selection through male body color and female preference
anagenesis
evolution of a population or species without a new species being formed (speciation)
morphological species concept and why it fails in nature
Linnaeus used an organism’s physical form to classify them into species. He figured that the more two organisms looked alike, they must be a similar species.
It fails in nature because of extreme sexual dimorphism, development stages w different morphology, and convergence
Biological species concept
Mayr surmised that appearance of an organism was secondary and that the way to classify a species is whether or not they can interbreed. Individuals that can successfully interbreed are a species.
different species are those which do not share genes with one another (different gene pools)
Convergence
the tendency of unrelated animals and plants to evolve superficially similar characteristics under similar environmental conditions.
Allopatric speciation or allopatry
speciation that occurs when biological populations of the same species become isolated from each other to an extent that prevents or interferes with genetic interchange.
sympatric speciation
speciation that occurs without a physical barrier or geographic isolation. Most commonly this occurs through chromosomal changes causing an individual to no longer be able to interbreed with the ancestral population
Pre-zygotic reproduction barriers that prevent two species from successfully interbreeding: (5)
- Habitat
- Temporal (the two species don’t occur in nature at the same time)
- Behavioral
- Mechanical (literally penis does not fit in vagina)
- Gametic isolation (egg and sperm come into contact but no fertilization occurs)
Post-zygotic reproduction barriers that prevent two species from successfully interbreeding:
- Hybrid zygote viability
- Hybrid adult viability (degree of health)
- Hybrid infertility
Hybrid organism:
An organism that arose from interbreeding of two “species”.
Possible outcomes of hybridization: (3)
Example
- If the hybrids are healthy and fertile, the hybrid zone will spread and the two “species” could meld into one
- If hybrids are less fit, there may be selection for further reproductive isolation. This is called reinforcement (aka reinforcing species boundaries)
- If the hybrids are only slightly less fit than the non-hybrids, a narrow hybrid zone may persist.
Example: Hybrid zone between European toads because of skeletal abnormalities. This could also be causing reinforcement.
What groups are able to speciate more rapidly?
- highly sexually selected organisms
- herbivorous specialists
- species with limited dispersal
Are genome size and eukaryote complexity correlated?
No. In fact, no genome (except for some viruses) varies more than two orders of magnitude (100x) in the number of protein coding genes
Rank genome size
prokaryotes < fungi (euk) < single celled euk < multi-celled euk
What is lateral gene transfer and in what ways can it occur? (3)
When parts of a genome seem to be traded to unrelated organisms
- Some bacteria pick up DNA from the environment or other bacteria
- Viruses can splice DNA in or out of organisms
- Hybridization, even if very rare, can input novel DNA
Is lateral gene transfer more common in prokaryotes or eukaryotes? Why?
More common in prokaryotes because eukaryotes have very sophisticated ways of isolating and destroying viruses and foreign DNA
gene duplication
DNA duplication produces an additional copy of a gene. Critical for allowing new gene functions to arise allowing one of 4 things to occur:
- both copies maintain their original function
- function continues but becomes more specialized or have different timing in different tissues
- One copy becomes a pseudogene, no longer producing a protein but accumulating changes to be turned on later
- One copy maintains original function but one evolves
Why study the history of life?
- some biological and evolutionary phenomenon can only be understood over very long durations
- Introduces us to the biodiversity of our planet
- The history of life is our story as well
- Shows that there is still room for God in this view
What two periods are the history of life split into?
Precambrian and the Phanerozoic
The precambrian is broken down into:
- 65-4 BYA Hadean period (no life)
- 9 BYA Emergence of oceans and some terrestrial areas
- 9-3.7 origin of organic chemicals and life
- 7 BYA first probable fossils
- 5 BYA first photosynthetic bacteria and begins O2 accumulation
- 1 BYA first aerobic bacteria
- 0 BYA First eukaryotes to evolve
- 2 BYA First photosynthetic eukaryotes
- 0 BYA First multicellular eukaryotes
What is the most important era within the Phanerozoic period?
The Paleozoic and, within that, the Cambrian are the most important eras for biological evolution. The Cambrian was the emergence of all major phyla of animals + nervous systems as well as the ancestors of modern plants and fungi.
Cambrian explosion
A series of radically novel body shapes and forms of animals evolved because of a genetic revolution that almost certainly evolved HOX genes.
Do biotic or abiotic conditions more strongly influence the history of life?
Both factors contribute and they are not independent of one another. Our understanding of these factors and the way they influence the history of life and each other is modest at best
The biomass of prokaryotes is more than _____ the biomass of all eukaryotes combined
10X
Prokaryote attachment
Though prokaryotes can float free in liquid, they prefer attachment to a solid surface
List the differences between prokaryotes and eukaryotes (7)
P E
- Cytoskeleton (lack/have)
- Division (binary fission/mitosis)
- DNA structure (circular/linear)
- DNA enclosure (not enclosed/enclosed in nucleus)
- Organelles (no membrane bound org/have)
- Cell size (small/large)
- Cell number (unicellular/multicellular (mostly) )
Why were bacteria and archaea grouped together for so long?
Because we knew very little about archaea and they appear SUPERFICIALLY similar
Domains
Taxonomic category above kingdom
How many taxonomical domains are there?
Some say 2 (Bacteria//Archaea and Eukaryotes) some say 3 (bacteria//archaea//eukaryotes). Others have argued that classifying them separately at all is an impossible feat because of gene transfer between domains
How do bacteria and archaea differ? (2)
How are they similar?
- Membrane lipids: different side chains and arch. have single lipid membranes
- They have different DNA and RNA polymerases and histone binding is much more similar to eukaryotes
How are bacteria and archaea similar? (5)
- Share genetic material (DNA) for protein production and it is often circular
- Their DNA replication is semi-conservative and they undergo binary fission, not mitosis
- Conduct glycolysis
- extremely in-folded membranes that function similarly to organelles
- Have plasma membranes and abundant 70s ribosomes
To date no archaean has been found as _____.
An animal or plant pathogen or to release free oxygen
What are the three shapes bacteria typically have?
spherical (cocci)
rods (bacilli)
helixes
Biofilms
assemblages of multiple species prokaryotes and some single celled eukaryotes. Biofilm formation is facilitated by the secretion of a polysaccharide gel matrix that covers (and protects) the cells and attaches them to the substrate. Single mol’s released from the biofilm attract other organisms which will reside in the film. Biofilms make it difficult for antibiotics to reach the target bacteria, this making bacteria in biofilms harder to attack.
Prokaryotes are much more diverse than eukaryotes in terms of their… (3)
biochemistry
metabolism
cellular structure
Example: cell walls
What are cell boundaries made up of in Plants, fungi, bacteria, and archaea?
Plant: Cellulose and polysaccharides
Fungi: Chitin (a protein)
Bacteria: Peptidoglycan
Archaea: variable but usually contains significant protein
Axial fillaments
produce a corkscrew like motion in in bacteria and archaea
Type IV pilus (or fimbriae)
short filaments that grab substances and pull the bacteria in that direction or attach the bacteria to a substance for anchoring
Bacterial flagella
rotate like a propeller
Do prokaryotes reproduce sexually?
Not in the typical sense: They do exchange genetic material though, even if unequally:
- via incorporation into their main chromosome (transformation) though the cell wall, or via a tube (conjugation)
- Via plasmids
- via phage (transduction)
A common misconception is that prokaryotes don’t communicate. Why is this incorrect?
Quorum Sensing: bacteria are trying to detect the density of individuals around them, usually of their own species. When a certain density is reached, movement or something happens.
Example: bioluminescence in some marine bacteria (Vibrio Harveyi)
Hadean period (no life)
4.65-4 BYA
Emergence of oceans and some terrestrial areas
3.9 BYA
origin of organic chemicals and life
3.9-3.7
first probable fossils
3.7 BYA
first photosynthetic bacteria and begins O2 accumulation
2.5 BYA
first aerobic bacteria
2.1 BYA
First eukaryotes to evolve
2.0 BYA
First photosynthetic eukaryotes
1.2 BYA
First multicellular eukaryotes
1.0 BYA
