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| using molecular bio to answer questions about human and primate evolution |
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| all the genetic material contained in an organism |
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| all the proteins encoded by the genome |
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| RNA to amino acids/proteins |
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| part of DNA that is transcribed and then translated to make proteins |
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| part of DNA that is transcribed and NOT translated |
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| several variants of one protein (isoform) from one gene |
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| when it's turned on and off, where, when, and how much |
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| protein that regulates for transcription of gene |
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| part of DNA that affects the transcription of a nearby gene, can include activators, repressors, enhancers, promoter regions, transcription factors |
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| what your genes look like |
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| what your appearance looks like |
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| the part of the chromosome/DNA that's being read to make proteins (from start to stop codon) |
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| chromosomes exchange chunks of their information during meiosis. this results in limiting the degree to which traits can be linked and breaks up straight lineage of chromosomes. y chromosomes don't recombine that much. |
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| alternate forms of DNA sequence at one locus |
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| when two or more alleles are present in the pop and the minor allele is at a frequency of at least 1% |
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| non-inhertiable mutations |
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| substitution of C to T or A to G |
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| any change that is not a transition |
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| a mutation that does not change amino acid produced |
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| non-synonymous mutation, missense mutation |
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| mutation that changes the animo acid produced |
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| substitution that changes the stop codon |
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| an indel that changes the ORF |
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| 10 to 30 repeats in the DNA, aka STRs or VNTRs |
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| up to several kbps, aka VNTRs |
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| like minisatellites but several 100kbps, aka VNTRs |
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| long interspersed nucleotide elements (6-8kbps) |
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| short interspersed nucleotide elements, 100-400bps |
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| enzymes that cut the DNA into pieces after seeing a particular sequence, used for DNA fingerprinting |
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| taking apart the strands of DNA with heat, melting |
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| creating the partner side of the DNA in the PCR machine to magnify the microsatellite, DNA synthesis |
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| getting the whole sequence of the genome by putting the terminators in w/ the PCR magnified portions of DNA, the radiation thing |
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| the type of genome sequencing where all the energy is released and that tells you what combined |
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change in allele frequencies from one generation to the next
forces of evolution are nonrandom mating, mutation, genetic drift, migration, and selection |
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| choosing a partner with similar traits to you, decreases heterozygosity |
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| choosing a partner with different traits than you, increases heterozygosity |
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| mating btwn 2 genetically related individs, decreases heterozygosity |
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changes to allele frequency due to random reasons, random walks
decreases heterozygosity esp in small pops where a certain allele goes to fixation
if s<<<1/(2N), drift will dominate over selection
if 4N(mue)<<1, drift dominates over mutation |
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| at a locus, everyone in the pop has the same allele |
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| temporary and drastic reduction in population size, then recovery. some alleles might get lost |
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people leave a population and the daughter population does not represent the allelic diversity of mother pop, some alleles will be lost
ex: Amish people who have an increased frequency of polydactyly |
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fixation index, measurement of pop differentiation
0=lots of gene flow
1=no gene flow |
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differential contribution of individs to next gen based on their ability to survive and reproduce
s>1/(2N)
occurs in 3 levels/stages
1. survival to reproductive age (viability)
2. attract a mate and fending off rivals (sexual selection)
3. fertility and fecundity |
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Definition
the dominant gene is favored AA, Aa > aa
ex: rock pocket mice
decreases heterozygosity |
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| where the homozygous dominant genotype is favored AA > Aa > aa |
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| additive selection (codominant selection) |
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| where the homozygous dominant genotype is favored AA > Aa > aa |
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| heterozygous advantage (overdominant selection) |
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where heterzygous genotype is favored Aa > AA, aa
ex: sickle cell anemia and malaria resistance
increases heterozygosity |
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| heterozygous disadvantage (underdominant selection) |
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Definition
where the heterozygous genotype is disfavored (not real) Aa < AA, aa
decreases heterozygosity |
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| lorsies (Asia), galagos (Africa), lemurs (Madagascar), and tarsiers (tarsiers are closest to monkeys and apes, they are found in Asia) |
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| humans, chimps, bonobos, orangutans, gorillas, gibbons, and siamangs |
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binocular vision, shorter snout, grasping hands, and color vision, Alu SINE
most closely related to flying lemurs |
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| the history of how exactly species descend from common ancestors, aka cladogram |
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| principle that drives the creation of phylogentic trees |
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| when branches on a phylogeny/cladogram diverge |
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| a species that you know has a common ancestor further back than the other species you're looking at |
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| keep it simple: the best phylogeny is the one that uses the least amount of evolutionary events to be created |
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| convergent characteristics |
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| traits that can be found in two species though the species aren't related (ex birds and bats both have wings) |
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| Sibley and Ahlquist in 1984 used this method to find out if chimps were more closely related to humans or gorillas, combined two species DNA and saw how much heat you needed to denature it |
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| chromosomal translocations |
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Definition
| huge mistakes in chromosomes, ex down syndrome |
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| ancient group of mammals. includes elephants, manatees, golden mole, tenrec, and hyrax |
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| the 12my old fossil of a human descendant. using this fossil, it seemed that humans were around at least 12mya. |
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genome is different by 1.2%, split 5-7mya
humans have 46 chromosomes, other great apes have 48 (on humans, chromosomes 12&13 of great apes is combined)
chimp brain is 1/3 size of human brain |
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| Tyrolean Ice Man, 5000y old mummy found in 1991, used aDNA to find out his diet and what weapons/gear he had |
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under 3 billion bp
humans and mice (and nematodes) have about 25000 genes
shape discovered in Cambridge, England in 1953 by Watson and Crick
it has 46 (23 pairs of) chromosomes. |
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| consists of a sugar, phosphate, and a base. bases are A (adenine), T (thymine), G (guanine), and C (cytosine)...then U (uracil) is added when DNA is transcribed into RNA |
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| proteins, codon codes for proteins, there are 20 important amino acids, poly peptide |
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| AUG, codes for methionine (Met) |
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| the 70% of our DNA that is not transcribed, some plays a role in chromosome structure or gene regulation |
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| certain variation of this gene leads to increased risk of having breast cancer |
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| if you stain DNA, it creates dark bands on the chromosomes. corresponds to regions of low GC content and each chromosome has a unique banding pattern |
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| y chromosome being special |
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Definition
| contains few genes, only small portions recombine (men usually have the same the same Y chromosome as their fathers...and their fathers' fathers...etc. |
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| location on chromosome where homologous genes are located |
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mitochondrial DNA.
several copies of this DNA in each cell.
mtGenome is circular, not chromosomes.
codes for genes involved in metabolism. it does not recombine.
includes the D-loop which contains highly variable in regions (HVRI and HVRII) |
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Definition
| when a mutation occurs because there is a misincorporation of nucleotides during replication |
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| when a mutation occurs because the involvement of other molecules that disrupt nucleotides |
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| when a mutation occurs because of particularly ionizing radiation and UV radiation |
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| type of mutation where instead of the "correct" sequence being there, its reverse compliment is there |
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IDIS
indels, duplications, inversions, and subsituations |
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| when mutations occur and are passed on to next generation |
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| when mutation occur in multiple species b/c of the environment they are living in |
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single nucleotide polymorphisms.
base subs are 10x more frequent than indels
transitions are 2x more frequent than transversions
G-C islands are more prone to mutations |
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| departure from normal chromosomal number (ex Down syndrome) |
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| exchange of chunks of chromosomes among non-homologous chromosomes |
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| chips with thousands of specific spots of our DNA on it, focuses on locating important SNPs in order to identity individuals. |
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| concerns expected ratios of offspring genotypes, given genotypes of the parents: one parent to their offspring |
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Hardie-Weinberg Equilibrium, nothing is going on.
p+q=1
p(squared)+2pq+q(squared)=1. |
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| studied the Karisoke Mountain gorillas in Eastern Africa |
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| males stay close to each other and stay w/in their natal region while female migrate farther from home (ex harem structure of western gorillas) |
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major histocompatibility complex, example of disassortative maing where people want to mate w/ people who have different MHC components than them b/c if deals with defense against pathogens.
t-shirt study |
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only source of completely novel genetic variation, increases heterozygosity
if 4N(mue)>>1, mutation dominates over drift |
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when neither allele is dominant or recessive, inheritance is additive
ex: AA=red flower, aa=white flower, Aa=pink flower |
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expanded Darwin's def of selection
also a statistician and founder of pop genetics and a Eugenicist |
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the degree of selection for (+s) or against (-s) a particular genotype
deviance from relative fitness (relative fitness = 1) |
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| egg laying mammales, split from humans about 190mya |
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| mammals that give live birth w/ particular development of embryo, split from humans 100mya |
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| placental mammals, the group primates are in! |
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| lemurs, lorsies, and galagos |
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| tarsiers, new & old world monkeys, and apes |
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divided into two types
1. colobines: mostly Asian
2. cercophitecines: mostly African |
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| grasping tails, Central and South America |
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| gibbons, siamangs, orangutans, tarsiers, and lorsies |
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belief that you can calculate how old last common ancestor is if mutations occur in clock-like frequency.
founders of the idea were Sarich & Wilson in 1967 |
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masillae darwinius
47mya, female who died when 9-10 months old
95% complete: guts help us determine its diet
discovered by John Hurun |
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ancient DNA, upper limit thought to be 1mya
400,000y old plant DNA from Siberian permafrost cores is the oldest DNA recovered
100,000y old Neanderthal molar form Belgium is the oldest primate DNA recovered
easily degraded so you need 3 things to have good preservation:
1. rapid desiccation (dry)
2. low temperature (cool)
3. high salt concentration
in 1997 a small segment of mtDNA from Neanderthal was sequenced |
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Definition
fossils discovered in Germany's Neander Valley in 1856
traits include no chin, large elongated brains, stocky bodies, cold adapted, lots of trauma
found in Europe & Asia 400,000-24,000ya
in 1997 a small segment of mtDNA from Neanderthal was sequenced |
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scientists discovered Bagheera Kiplingi jumping spider, inhabits a region in SE Mexico and Costa Rica
maybe a case of horizontal gene transfer |
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| domesticated in China about 11,000-14,000ya |
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| looked at species and gene trees of chimps, gorillas, and humans to solve trichotemy |
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| knuckle walker, small brain, 4.4mya |
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infant is homozygous for a gene variant that is known to cause congenital chloride diarrhea.
used microarrays for the test |
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| human uniqueness is due to rapidly evolving proteins; changes to exons |
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| deletions or copy number changes |
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Definition
| difference btwn humans and chimps is because we have lost or duplicated key genes |
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| gene regulatory evolution |
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| differences btwn chimps and humans are due to differences in the expression (when and where) of particular genes |
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Definition
chunks of RNA that are just 21-23 bases long
highly conserved throughout evolution
don't code for proteins,but seem involved w/ gene regulation
RNA silencing/interference |
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Definition
| compared 7645 coding genes in chimp, human, and mouse and found genes associated with immune defense, cell signaling, amino acid metabolism, olfaction, hearning (ex TECTA) |
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| comparing gene expression profiles, used micro-arrays to analyze gene expression differences and found out that humans have more mRNA, so more expression, in their blood, liver, and brain tissues than do chimps or rhesus monkeys |
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gene related to jaw musculature
humans have a frameshift mutation so that they don't have this protein in their jaw muscles
change perhaps due to change in diet |
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gene related to brain size and development
associated with microcephaly |
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gene associated with development of speech and language
discovered via study of KE family (British family)
conserved amino acid sequence (only 1aa change from mouse to chimp, but 2aa change in humans)
2aa changes went to fixation about 200,000ya
Enard et al 2009 tested FOXP2 variant in mice |
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Definition
Aussie family w/ speaking disorder had a variant on chromosome 8
production of tospeak RNA was involved w/ larynx development
breakdown btwn tospeak and GDF6 can lead to fused bones in wrist and feet |
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| put human variant of FOXP2 in mice and it increased neuron plasticity and connectivity and changed the pitch of ultrasonic vocalizations |
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Evans et al 2004, Kouprina et al 2004, Zhang 2003
loss of function mutations at this gene cause microcephaly (reduced brain size) |
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hair keratin gene
in humans this gene is inactive |
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olfactory receptor
in humans there is an amino acid substitution |
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gene associated w/ brain development
in humans there is a regulatory change |
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gene associated w/ pathogen resistance
in humans this gene is lost |
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| monkeys are better at estimating |
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research at Brannon Lab @ Duke
monkeys better at fuzzy math whereas humans are good at precise math
monkeys were two females named Boxer and Feinstein |
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| good preservation conditions for aDNA |
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Definition
rapid desiccation (dry)
low temp (cool)
high salt concentration |
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Definition
chemical change to structure of the nucleotides that occurs post-mortem
leads to insertions of an extra nucleotide or change a nuceoltide after death |
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Definition
| type of aDNA control where you run tests to see if there are amino acids presents in the sample |
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Definition
| control used for aDNA where you create mock controls of extraction and PCR reactions with no DNA in them to allow to test for false positives (a false positive would mean that your sample is contaminated) |
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18,000y old fossil discovered in 2003 on Flores Island, Indonesia
female adult, 3ft tall, huge feet, small brain |
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| Anatomically modern humans |
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Definition
earliest fossile 200,000-150,000ya in Africa
first appear in European fossil record 40,000ya
traits include: round tall skull, vertical forehead, small brow ridges, small face and teeth, gracile skeleton and skull |
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Definition
| humans evolved more or less simultaneously across the entire Old World from several ancestral populations |
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rapid-replacement model
modern humans evolved in Africa and then migrated throughout Old World
AMH migrated out of africa 1.8mya |
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Definition
split 290,000-440,000ya
still debating about interbreeding, but looks like no interbreeding |
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| domesticated in the New World 4,000-7,000ya |
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preceded AMH
Africa-350,000-200,000ya
Asia-350,000-130,000ya
Europe-350,000-130,000ya |
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Definition
Cann et al. 1987
first major construction of human phylogeny |
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flip side of divergence
tracks the genetic history of a particular genetic locus back in time |
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Definition
| group of modern humans with smallest amount of genetic diversity |
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Definition
a particular set of alleles, linked on the same chromosome, that are transmitted together
when chromosomes recombine, they recombine in chunks: these chunks are called haplotypes |
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Definition
groups of haplotypes
Y chromosome haplogroups: organized using alphabet, A being the oldest
mtDNA haplogroups: organized using L, L1 being the oldest |
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| Migration using haplogroups |
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Definition
1. 150,000ya L1 mtDNA lineage spreads thru Africa
2. 75,000ya L2 and L3 spread thru Africa
3. 60,000ya L3 migrate out of African giving rise to M and N
4. 30,000-50,000ya migration throughout Eurasia (including Aussie by 45,000-50,000ya) |
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Definition
fossil dating 40,000ya
oldest human skeleton in Aussie |
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| four major regions particularly influences by changes in sea level |
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Definition
BESS
1. Bering Strait
2. English Channel
3. Sahul
4. Sunda Shelf |
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| hypotheses regarding the peopling of the Americas |
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Definition
BAPP
1. Bering Land Bridge (interior)
2. Atlantic Crossing
3. Pacific Coastal (coastal)
4. Pacific Crossing
major migration happened 20,000ya |
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early Americans
traditional idea: clovis (spear point) first
earliest ones dated about 13,000ya
big game hunters
appeared suddenly in short period of time |
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Definition
David Teie, cellist for National Symph Orch & Chalres Snowdon, physcologist
composed music tailored to the pitch, tempo, and tone of monkey calls
monkey's only response to human music was being calmed by Metallica's "Of Wolfe And Man" |
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Definition
| goal was to collect and sequence DNA of 10,000 vertebrate species |
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| division of the human species based on differences in phenotype that are determined by genotype |
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Definition
in 1775 he created a systematic classification system for humans based on size of crania
4 major groups:
1. African
2. Asian (or Mongoloid)
3. Caucasian
4. American Indian |
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Definition
early 20th cent, studied immigrant families in America and found no support for the taxonomy of human variation
cranial proportions are largely influence by environment |
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study in 1972 showing that there was little genetic variation w/in pop, btwn pops w/in a race, and btwn races
most human diversity found w/in pops (85%)
diversity btwn pops w/in a race was 8.3%
diversity btwn races was 6.3% |
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Definition
| 0.092 for ACE Alu insertion |
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Definition
sequencing of horse named Twilight began in 2006 for $15 billion sequencing 2.7billion bps
horses were domesticated btwn 4,000-6,000ya
centromere: part of chromosome that contain satellites
larger than dogs', but smaller than cows' and humans' and have 53% similar to humans' |
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Definition
gene on chromosome 15 associated w/ and likely causative of blue vs. brown eye color in humans
it's an intron! it probably effects regulation of OCA2 |
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Definition
| codes for P protein which helps determine pigment |
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Definition
| codes for Tyrosinase that affects pigment. Siamese cats have C allele there which causes dark pigment production but how much pigment is produced depends on temp of skin |
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Definition
effects melanocite production
in red heads, they have recessive alleles which means more phaeomelanin then eumelanin is produced
same allele effects UV radiation sensitivity
these haplotypes arose 30,000-80,000ya in Europe |
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Definition
| when a single locus influences more than one trait |
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Definition
polygenic traits
traits that very in phenotype along the cline (ex skin color, eye color)
bell curve distribution |
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Definition
| clearly defined categories of phenotypes |
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Term
| stabilizing/balancing selection |
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Definition
| if average is more fit than others, then bell curve will span over a smaller variety of the trait |
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Definition
duffy locus which encodes a blood group antigen that confers resistance to malaria.
has a high Fst |
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Definition
| gene associated w/ Asian flush, high Fst value |
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Definition
| codes for enzyme Amylase which helps break down starch, more copies means more amalyse in saliva |
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Definition
| codes for lactase and enables your body to digest lactose |
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Definition
strongly influenced by a single gene
follows Mendelian inheritance
individs w/ mutation usually manifest the disease phenotype |
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Definition
influenced by many genes and environment
do not follow straightforward Mendelian inheritance
individs w/ mutation may not manifest phenotype |
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Definition
| number of people who develop a disease over a particular period |
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Definition
| number of people who have the disease at any one time |
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Term
| Duchenne Muscular Dystrophy (DMD) |
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Definition
extreme muscle weakness
indidence 30/100,000 males
usually caused by defect at the gene for dystrophin (largest gene in genome!) |
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Definition
largest gene in the human genome (70 exons, 2.4Mb, .1% of genome)
associated with DMD (Duchenne Muscular Dystrophy) |
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Definition
lung congestion
common among Europeans
affected individs carry 2 inactive copies of CFTR on chromosome 7 |
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Definition
gene on chromosome 7
helps regulate fluid secretion across cell membranes
associated with Cystic Fybrosis
has deletion of a single amino acid (phenylalanine) at position 508 |
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Definition
gene associated with HIV resistance
found mostly in Northern Europe and NW Asia |
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Definition
gene responsible for developing enzymes/proteins that metabolize stuff
more copies you have, the better your are at metabolizing |
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Definition
serotonin transporter
social anxiety, depression, alcoholism |
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Definition
dopamine receptor
risk taking and novelty seeking, ADHD |
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Definition
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Definition
degrades serotonin
leads to aggression |
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Definition
vasopresisn receptor
male "bonding" behavior
monogamy gene (ex prairie voles who are monogamous have longer variant than mountain and meadow voles who are promiscuous) |
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Definition
| ethical, legal, and social implications research program |
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marrying within in the same cultural group
decreases heterozygosity |
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type thousands of markers thruout genome for numerous affected and unaffected individs
helps find candidate genes for certain diseases |
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genetics perspective on individs variation in response to pharmaceutical drugs
ex studies CYP to find out how good people are at metabolizing medicines |
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changes in genome to deal w/ geographic area where you live
for example, DARC (duffy locus), MCR1 making pale skin in Northern Europe |
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a species that is extensively studied, usually experimentally, to understand biological processes
mouse is a good example of this |
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influence the activity of nearby genes
3% of genome is actual genes
tandem repeats allows animals to adapt quickly |
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defined by advanced in tool construciton
change in economy and human lifeway (people start making pottery!) |
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ancestor of maize
domesticated btwn 7,000-4,000ya
increased number of kernels per cob and cob size |
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| new pops learn agriculture from neighboring groups |
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Corey Haas had Leber's Congenital amaurosis (LCA)
affected by RPE65 gene |
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| most common recent ancestor for homo sapiens from diff regions |
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Definition
90,000-180,000ya
original pop size was about 10,000 |
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