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288 Cards in this Set

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Coevolution:
The reciprocal evolutionary change in two or more interacting species, resulting from their influences on one another.
3 requirements for coevolution:
1. There must be genetic variation for characters in both species that influence their interaction.
2. Each species must be a selective force on the other species (ie affect the other's fitness).
3. There must be a response to this selection in each species.
Coevolution can lead to the fixation...
of mutations in species or the maintenance or polymorphism within species.
3 kinds of interactions that lead to coevolution:
1. Mutualistic
2. Competitive
3. Antagonistic
What are mutualistic interactions?
Both lineages benefit from the interaction, evolve to maintain it, and increase the benefits to themselves. Note that even mutualists can have conflicts of interest.
2 examples of mutualistic interactions:
1. endosymbionts
2. pollination
Competitive interactions:
Competitors may evolve to limit niche overlap or to compete more effectively for the same resource.
Example of competitive interactions:
Species using the same resources.
Antagonistic interactions:
Members of one lineage exploit members of the other: exploiter evolves to overcome defenses and victim evolves to escape or defend itself.
3 examples of antagonistic interactions:
1. Predator-prey
2. Parasite-host
3. Pathogen-host
2 observations suggesting coevolution:
1. Tight correspondence between features of interacting species.
2. Patterns of ecological specialization and diversity
Name 2 examples of a tight correspondence between features of interacting species suggesting coevolution.
1. The long nectar spur in a plant matches the long tongue of the pollinating moth.
2. Specialized bacteria called buchnera live in aphid hosts. Buchnera is passed down from mother to baby. Aphids can't live without buchnera and buchnera can't live without aphids.
Why do aphids need buchnera?
Aphids feed on the phloem sap of plants and their diet is deficient in essential amino acids. Buchnera make essential amino acids that aphids need.
Essential amino acids:
Amino acids not produced by animals, must be obtained from other sources.
Example of patterns of ecological specialization and diversity:
The queen butterfly caterpillar eats milkweed as its host plant. The caterpillar has adapted to avoid the effects of the cardenolide toxins in the milkweed plant.
cardenolide toxins:
defense mechanism in milkweed.
What's so special about the parsnip webworm?
It feeds on wild parsnip and can overcome furanocoumarin toxins in its host.
furanocourmarin toxins:
defense mechanism in wild parsnip plants.
5 points of the Ehrlich and Raven coevolution hypothesis:
1. Plants are attacked by insect herbivores and selection favors the evolution of protective chemical defenses (toxins).
2. Protected plants increase in abundance and diversify (speciate).
3. Insect lineage evolves ability to overcome plant defense.
4. This insect lineage becomes abundant due to lack of competition.
5. Plants evolve a further defense against the new herbivore type, etc.
Example of one-on-one coevolution:
Buchnera - aphid host
Diffuse coevolution:
Coevolution can involve several competing species and/or several prey evolving defenses against several predators.
Why do mutualisms occur?
Mutualisms can benefit both partners. For example, acacia plants can house ant colonies. The ants get a home and in return, the acacia plant gets protection from the agressive ants. Natural selection WITHIN each species favors the interaction.
Why did Darwin not agree with mutualism?
He didn't think that natural selection would favor beneficial mutualistic interactions.
How could a species interaction be bost mutualistic and antagonistic?
Selection will favor traits that give higher fitness within a species, for example a parasite. Some of the parasite's favored changes could benefit the host while others harm the host.
What is an example of a species interaction that is both mutualistic and antagonistic?
Yucca moths are the exclusive pollinators of yuccas, but their larvae eat some of the seeds of the yucca.
What is a cheater species?
It's a species that has evolved to eat the seeds of a plant, but not pollinate the plant even though its ancestors were pollinators.
How are ant-aphid interactions mutalistic and antagonistic?
Aphids poop excess sugar called honeydew. Ants eat out of aphid butts, collecting honeydew. Ants will actually protect aphids from enemies like ladybugs and parasitic wasps, but when ants are limited by nitrogen in their diet, they'll just munch on aphids.
How have aphids evolved from their interaction with ants?
They have a specialized butthold that presents honeydew to ants like it's a present. Weird.
What is coevolution among competing species?
Let's say you have an abundance of variable resources. Several different species will evolve to feed on a niche portion of these resources to keep from directly competing with the other species. This is called character displacement.
Character displacement:
Divergence among several populations when their is an abundance of resources. It leads to specialized feeding niches so that species do not have to directly compete with one another.
What's an example of character displacement?
Darwin's finches. They develop different beak sizes for different seeds.
What are 3 examples of antagonistic coevolution in response to diffuse coevolution?
Evolving camouflage (gecko that looks like leaf) or warning coloration (blue frog). It can also include creating a spikey/sharp hard shell as protection from predators like molluscs.
5 kinds of parasites:
1. Leishmania (parasite that affect humans and other mammals)
2. Eyelash mite
3. Dwarf mistletoe (parasitic plant that grows under bark of another plant)
4. T4 bacteriophage (acts on bacteria)
5. Cowbird (puts eggs in other birds' nests and has bigger mouth so it's fed more/preferentially)
What's the arms race?
Step-wise coevolution for antagonistic pair of species (ex: host-parasite)
What are the 5 needs of arms race?
1. There must be genetic variation of characters in both species that influence their interaction.
2. Each species must be a selective force on the other species (affect the other's fitness)
3. There must be a response to this selection in each species.
4. This can lead to the successive fixation of alleles in each of the species.
5. Runaway escalation or "arms race" may result ("Red Queen hypothesis")
What can an arms race between two species lead to?
It often leaves signature of positive selection in genes underlying resistance.
What is the Red Queen hypothesis?
"...it takes all the running you can do, to keep in the same place." It's the idea that the environment is ever-changing and you have to keep evolving to stay fit.
How does the Red Queen hypothesis relate to parasites/pathogens?
Parasites and pathogens specialize in rapidly changing their genotypes, which are represented by parental genotypes. Anything new and different may be better for the organism.
What are 4 points on inverse frequency dependence?
1. Depends on antagonistic coevolution: parasite or pathogens evolve to use common genotypes.
2. Common host types disadvantaged because they are more susceptible to pathogens.
3. Parasites and pathogens usually have shorter generation times than hosts, may be able to evolve quickly to specialize on abundant types.
4. Can be a force maintaining sexual recombination, since sexuals produce novel genotypes every generation.
Why would coevolution favor sex?
Sexual species can use sexual recombination to produce novel genotypes every generation which may be better at combatting pathogens.
What is inverse frequency dependence?
High frequency of a resistance locus in hosts leads to high frequency of corresponding infectivity locus in parasite.
What is the arms race in cone snail toxins?
A single snail may deliver 100+ different peptide toxins. Some paralyze muscles, others affect the CNS, others prevent transmission of pain signals. They're called conus toxins.
How do conus toxins relate to coevolution?
Positive selection on toxin region of peptide show a high rate of amino acid replacement. You can tell by looking at the high Ka/Ks value in the toxin part of the molecule. This is leading to fast response to the prey evolution.
What is gene-for-gene coevolution?
A pathogen will create an Avr gene which infects a host. In return, the host evolves an R gene which leads to resistance to the pathogen. The Avr and R genes will evolve in response to one another.
How can you tell there are a lot of R genes in arabidopsis under positive selection?
They have a high Ka/Ks value.
What is symbiosis?
Members of more than one genetic lineage associate closely, usually for mutual benefit.
5 possible benefits of symbiosis:
1. Nutrients
2. Metabolic products
3. Protection
4. Transport
5. Structural integrity
2 players in symbiosis:
1. The host (usually the larger partner)
2. The symbiont (smaller partner)
Coinheritance:
symbiont benefits when the host reproduces.
Long-term infection:
Symbiont benefits if host lives longer.
Symbiosis in evolution:
A creative force underlying the origin of major adaptive radiations.
How is symbiosis in evolution possibly favorable?
New combinations of capabilities allow for the exploitation of new niches.
3 changes that occur from symbiosis in evolution:
1. Different genomes have to be coordinated.
2. Genomes subject to distinct population genetic processes
3. Different membrane-bound compartments; products to be transported between them.
6 evolutionary innovations through symbiosis:
1. Eurkaryotic cells (mitochondria)
2. Photosynthesis in eukaryotes (plastids)
3. Colonization of land by plants (mycorrhizae)
4. Nitrogen fixation by plants (rhizobia)
5. Chemoautotrophic life at deep sea vents (life without sunlight)
6. Use of many nutrient-limited niches by animal lineages.
How long ago did buchnera infect aphids?
150+ mya.
How can you use a phylogenetic tree to look at symbiosis?
You see a correspondence between phylogenies of interacting species that reflects codiversification of host and symbiont over the same time frame.
How did buchnera get transferred into aphids?
Through vertical transmission 150 mya.
Aphid mothers pass...
buchnera to their kids.
3 ways symbiosis is a parallel to gene uptake:
1. Confers ecologically significant traits that are heritable if transmission is vertical.
2. Many examples in which inherited bacterial symbionts expand insect capabilities and ecological niche.
3. Also cases in other invertebrates, plants, fungi.
8 effects of symbiotic bacteria on hosts (insect examples):
1. provide nutrition
2. defense against wasp parasitoids of aphids
3. defense against fungal pathogens of aphids
4. defense against spider predation of staphylinid beetles
5. tolerance to heat stress in aphids
6. protection against parasites in bumble bees
7. parthenogenesis (all female production) in wasps
8. digestion of food (termites)
What is H. defensa?
It's a maternally inherited bacterium that keeps wasps from laying eggs in an aphid.
What does the bacterial symbiont of paederus beetles do?
It produces a polyketid synthase (peptide sythetase) which keeps wolf spiders away from the beetle.
The total microbial population on humans is more...
than all our somatic and germ cells by an order of magnitude.
What happens in the termite gut?
It has complex bacterial communities which fix N and provide enzymes for the termite to break down wood.
What happens in the cow gut?
It has complex bacterial communities that produce methane and break down cellulose.
What did Coyne and Orr study?
They examined the degree of genetic divergence between populations or species of Drosophila to look at the temporal patterning of the evolution of reproductive isolation.
What 3 things did Coyne and Orr measure?
1. Prezygotic isolation by observing if mating occured when flies of different populations were reared together (looking at female mate preferences)
2. Postzygotic isolation by examining survival/fertility of hybrids.
3. Measured genetic distance based on molecule genetic divergence across the genome (Genetic distance reflects time since divergence).
4 findings of the Coyne and Orr study:
1. Prezyotic and postzygotic reproductive isolation increases over time.
2. Full reproductive isolation is highly variable but takes 1-3 million yrs.
3. Premating isolating mechanisms are stronger that postzygotic mechanisms in recently diverged populations.
4. In early stages of speciation, hybrid sterility is almost always seen in males only.
Postzygotic isolations evolve more rapidly in...
males.
Dobzhansky-Muller incompatibility:
Disharmonious interactions between the different genes inherited from the two parents (epistasis).
How are the Dobzhansky-Muller incompatibility hypothesis and the Coyne-Orr study at odds?
In the early stages of speciation, hybrid sterility is almost always seen in males only even though incompatibility is supposed to be due to different genes inherited from the two parents.
Haldane's rule:
Hybrid sterility is often limited to the heterogametic sex. Heterogametic is the diploid genotype with two types of sex chromosomes. In fruitflies and mammals, males are heterogametic (XY), but in birds and butterflies, females are heterogametic (WZ).
Why is the heterogametic hybrid sex at a disadvantage?
Probably due to dominance. If recessive genes with negative effects on hybrids are present on the sex chromosomes, then their effects are manifested in heterogametic sex and masked in homogametic sex.
How does Haldane's Rule compare to cases in which one hybrid sex is at a fitness disadvantage?
It's seen in almost all cases where one hybrid sex is at a disadvantage.
Many loci of postzygotic isolation map to...
the X chromosome.
2 examples of sympatric speciation:
1. Nicaraguan crater lake cichlid fish
2. Palms on an oceanic island.
What is the rhagoletis speciation case?
It's a case of sympatric speciation. Because apples are not native to North America, the native species was the Hawthorne maggot fly and it feeds on hawthornes. When apples were introduced to the United States in the 1700s, some populations moved to the apples and became the Apple Maggot flies. Mating occurs on the fruit and larvae develop in the fruit so there are difference in mating time.
How many species are there currently on Earth?
100 million
How many species have gone extinct?
1 trillion probably
Three ideas on how diversity generated:
1. Each species arose independently by special creation.
2. Most species evolved from simpler lifeforms, but humans are somehow unique.
3. All lifeforms are interrelated and descend from a single common ancestor.
3 things Darwin could not explain:
1. How traits were transmitted from parents to children (didn't know about Mendelian genetics)
2. How new variation is generated (did know about mutation)
3. How life originated in the first place
How did Darwin think life originated?
He thought it came form one origin.
What are the 4 pieces of evidence for a common origin
1. The transition of forms in hominid fossils
2. Relationship in cellular characters
3. Presence of vestigial features (pelvis in whales)
4. Universality of certain molecular structures (DNA, RNA, proteins)
What human chromosome points to a common ancestor?
Human chromosome 2 was caused by a fusion of chromosomes present in contemporary apes.
What are the 4 points of universality of certain molecular structures in life?
1. Use of DNA heritable genetic material, with DNA transcribed into RNA, which is translated into proteins
2. the genetic code; around 20 amino acids
3. Same metabolic pathways based on same enzymes
4. ATP as energy currency in all organisms.
What are the 4 criteria for life?
1. Replication
2. Variation
3. Heredity
4. Metabolism (draws nutrient from the environment)
What is life?
Life is a self-sustaining chemical system capable of Darwinian evolution.
What are 5 assumptions about life?
1. Life is 4bya
2. All life comes from a common ancestor
3. Life originated on Earth
4. Biochem of previous lifeforms is similar to the present
5. Life comes from complex molecule precursors.
How can the process of life be understood (2 ways)?
1. Mimicking the prevailing conditions in the lab
2. Examining the properties of existing molecules and lifeforms
What did Haldane and Oparin postulate?
They both postulated in the 20s that life started in a reducing anaerobic atmosphere and that life probably arose in the ocean where there was water and simpler molecules.
What kind of molecules were in the ocean when life began?
water, H, N2, hydrogen sulfide, carbon monoxide, CO2, ammonia, and methane.
What did the Miller-Urey experiment show?
They found that by creating a hot, reducing atmosphere, they could end up making simple amino acids like glycine that are integral to all lifeforms without having O2.
What is the support for DNA being the first molecule?
1. It's an informational macromolecule
2. It has heredity
What is the support for proteins being the first life molecules?
1. They were made by abiotic so maybe you can make a nitrogenous base?
2. It takes proteins to make proteins
3. Meteorite: found similar amino acids in a meteorite that were made in the Miller experiment
What's the support of the RNA world hypothesis?
1. To copy DNA, you need short RNAs to prime the synthesis (RNA primer)
2. Info encoded in DNA needs ribosomes for processing
3. Ribose (not deoxyribose) have been formed in abiotic synthesis experiments
4. RNA can act as its own template to make its own copy
5. RNA has a phenotype (3D folding structure)
6. RNA can act as an enzyme (Ribozymes) - eliminates the need for proteins
4 problems with RNA world hypothesis:
1. Although ribose forms from simple precursors, it is highly unstable.
2. How to get the nucleobase + sugar + phosphate together to generate a nucleotide?
3. When, why, and how did proteins and DNA appear?
4. When and how did cells form?
What are the 4 steps of the evolution of life from RNA entities?
1. Evolution starts: the first protocell is just a sac of water and RNA and requires external stimulus to reproduce
2. RNA catalysts: Ribozymes arise and speed up reproduction and strengthen the protocell membrane. Protocells can now reproduce on their own.
3. Metabolism begins: Other ribozymes catalyze metabolism which allows protocells to take nutrients from the environment.
4. Proteins appear: Complex systems of RNA catalysts begin to translate strings of genes to make amino acids. Proteins later become more efficient catalysts.
When did Earth form?
4.5 bya
When is the first clear sign of life in the fossil record?
3.5bya
4 ways fossils are created:
1. Compression
2. Permineralized fossils
3. Casts or molds
4. Unaltered hard parts (shells, bones) and soft parts (permafrost)
What is fossil compression?
Chemical decomposition of organic materials that leave an impression like ferns
Permineralized fossils:
Where minerals from groundwater fill precipitate in spaces.
Fossil casts or molds:
Original remains decay after being buried in sediment
What is the taxanomic fossil bias?
Hard parts like bone last longer than soft parts like skin.
First fossil evidence is...
something similar to cyanobacteria found in stromatolites.
Relative dating:
associating fossils with geological and biogeographic events.
Radiometric dating methods:
provide the absolute age of a fossil
Molecular clocks:
age infer by degree of molecular divergence.
What are the 3 main dating methods?
1. Relative dating
2. Radiometric dating
3. Molecular clock
How can you find the relative age of an organism by the rocks it's around?
The organisms are limited to rock layers where they occur. You can align a common time series to different sites world wide. Specific organisms provide a signature for a particular time period.
The strata of the Grand Canyon are from what age?
The Precambrian through the Paleozoic era.
How did they get the timescale of the strata?
radiometric dating
How does radiometric dating work?
Unstable isotopes are present in newly formed material and decay at constant rates. The amount of parent and daughter isotopes present in the material can be measured and the age can be determined based on the decay rate.
What is the half-life?
The time required for half of the parent isotope to become the daugher isotope.
How did we figure out how old Earth is?
Clair Patterson used uranium isotopes which decay to form lead. Based on the half-life of uranium, the Earth is about 4.5 bya?
What is the range that it's best to use C14 dating?
C14 has a half life of 5730 years so the method is most accurate for materials <40K years old
How does C14 dating work?
Living organisms incorporate a certain level of atmospheric C14 which is really really low. When they die, the C14 in the organism begins to degrade. You can measure the degradation to figure out how old the organism is.
Three kinds of radiometric dating
1. Uranium - lead (good for really old stuff)
2. C14 (good for <40K years)
3. K/Ar (used for rocks)
How does K/Ar dating work?
40K decays into 40Ar and 40Ca. Only 40K is in newly formed rocks. 40K has a half life of 1.26by. You mostly use it for rocks.
Fission track dating:
Based on the damage trails made by spontaneous decay of 238Ur. When volcanic rocks form, it's clear and then fission tracks accumulate over time.
Amino Acid racemization dating:
Methods based on relative ratios of the different D and L forms of amino acids. Living organisms keep al their L-form amino acids and when the organism dies, the ratio of D to L goes to 1:1.
What kind of gene should you study for looking at human evolution?
Look at homologs.
Homolog:
Genes related by descent from a common ancestral gene sequence.
2 kinds of homologs:
Orthologs and Paralogs
Ortholog:
Genes in different species or organisms that evolved from a common ancestral gene in their last common ancestor
Paralog:
Genes that arose by duplication within a genome.
The selection of the proper molecule for studying evolution depends on (3):
1. how quickly the sequence evolves
2. which organisms are being compared
3. how easy it is to obtain the data
How did mitochondria happen?
Mitochondria originated from endosymbiotic bacteria and contain a genome separate from the nuclear DNA.
7 properties of mtDNA:
1. Small (16.5 Kb) circular genome (only 37 genes mainly involved in oxidative energy production)
2. Genes have no introns; largest non-coding region is D loop
3. Altered genetic code
4. Multiple copies of mtDNA per cell
5. Doesn't recombine; new change only occur via mutation
6. mtDNA has a fast rate of evolution
7. Mitochondria are only passed down from mother
Why is mtDNA useful for exploring the human past? 5 things.
1. High mutation rate makes it easy to assay diversity in samples efficiently.
2. Low effective population size leads to increased genetic drift, which generates geographic structure
3. Lack of recombination, so lineages are not reassorted and obscured each generation.
4. Exclusively maternal inheritance allows access to female-specific processes.
5. High copy of mtDNA/cell facilitates analysis of degraded contemporary samples and ancient DNA.
What's so special about African mtDNA?
There is more mtDNA diversity in Africans than in other groups which proves that the Out-of-Africa model is correct. Because Africans have the most sequence diversity, they are considered the most ancient such that small groups left Africa and colonized in other parts of the world.
Out-of-Africa model:
Erectus left Africa 2mya, but sapiens arose in Africa and migrated throughout the world to replace other hominids.
Multiregional Model:
Erectus left Africa 2mya and became sapiens in different parts of the world.
mtDNA is traced by what lineage?
mtDNA is maternally inherited, so it traces back to the original African female that gave rise to all present day mitochondrial lineages (Eve).
Why is "Eve" important?
Eve is the original African female that gave rise to all present day mitochondrial lineages.
What are the mtDNA divergent times based on?
Divergence times based on a substitution rate of 2-4%/mya. It's calibrated from human-chimp split and fossil evidence of colonization of New Guinea, placed ancestor of all mtDNA ("Eve") in Africa 200K ya.
How old is Eve?
200,000 years old.
How can you get highly resolved human phylogenies?
From complete mt genome sequences.
3 things fossils can tell you if you can get the DNA sequences:
1. Phylogenetic relationships of ancient hominids from DNA sequence data
2. Analysis of the ancient sequences of candidate genes involved in human-specific traits like language.
3. Direct understanding of mutational dynamics by sampling loci.
4 examples of fossil materials that can be used to extract informational macromolecules:
1. Peptide bonds in shells that are 50mya
2. Cellular structures seen in amber-encased insects
3. Collagen in human bones from 1mya
4. Albumin in wooly mammoths form 40Kya
How much protein survives in fossils?
<<<<<1% not much
How can you find out if DNA is present in a sample?
1. Stain with dyes specific to DNA (not very sensitive)
2. See if there is a template (DNA molecule) to synthesize with radiolabeled DNA.
How is the DNA of organisms 10,000s of years old?
It can be detected, but is often degraded (pieces are only 100-300 bps long)
How can we figure out the origins of DNA in a fossil sample?
You have to place the DNA in a phylogenetic context. Obtain a sequence of homologous genes from the sample and its relatives and infer a phylogenetic tree.
How did you obtain DNA from a sample before the 80s?
You had to clone the DNA into a bacterial vector. It's difficult to obtain a specific region with fresh DNA and even harder is old DNA.
What technique did they use to figure out about the quagga?
They examined the mtDNA and related it back to horses.
DNA cloning was hard before the 80s. What changed it?
PCR which amplifies DNA fragments without needing to clone into a plasmid.
3 ways PCR is so freaking great:
1. Specific sequence amplified
2. Sensitive to very low amount of DNA
3. Very rapid results
What did researchers find when sequencing neandertal mtDNA?
It indicated the sequence was endogeneous to the species. It didn't match the mtDNA sequence to show. The age of the common ancestor ended up looking to be four times previously thought. This points to neandertals going extinct before they could interbreed with humans.
What does the multi-regional hypothesis state about neandertals?
They thought that they bred extensively with humans and that they should be considered one species. This is based on fossils with intermediate characteristics, and shared aspects in their culture that they coexisted.
What does the Out-of-Africa hypothesis think about neanderthals?
They think that neanderthals and humans are separate species that never interbred.
Based on mtDNA, when did it look like neanderthals formed a distinct clade from humans?
350Kya
What did they find out after sequencing the full neaderthal genome?
Neanderthalas are the closest evolutionary relatives to humans. They lived in large parts of Europe and Asia and disappeared 30K years ago. They share more genetic varients with humans in Eurasia than Africans.
Who has Neanderthal DNA?
Europeans and Asians, not Africans.
What are Denisovans?
They come from a small finger bone found in the Denisova Cave in Siberia. mtDNA showed that it was neither neanderthal or sapiens, but was more closely related to neanderthals.
How long ago did Denisovans live?
1 million ya
Who has Denisovan genes?
5% of the genome of Melanesians is Denisovan, but not the modern Asian populations that live close to Siberia.
Who bred with Denisovans?
Denisovans interbred with ancestors modern Melanesians.
Where did Denisovans live?
Probably in Eastern Asia. They could have lived in large parts of East Asia when Neanderthals were present in Europe and western Asia.
What does Ka/Ks < 1 mean?
Purifying (negative) selection. It's the most common. Selection is acting to preserve a function.
What does Ka/Ks > 1 mean?
Positive selection. It's infrequent. It denotes adaptive changes within a species.
What does Ka/Ks = 1 mean?
Neutral evolution. It's infrequent. It means that the protein is nonfunctional.
What is Ka?
Number of nonsynonymous mutations.
What is Ks?
Number of synonymous mutations.
Ways that humans differ from chimps:
Language, brain size, intelligence, culture, reduced hair cover
What do you see about most positively selected genes that differ between humans and chimpanzees?
They're mostly involved in immunity and defense. The biggest portion of the genes are unclassified - we don't know what they're there for.
How many human-chimp orthologs have a Ka/Ks > 1?
585 out of 13K
What does FoxP2 do?
It's involved in fine motor control of larynx and mouth as well as linguistic and grammar skills.
How is FoxP2 different in humans?
Human FoxP2 has changes in amino acid coding and a pattern of nucleotide polymorphism which suggests that the gene has been a target for selection.
How does the Pituitary Adenylate cyclase-activating polypeptide precursor gene have to do with human evolution?
It has a Ka/Ks > 3 in humans and is much greater than any other lineage. It's involved in intelligence and neurological processes.
Size of human and chimp genome?
Human = 3.1 billion bps
Chimp = 3.35 billion bps
What are the new genes from in the difference between the human and chimp genome?
Probably from non-coding DNA and somehow we got 3 new proteins.
Evolution:
Change in allele frequencies over time.
What 4 forces act on populations?
1. Mutation
2. Selection
3. Drift
4. Migration
Are there changes in effective population size and allele frequencies of humans?
Countries all over the world have different population sizes. These populations will experience huge change in allele frequencies. Higher birthrate means more allele frequency change.
What three alleles will change in frequency in response to global population change?
1. R1b will decrease a bit because it's primarily in Europe will increase a bit because of African population.
2. E3a will only increase because it's from Africa.
3. CCr5change32 will flatline because the world can't get an AIDS break.
What happens when the global Ne population increases?
1. Decrease in drift influence
2. increase in efficacy of selection
3. Increase in genetic diversity
Endogenous mutations:
DNA repair/replication errors
Exogenous mutations:
X-rays/UV/chemicals
Number of cell division in female gametes:
32 divisions
Number of cell divisions in male gametes:
35 cell divisions up to the age of puberty and 23/year thereafter.
How are de novo mutations related to the father?
On average there are 63.2 new mutations per trio, but older fathers can have kids with twice that.
What is the difference between Han Chinese and Tibetans?
Their genomes are basically the same except for EPAS1 which is an hypoxia-inducible factor related to lower erythrocyte count and hemoglobin concentrations. This is opposite of what you'd think.
6 diseases that account for 90% of deaths?
1. Acute respirator infections
2. AIDS
3. Diarrheal diseases
4. TB
5. Malaria
6. Measles
What is malaria?
Disease caused by a parasite that reproduces in red blood cells. The parasite is vectored by mosquitoes. People who have normal RBCs are good hosts, but people hetero for sickle-cell can survive malaria.
What is the survival rate of malaria?
10% of the world population is infected by malaria and 90% of cases in Africa - was the major cause of death until AIDS.
Whawt is sickle cell due to?
It's an altered hemoglobin protein (HbS) which has a single replacement substitution - GAA to GUA.
Why was the Black Death a big deal?
It killed off 30-60% of Europe's population and reduced the world population from 450 to 350 million in the 1300s.
How many people live with HIV in the world?
33.2 million
What is CCR5?
It encodes for a cell-surface receptor that is required for entry of HIV into the cell.
What is CCR5-change32?
It has a 32-bp deletion that disrupts the formation of CCR5 receptors on the cell which results in nearly complete resistance of HIV infection.
What happens if you have the ccr5-change32 gene?
If you're homozygous, you're resistant to HIV and with heterozygous, you have reduced viral loads and slower progression to AIDS
Was ccr5-delta32 related to the Black Death?
No - the allele probably rose up about 700 years ago, but it's not related to the Black Death resistance.
What was the Black Death a result?
It comes from bacterium Yersinia pestis
What's the big deal with small pox?
It killed 400K Europeans at the end of the 1700s. Caused 300-500 million deaths in the 20th century.
Is ccr5-delta32 related to smallpox?
No - they thought that resistance may be tied to people with ccr5-delta32. Both HIV and smallpox infect lymphocytes, but smallpox originated outside of Europe so why would that gene be confined to Europe?
What's the average duration of a mammalian genus?
5 million years.
What is balancing selection?
Heterozygotes at a locus are favored over both homozygotes.
3 factors that could cause human extinction?
1. biotic
2. abiotic
3. anthropogenic (man-made causes)
5 possible things that could cause human extinction:
1. Massive disease event - small because there are isolated populations
2. Asteroid/natural disasters - rare, risk is small
3. Nuclear war - slightly higher risk
4. Overpopulation - much higher risk, but not worst
5. Climate change - greatest risk to humanity.
Why is Ramapithecus important?
It had jaws and teeth similar to humans. Based on this fossil record, they placed human origins in Asia and timed the divergence from great apes at 15 million years ago.
2 ramapithecus' teeth/jaw was similar to humans?
1. Their premolars and molars were relatively large compared to their incisors/canines like humans
2. Although the middle portion of the palate was missing, it had a human like palate shape.
What is the Sarich and Wilson experiment?
They used immunology to determine divergent times of apes. They stuck human blood in a rabbit. The rabbit made antibodies and then they took the antibody and added human serum and then chimp serum and found out how much the antibody attached to the chimp-human serum. That tells you how much they're related.
What's the difference between the pre-molecular and post-molecular view of human divergence?
Pre-molecular: They thought we diverged 15-30mya.
Post-molecular: We diverged from African apes 5mya. Ramapithecus was 10mya and was more related to Asian apes.
How similar are chimps and humans?
They're identical in 98.8% of their sequences.
How many human-chimp sequences are identical?
Over 30%.
4 reasons to believe molecular data:
1. Well-defined characters (quantitative)
2. Large # of definable characters
3. Genotypic evolution continues (when morphological evolution ceases)
4. Genetic bases of many morphological traits is unknown
Disadvantage of molecular data:
Only a few nucleotides studied so there might be convergence from homoplasy in the tree or incomplete lineage sorting.
Compared to chimps, human heads are:
flatter, fragile, bigger brain case, chin, no brow ridge, have foramen magnum.
Foramen magnum:
The hole in your skull for your spinal column.
Compared to chimps, other human body features:
Low pelvis, curved spine, no apposable toe, bipedal
3 disadvantages of fossil evidence for human evolution:
1. Fossils provide very fragmentary info
2. Fossil may be from taxon that went extinct
3. Rate of morphological change is variable.
Hominins:
Organisms that are more closely related to humans than to chimps.
Hominids:
Organisms along the lineage leading to humans capable of bipedal locomotion.
3 main classes in human evolution:
1. Ardipithecus
2. Austrolopithecus
3. Homo
The first putative hominin:
Toumai. Discovered in Chad. Dated to 7mya. Small cranium, sloping face, had foramen magnum, small canines.
Millenium man:
Discovered in Kenya from 6mya. It's orrorin tugenesis. Was bipedal off of femur bone. Small teeth. Reduced canines.
Astralopithecus africanus:
Found in South Africa. 2.5mya based on ventral position of foramen magnum, it walked upright. Had small canines, but small brain and snout.
Tuang child:
Astralopithecus africanus.
Australophithecus afarensis:
Discovered in Ethiopa 3.2mya. We have around 300 individuals. Lucy is an example.
Lucy:
Australopithecus afarensis
Footprint in Tanzania;
They were in volcanic ash dating back to 3.6mya. There were footprints of hominids and they think it was A. afarensis.
Compared to humans, australopithecus had...
flatter feet, angled spinal skull hole, smaller brain case.
Oldest true hominid:
Ardipithecus at 4.4mya.
How many species of homo?
7 and the only one that exists now is homo sapiens
Earliest member of homo:
Homo habilis 1.7-2.3mya.
Features of homo habilis:
Thin walled skull
smaller jaw
reduced canines
precision grip
bipedal
toolmaking
Homo erectus:
Dates to 700Kya. One in China from 500kya (Peking man).
Why'd they think humans originated in Asia?
They found Peking man in China and then in the 70s found several H. erectus fossils in Africa which led origins back to Africa.
Features of H. erectus:
Brain case 800-1100 cc
Bony bump on head
Brow-ridge
Modern hands and feet
Developed speech center
Had fire
Made tools
Homo heidelbergensis:
Lived 600K - 200K ya. Had small molars and heavy build.
Homo neanderthalensis:
Lived in Europe, Middle East, and Asia 300K - 30Kya.
Features of H. neanderthalensis:
Large brain
Bony bump
Prominent brow-ridge
No chin
Inflated cheeks
When did neanderthals go exinct?
Like 25K ya.
4 possible reasons for neanderthal extinction:
1. Disease
2. Competitive replacement by humans
3. Interbreeding to humans
4. Climate change.
Homo floresiensis:
Found on Flores island. Lived probably 1mya - 12Kya. Viewed as a descendent of Indonesian erectus.
5 features of modern humans
1. vertical forehead
2. no prominent brow-ridge
3. rounded cranium of thin bone
4. flattened face with chin
5. small teeth and reduced jaws
5 facts about the multiregional model:
1. erectus left Africa 2mya and became sapiens in different parts of the world
2. Original form had erectus in each population form a different race
3. Now allows for some mating between populations to prevent speciation
4. Natural selection in geographic populations is responsible for races we see
5. Emergence of homo sapens was not restricted to one area, but whole world.
4 facts about the Out-of-Africa model:
1. erectus left Africa 2mya. However, sapiens arose in Africa and migrated throughout the world to replace other hominids.
2. After erectus left Africa, the different populations became reproductively isolated, evolving independently.
3. sapiens arose in one place
4. Modern human variation is a relatively recent phenomenon.
When Earth formed:
4.5bya
First life forms, as in replicating molecule:
3.8bya
First cellular life was:
3.5bya
Date of Great oxidation Event:
2.4bya
First eukaryotic cells was:
2bya
Cambrian explosion was:
543mya
Verebrate fish appear when:
480mya
When arthropods colonize the land:
450mya
When plants colonize the land:
440mya
When tetrapods evolve and colonize the land:
360mya
When Pangea breaks up:
225mya
When cretaceous/tertiary mass extinction, end of dinosaurs occured:
65mya
When Lucy lives in Africa:
4mya
How did the Great Oxidation event occur?
Photosynthesis of cyanobacteria increased oxygen in oceans and atmosphere. This enabled the dominance of aerobic metabolism and emergence of eukaryotes.
How did we figure out the timing of GOE?
Banded iron formations are deposits of iron embedded in a silica matrix. They come from precipitation of iron out of water when dissolved ferrous iron is converted in the presence of oxygen to iron oxides. Once dissolved oxygen was used up, it could escape in the atmosphere.
What are red beds:
Iron from volcanoes was oxidized on land which made red beds that are shallow-water or soil deposits in which the iron was combined with O2.
When was the Proterozoic Eon?
2.0-0.5bya
2 first multicellular organisms:
1. Gabon fossils (2.1mya)
2. Edicaran fauna (640-544mya)
What are the 6 parts of the Phanerozoic eon?
1. Cambrian
2. Ordovician
3. Silurian
4. Devonian
5. Carboniferous
6. Permian
Cambrian explosion:
The relatively rapid (30mya) appearance of many animal phyla in the fossil record.
Major site of Cambrian explosion:
Burgess shale where there was a bunch of marine fauna
When first winged insects appeard:
In Devonian era near 360mya
Why is tiktalik important?
It was a transitional form between primitive fish and tetrapods - walking fish!
What did Shubin and Coates find?
Tiktalik which had a fossil humerous. It's 365 myr-old.
3 subdivisions of the Mesozoic era:
1. Triassic
2. Jurassic
3. Cretaceous
What did Alfred Wegener propose?
That the continents were once a single landmass and then drifted. He was initially ridiculed.
Evidence of Pangea?
Continental shape fit one another and the rock types match. Like Ireland and Newfoundland. They found out in the 60s the seafloor spreading proposed a mechanism underlying plate movement.
During what era did the dinosaurs appear?
Triassic.
What era did the birds appear?
Jurassic
What era did the first placental mammals appear?
Cretaceous
When did angiosperm come about?
In the early Cretaceous (135mya) era.
When did angiosperm become dominant?
65mya
How many species of angiosperm?
250K
Time of first bird in the Jurassic?
206-144mya
What group did mammals arise from?
A group of reptiles called synapsids.
When did synapsids happen?
200mya in early Jurassic. Became diverse and abundant in the Mesozoic.
6 stages of Cenozoic era
1. Paleocene
2. Eocene
3. Oligocene
4. Miocene
5. Pliocene
6. Quaternary
Mass extinction:
When a substantial amount of species goes extinct. Like >60%
5 mass extinction events:
1. Ordovician
2. Devonian
3. Permian
4. Triassic
5. Cretaceous
Most severe mass extinction:
Permian
3 high speciation events:
1. Cambrian explosion
2. Early Triassic after Permian extinction
3. Early Tertiary following KT extinction
Why would you have explosion in increase of species after a mass extinction?
1. Empty niches - maybe a bunch of species have died off and it makes room for new ones.
2. New niches - maybe new niches are formed.
3 possible causes of mass extinctions:
1. Extraterrestrial impact - altering the atmosphere, ocean chemistry, amount of light, temp, which can cause huge environmental changes.
2. Massive volcanic activity on Earth
3. Extreme climate
When was the Permian mass extinction and what happened?
>50% of all familes and >90% of all species disappeared. At the time there was only Pangea and it was really hot because it didn't have the cooling down of the oceans. There were massive changes in sea level, ocean chemistry, climate and atmosphere.
3 possible causes of Permian mass extinction:
1. Multiple-causation hypothesis
2. Extra-terrestrial - high impact event
3. Volcanic activity leading to atmospheric change
What are 3 evidence of climate change in Permian mass extinction?
1. Evidence for massive shift in carbon cycle, release of methane deposits.
2. Evidence for widespread ocean anoxia (low O2) and drop in sea level
3. Low O2 favored sulfate-reducing bacteria which made hydrogen sulfide --> plant extinctions.
What is the cause of the KT mass extinction?
Alvarez examined the clay layer and proposed meteorite impact, causing demise of dinos. There was just a bunch of iridium in this area and there is a bunch of iridium in meteorites.
Evidence behind Alvarez hypothesis of KT mass extinction?
Found Chicxulub crater by the Yucatan Mexico dating back to 65 mya
Are older or younger species more likely to go extinct?
Neither - think about Red Queen hypothesis.