envs lecture 5 Flashcards
what provides material that selection acts on
mutation and variation
what would happen without variation in phenotype
nothing for natural selection to act on
what provides new variation
mutation
chromosome
strings of DNA bases bound together by proteins
what is main structure in machinery of inheritance
chromosomes
what are proteins in chromosomes
histones
do all species have same number of chromosomes
no
locus
position on a chromosome
gene
physical unit of heredity
what is gene composed of
DNA
what is gene the code for
proteins and RNAs
what is gene used interchangeably with
locus
does a locus always code for protein
not always
is locus always part of a gene
not always
codons
sets of 3 DNA bases that are translated to AAs in protein-coding genes
synonymous codon/mutation
doesn’t change amino acid and thus protein
non-synonymous codon/mutation
changes amino acid, can cause sickle cell anemia etc.
allele
alternative forms of a gene
homozygotes
carry exact same form on both chromosomes
how many alleles for a given gene can an individual have
no more than two alleles
how many alleles for a given gene can a population have
many different alleles
what is genetic basis of variation in populations
population having many diff alleles for a given gene
central dogma
DNA –> RNA –> protein
what does dNA code for
codons
what are codons transcribed to
RNA
what is RNA translated to
proteins
SNP
single nucleotide polymorphism
what is SNP
single DNA base that defines alternative alleles at a locus
example of SNP
likeee 2 alleles of gene XYZ differ at a SNP at position 242
homologous chromosomes
pair of chromosomes
basically what is SNP
when a single base pair difference causes difference b/w two alleles
exon
segments of a gene that code for amino acids
introns
noncoding DNA segments in between exons
what is 1st step of protein synthesis
cell first transcribes DNA from genes into RNA (pre messenger RNA)
2nd step
pre mRNA is spliced, so parts of molecular are removed to form a mature mRNA
3rd step
mRNA translated into a string of AAs that make up a protein
what happens in genomes where this process happens
segments of gene that are spliced out b/c they don’t encode AAs are introns
what are regions that do encode for AAs
exons
purpose of introns?
variable, but we know they impact gene expression
how do introns impact gene expression
alternative splicing
alternative splicing
allows a single gene to encode for more than one protein
summary of chromosomes & machinery of inheritance
organisms have chromosomes, within which are found protein coding genes, which are composed of codons, which can be changed to form diff versions of the same gene called alleles
phneotype
observable characteristics of an organism
what does natural selection act on
phenotype
when does evolutionary change only occur
if phenotypes are heritable
genotype
unique genetic makeup of an organism
are genotype and phenotype completely linked
not necessarily; b/c phenotype can be influenced by environment as well as genetics
what happens if there’s no genetic variation and inheritance
no evolution
segregation
separation of alleles during meiosis so that each gamete carries only one allele for each locus
why is segregation important
all alleles have an equal change of being inherited in next gen
hardy weinberg equilibrium
HWE characterizes distributions of genotype frequencies in populations that are NOT EVOLVING
what happens if genotypic frequencies in the population we’re studying are not at HWE
we need to explain this pattern via one of many processes causing evolutionary change in populations
what does HWE provide
null model from which to understand process of genotypic & phenotypic evolution, based on what we expect due to chance alone
when a population is in HWE, what is needed for equilibrium to be reached
when segregation is the only factor that influences genotype frequencies
formula for genotype frequencies after one generation of random mating
p^2 + 2pq + q^2 = 1
what is p
frequency of homozygous genotypes (allele 1)
what is 2pq
frequency of heterozygous genotypes
what is q^2
frequency of homozygous genotypes (allele 2)
what is HWE
null model, reached under specific set of conditions
first HWE condition
mating is random
second HWE condition
population size is very large (inifinte)
3rd HWE condition
gene flow does not occur
4th HWE condition
mutation doesn’t occur [negligible anyway]
5th HWE condition
locus concerned is not under selection (no fitness difference b/w alleles)
why is this null model even useful
observed in natural populations; find it in nature when mating is random w/r to genotype at most loci in genome
so basically why is HWE interesting
deviations from HWE tell us that a locus is involved in an interesting evolutionary process
how to find frequency of A allele
add freq of homozygotes and half freq of heterozygote
a mechanism by which genetic variation is produced & inherited (i.e. evolution is allowed to occur)
recombination
recombination
occurs in meiosis & gamete production –> produces new genetic combos within a gamete
how does recombination occur
by independent assortment or crossing over
law of independent assortment / crossing over
the allele a gamete receives for one gene doesn’t influence the allele it gets for a different gene
what does law of independent assortment produce
novel combos of alleles in gametes
what two mechanisms can recombination occur through
independent assortment or crossing over
what is crossing over
when homologous chromosomes swap segments of DNA
what happens to loci in crossing over
loci on same chromosome can recombine by crossing over
basically what is crossing over
process that involves genes linked on the same chromosome undergoing recombination
what happens to chromosomes in meiosis
homologous chromosomes are aligned, crossing over occurs, exchanging pieces of the homologous chromosomes (which might be carrying different alleles)
what does crossing over prodouce
both recombinant and non-recombinant chromatids
what happens to recombinant ones
the ones resulted from exchanging pieces of chromosomes during crossing over
what does process of crossing over do
produces new associations and combos of alleles in multiple genes on a given chromosome, thus increases genetic variation
recombination & segregation
powerful tools that promote novel genetic combinations that can be inherited in future generations
what do both recombination and segregation do
produce and promote novel genetic combos that are inherited by future generations
recombination rate (r)
probability that recombination occurs between a given pair of loci
what happens of two loci are on different chromosomes
r = 1/2
if two loci are on the same chromosome
r < 1/2
what happens of loci are on different chromosomes
50% chance that when an individual makes a gamete one of the chromosomes it carries will be from the mother and other from the father
what happens of the loci are on the same chromosome
closer the loci are, smaller r
what happens to loci right next to each other
r = 0
linkage disequilibrium
alleles of multiple loci are found together more often than you would expect based on independent assortment
another way to think about LD
allelic association
what does LD suggest
different loci are physically linked on the same chromosome
is LD actually the case
not necessarily (often isn’t)
when does linkage disequilibrium occur
when recombination rate is low
why does LD occur when recombination rate is low
b/c it acts to mix the association of alleles at different loci
what happens to loci close together in linkage disequilibrium
loci closer together experience less recombination (lower r) and higher linkage
what causes linkage disequilibrium
linkage disequilibrium can result from other processes besides physical proximity on a chromosome
what else can cause LD
natural selection, genetic drift
example of nat selection causing LD
epistasis
epistasis
when the effect of an allele at one locus depends on the allele at a second locus
when does selection promote linkage
when combos of alleles have high fitness
example of LD in primrose
plants either have low anthers/high stigma or high anthers/low stigma; two traits are at linkage disequilibrium b/c specific combos have higher fitness
gene mixing without inheritance
horizontal gene transfer (HGT)
HGT
movement of DNA between individuals without sexual reproduction
what is HGT common in
prokaryotes
vertical gene transfer
how genetic variation is produced in sexually reproducing organisms
why is HGT iimportatn
how antibiotic resistance is spread and transferred across bacteria
bacterial transformation
spread of antibiotic resistance; donor cell releases DNA that is taken up by a recipient cell
how is that variation ultimately produced
mutations
mutation
ultimate source of genetic variation in all organisms
what would happen w/o mutations
no variation, no evolution
types of mutations
point mutation, structural mutation
point mutation
single base pair mutation
structural mutation
insertions/deletions (single to multiple bases), inversion (DNA segment), fusion/fission (chromosomes), whole genome amplification (all DNA in genome)
what are point mutation
single nucleotide changes
what can point mutations be
synonymous, nonsynonymous, can cause stop codon
what do stop codons produce
pseudogenes (nonfunctional)
ice fish
colorless blood b/c it lacks hemoglobin; either genes are deleted or rendered nonfunctional (point mutation) (pseudogenes)
what are most mutations at 3rd codon position
synonymous
what are all mutations at 2nd position
non-synonymous
what is synonymous
don’t change AAs
what are nonsynonymous
change AAs
types of chromosomal mutation
deletion, duplication, inversion, fission, fusion,
deletion
DNA segment is removed
duplication
DNA segment is copied and inserted in the genome/chromosome
inversion
chromosome segment is reversed
fission
one chromosome breaks into two
fusion
two chromosomes become 1
what do fission/fusion do
alter number of chromosomes in the genome
what is whole genome duplication
occurs when meiosis produces gametes that carry a diploid genome which then undergo fertilization
which organisms have whole genome duplications?
common in plants; occurred deep in evolutionary history of many plant lineages
whole genome duplication is important source of what
evolutionary novelty
what does double the genes mean (WGD)
opportunity for new functions to evolve
why is WGD important source of evolutionary novelty
b/c having double the number of genes provides opportunity for new functions to evolve
is DNA replication accurate
extremely
what do mistakes in DNA replication lead to
mutations
how much of DNA bases are a mutant in humans
1 out of every 10^8 (100 million) bases
given 3 billion base pairs, each gamete has how many mutations
approximately 30 mutations
is mutation rate variable among tree of life
yeah
who has more mutation rates
parasites and viruses have higher mutation rates than hosts
why might it be advantageous to have high mutation rates
produces novel variation, allows them to evolve and keep evading hosts
fitness
number of offspring an organism produces
beneficial mutations
increase fitness
are beneficial mutations rare or common
rare
what are beneficial mutations acted on
acted on by natural selection
what are deleterious mutations
decrease fitness
are deleterious mutations rare or common
more common
are deleterious mutations acted on or selected against
selected against
pleiotropy
occurs when single mutation affects multiple traits
what is currency of natural selection
fitness
what do most genetic changes likely have
pleiotropic effects (side effects)
do synonymous mutations have an effect on fitness
not really; almost no effect
what do majority of mutations have
negative effects; deleterious
are beneficial mutations common or rare
rare; very few mutations are beneficial
germ line mutations
mutation in gamete (germ cell –> egg or sperm)
are germ line mutations inherited
yes
what are germ cells
egg or sperm
what is gamete
germ cell; egg or sperm
are somatic mutations inherited
no
who does somatic mutations effect
the bearer
somatic cell
body cell
is mutation random
yes and no
how is mutation not random
not random because certain types of mutations are favored
what types of mutations are favored
transitions are more common than transversions, even though there are twice as many transversion mutations
transitions
mutations between A and G or C and T (purine to purine, pyrimidine to pyrimidine)
transversions
all other mutations
how is mutation random
fitness effects of mutations are truly random
how is fitness effects of mutations truly random
organism isn’t more likely to evolve beneficial mutations b/c of a strong selective pressure (but selection will act if a mutation is beneficial)
when will selection act
if mutation is beneficial
HOWEVER; what’s up w/ mutational hotspots
mutational hotspots may make adaptation more likely if a mutational hotspot lies within a locus w/ important function
non genetic inheritence
epigenetics
epigenetics
study of changes in expression of genes
what is non genetic inheritance
form of inheritance that does not require changes to DNA
what is expression
transcription of DNA into RNA; first step of formation of protein
what can prevent genes from being expresed
methylation and histone modification of DNA
can these methylation and histone modifications be inherited
yeah
are these non genetic inheritance long term??
not rlly for long term evolutionary chage
