Lecture 1 Flashcards
Population Genetics
study of how evolutionary forces result in genetic changes in species through time.
Study genetic diversity within and between population
locus
the position on a chromosome where a given gene (or other structure) occurs.
alleles
different forms of a gene or DNA seq
neutral alleles
alleles that do not have any noticeable physical effects
Evolution
A change in the frequencies of alleles (genetic types) over time, opportunity for complexity
Forces of Evolution
Mutation, Gene Flow, Genetic Drift, Natural Selection
-Cause allele freq changes
Mutation
a change in the DNA sequence (error in DNA repair or replication)
Gene Flow
the exchange of alleles between populations
Genetic Drift
changes in allele frequency that occur at random
nature’s sampling effect
Natural Selection
process that produces adaptation
- loci w/ functional consequences may affect individual’s fitness» one gene type (allele) to be favored over another
- the dice can be loaded
Rapid Expansion
look, genetically, like a small population for a very long time because mutations are rare
Nucleotide Diversity+ Mismatches
Probability that two nucleotides are different when comparing two DNA sequences
- Averaged for sequences within population, and between different populations
- diffs between all seqs to ea other.
Features of Human Genetic Diversity- 1
1) amount of diversity in humans is much smaller than for a typical species with 6 billion members.
level of variation in -humans is consistent with that of a population of only 20,000 individuals
Features of Human Genetic Diversity- 2
2) genetic variation of the people outside sub-Saharan Africa is mostly a subset of the genetic variation within sub-Saharan Africa
- Africa-Africa more diverse than Africa-Europe or Africa-Asia!
- Europe-Europe and Asia-Asia nearly the same as Asia-Europe!
Features of Human Genetic Diversity- 3
3) If allele is common in one population, it is typically common throughout the world
Genetic Variation- Ppling the world
Total pattern of genetic variation is consistent with serial founder effects. beginning in sub-Saharan Africa and extending to the rest of the world
Bio Definition of Race
a group of individuals more closely related to one another than they are to individuals outside their group.
-categorize Western honey bees in North America
Levels of diversity- Chance
each gene may be affected by mutation, gene flow and genetic drift similarly
-each genetic locus is evolving independently (a different roll of the dice, sort of speak)
Independent Segregation
gene alleles segregate into gametes= 1 allele o each gene in each gamete.
Independent Assortment
genes/ chromosomes are distributed randomly into gametes during meiosis. (i.e. each gene is equally likely to be transmitted when gametes are formed)
Hardy-Weinberg principle
Genotype frequencies in a population remain constant from generation to generation unless specific disturbing influences are introduced
-influences= non-random mating, finite population size, mutations, genetic flow, genetic drift, and natural selection
Bio Pop concept
A group of individuals from the same species who, excepting barriers imposed by sex and developmental stage, are likely to mate and reproduce.
-group of inds share gene pool
Law of Dominance
Some alleles dominant. If have at least one dominant allele= will be expressed
Variation- discrete
distinct classes
Variation- continuous
measured scale or grade
-attributed to 1) multiple genes, 2) gene-environment
Probability Distribution
equation that assigns the probability to each possible measurable set of values for a particular random experiment.
Probability density function
probability distribution for continuous random variables
Central Limit Theorem
iterating independent random variables with expected values and variances will converge to the normal distribution.
-Independent= information about one iteration provides no information about the others.
Measures of Variation- Monomorphic
absence of variation -every copy of the locus in the population has the same nucleotide sequence
Measures of Variation-Polymorphic
more than one common allele at the locus
-A polymorphism is an allele that is in too high a frequency to be a new mutation.
Gene diversity
H
-probability will draw different alleles of the locus at random from the gene pool.
Gene identity
J
-probability will draw same alleles if drawn at random
Effective number of alleles
of equally frequent alleles that would provide given level of diversity
- difficult to determ if many alleles at a locus
- predicted from underlying pop characteristics (# o inds, mut R, mode of NSel)
of segregating sites
S
-number of nucleotide sites that are different for a particular set of aligned
sequences
Seq variation- pie, pairwise comparisons
π = (total # differences) / (# pairwise comparisons)
Size of the sequence
-pairwise comparisons =
n(n-1)/2
STRs
runs of simple nucleotide motifs
- mammals have many
- diffs in copies o repeat motif b/w alleles pair is roughly proportional to # o muts in their history.
