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Definition
| any type of change to the genome. The only source of completely novel genetic variation. Increases heterozygosity. Mutation rate=mu. Changes very slowly. |
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| when two or more alleles are present in the population and the minor allele is at a frequency of at least .01 |
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| Mutations that contribute to evolutionary change are: |
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Definition
A) in the germ-line
B) non-lethal, compatible w/fertility |
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Definition
A) Endogenous-misincorporation of nucleotides during replication
B) Chemical mutagens-involvement of other molecules that disrupt nucleotides
C) Physical mutagens- ionizing and UV radiation |
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Definition
A)substitutions
B)Duplications
C)Indels
D) Inversions |
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Definition
| Single Nucleotide polymorphisms. Usually substitutions, but also includes indels. substitutions 10x as common as indels |
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| change between pyrimidines (C,T). 2x as common as transversion |
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Definition
| change from a pyrimidine to purine (A,G). |
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| substitution that does not alter amino acid. e.g. many substitutions in 3rd position of codon. |
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Definition
| substitution that changes amino acid into a stop codon |
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| indel that changes the reading frame |
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| Short Tandem Repeats. Mutation by short duplication-microsatellites. High mutation rates, lots of alleles, lots of variation. usually neutral. |
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Definition
repeat units of 8-100bp of 5 to ~1000 times.
satellites-repeat units of several 100 bp. not used much. |
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Definition
| Variable Number Tandem Repeats-micro, mini, and satellites |
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Definition
A) LINEs-long interspersed nucleotide elements. 17% of genomes
B) SINEs-short interspersed nucleotide elements. 100-400 bp. ex. Alu elements. 10% of genomes |
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Term
| chromosomal rearrangements |
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Definition
Aneuploides-departure from normal chromosomal number. e.g. trisomy
Translocation-exchange of chunks of chromosomes among non-homologous chromosomes. |
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Definition
| Chromosomal anomalies >satellites >LINEs >minisatellites >SINEs >microsatellites >SNPS |
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| mutation rate varies across |
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Definition
A)marker/mutation types-SNPs, microsatellites, minisatellites
B) Age and sex-older more than younger, men more than women
C) Genome regions- mtDNA>nuclear DNA |
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| Sources of DNA (from best to worst) |
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Definition
| semen, blood, cheek cells, hair, shed skin, feces, urine |
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Term
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Definition
| W/ enough DNA, use restriction enzymes to cut DNA into chunks of various sizes. Then, gel electrophoresis-put DNA into gel, stain it, send current through it-DNA moves towards positive pole. Larger chunks move slower. Everyone has a diff. DNA badning pattern (except twins). |
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Definition
| Polymerase Chain Reaction-way to making many copies of a DNA segment(specific microsatellite). Used w/low quality DNA. Primers flank the target sequence. Also add individual nucleotides, enzyme (polymerase) and buffers and ions to help the enzyme function. Denature, anneal, extension (heat, cool, heat) 35 times. Creates 1000s of copies |
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| microsatellite genotyping |
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Definition
| has replaced DNA fingerprinting. Targets specific microsatellites, other than that basically the same. |
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Definition
DNA sequencing- purify DNA, set up sequencing reaction, perform cycle sequencing in PCR machine, resolve the 1-bp differences among fragments using electrophoresis, read output to determine the DNA sequence.
-Do a modified PCR with normal and terminal nucleotides. generate products of all possible sizes. Use elctrophoresis to separate by size. read sequence. |
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Definition
| Sequencing by synthesis, when a nucleotide is added during DNA synthesis, pyrophosphate is released. Pyrosequencing sequences as new base pairs are recorded. Keep adding nucleotides one at a time and see which one glows (releases pyrophosphate). MUCH faster than Sanger b/c no electrophoresis step. 500 million nucleotides a day. |
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Definition
| No need to sequence region. Type using microarrays. Faster and cheaper. |
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Definition
| explicitly modeling changes in genotype and allele frequencies in diff. generations in a population. It's a way of studying evolution. |
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Definition
| community of individuals where mates are usually found |
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Definition
| expected rations of offspring genotypes, given genotypes of parents. |
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Definition
| change in allele frequency from one generation to the next |
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Term
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Definition
A) Mutation
B) Migration
C) circumstances that prevent individuals from contributing to subsequent generations |
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Term
| Hardy-Weinberg Equilibrium |
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Definition
model of a population where no evolution is occuring. p^2+2pq+q^2=1. Assumptions:
A) no mutation
B) no migration
C) no natural selection
D) no accidental deaths
E) Random mating |
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Definition
A) Nonrandom Mating
B) Mutation
C) genetic drift
D) migration
E) selection- sexual and natural |
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Definition
Assortative- choose partners w/similar phenotypic traits. Decreases heterozygosity.
Disassortative- opposites attract.
Increases heterozygosity
Inbreeding-mating between genetically related individuals, decreases heterozygosity |
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Term
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Definition
| changes in allele frequencies due to random factors. Random walk. Allele frequency change independent of fitness. Only a factor in small populations. Reduces heterozygosity |
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Definition
| For the locus in question, there is only one type of allele and every chromosome has it. |
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Definition
| temporary and severe reduction (then recovery) in population size. Alleles can be lost due to drift during the bottleneck. |
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Definition
| daughter population has a different and less diverse allelic constitution than the parent population. ex. immigrant populations. |
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Definition
| gene flow. Can change allele frequencies within a population. Subpopulations might differ in allele/gentoypic frequences b/c of localized mating, drift, differential migration. Drift will fix different alleles in different subpopulations that don't interact. Lots of migration makes subpops essentially one large pop. |
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Term
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Definition
Fixation index. Fst= (Ht-Hs)/Ht
Ht=expected heterozygosity of total meta population.
Hs=observed average heterozygosity of subpopulation.
Fst=0 w/lots of gene flow, 1 w/ complete isolation.
Measure of gene flow, genetic differentiation, genetic diversity, genetic distance. |
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Definition
differential contribution of individuals to the next generation based on ability to survive and reproduce (Darwin and Fisher). Fertility and fecundity also factors. Selection occurs w/differences in fitness.
S-selection coefficient. Measures devation in relative fitness or degree of selection for/against a particular genotype.
Directional selection decreases heterozygosity
Overdominant selection increases heterozygosity.
Underdominant selection decreases heterozygosity. |
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Term
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Definition
A) New World Monkeys-South and Central America
B) Old World Monkeys- Colobines (mostly Asian_ vs. Cercopithecines (mostly African)
C) Apes- Asia and Africa. use tools. Hunt in teams.
D) Lemurs-madagascar,
E) Lorises and galagos-Asia and Africa
F) Tarsiers-Asia |
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Term
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Definition
Only primates have Alus- type of SINE
Physical traits-binocular vision, color vision, shorter snout (use sight more than smell), grasping hands/feet, nails instead of claws, large brains, extended juvenile period |
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Term
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Definition
A) Gibbons and siamangs- lesser apes, Asian
B) Orangutans- Great apes, Asian
C) Gorillas- Great apes, African
D) Chimps and Bonobos- Great apes, African
E) Humans-Great apes, African |
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Term
Phylogeny
Phylogenetic tree |
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Definition
-History of how a group of organisms descended from common ancestors
-representation of that history |
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Definition
-Principle that guides production of phylogenetic trees (cladograms, phylogeny)
-lineage, an entire branch |
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Term
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Definition
Step 1) make a character matrix/table for relevant taxa
Step 2) ingroup (group whose relationships we're trying to resolve) vs. outgroup (species known to have an older most recent common ancestor predating the ingroup). Outgroup helps identify ancestral vs unique traits. |
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Definition
| Tree that requires the fewest evolutionary events |
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Convergence
Convergent evolution |
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Definition
-similarity among taxa can lead to convergence (ex. wings-bats and birds)
-produces superficially similar traits |
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Definition
| amount of genetic difference b/w sequences is a function of time since separation. Rate of change is constant enough to predict time of divergence. |
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Term
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Definition
denature DNA from two diff. species, then combine. How much heat is needed to denature the heteroduplex (hybrid) DNA?
-Helped figure out that humans-chimps are sister taxa |
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Term
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Definition
Chimps- 1/3 brain size, jutting face, larger teeth/ sexually dimorphic, jutting face, knuckle walking, relatively short legs, straight spine
humans-stronger chin, more spherical brain case, smaller snout, smaller teeth. hair is finer, thinner, w/a shorter growth cycle (except for scalp hair). Bipedal, long legs, knees angled in, rounded hips, big toe aligned, arms can rotate 360, s-shaped spine, knock-kneed, arched foot |
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Term
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Definition
Ardi- first clear biped w/nearly complete specimen
australopithecus afarensis-Lucy, used to be first clear biped
australopithecus africanus-smaller face
homo habilis-first stone tools
homo ergaster/erectus-first long migrations |
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Definition
| transfer of genes between non-mating species. happens in bacteria, rare in multicellular eukaryotes. mechanism not clear. makes phylogenetic tree construction difficult. |
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Term
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Definition
| Tarsiers, lemurs, and lorises & galagos. part of phylogenic tree. |
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Definition
NW monkeys-spider monkey
OW monkeys-rhesus macaque, olive baboon,
Apes-humans, chimps, gorillas |
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Term
| comparative primate genomics |
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Definition
| understand human genome by comparing it to other (primate) species. similarities, differences. Goal-reconstruct the evolutionary history of every gene and segment of genome. |
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Term
| Gene trees vs species trees |
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Definition
| molecular divergence and species divergence are not always the same. When sequential splits happen over short time period, not all gene trees will match species trees. Need to examine numerous loci in all sepcies. |
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Definition
| controversial b/c it's difficult to define species/subspecies. |
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Definition
humans>> pop size and diversity.
humans<< genetic diversity
Exception- humans have more genetic diversity in y chromosome than gorillas. |
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