Evolution Exam 3

central dogma

DNA → RNA → Protein → Phenotype

Transcription

DNA → RNA, coding region of DNA molecule is used as a template to synthesize an mRNA sequence

Translation

RNA → protein, coding information is read and translated, with the use of charged transfer RNAs, into the ‘language’ of amino acids to make a protein

Synonymous

codon changes but amino acid stays the same, accumulate freely, mostly invisible to selection

nonsynonymous

codon and amino acid change

nonsense

codon changes to a stop codon, truncating the protein, usually devastating

transitions

purine <-> purine (A <-> G) or pyrimidine <-> pyrimidine (C <-> T)

transversions

purine <-> pyrimidine (A/G <-> C/T)

frameshift mutation

when an indel is not a multiple of 3 bp, the entire reading frame shifts downstream, every codon after the indel is misread, usually produces a completely non functional protein

gene duplication

an entire gene is copied, producing two copies in the genome, one copy maintains function, the other is free to diverge or specialize (hemoglobins, hox genes, opsins)

homoplasy

identity by state but not by decent, independent evolution of similar traits, don’t share common ancestor

dS

rate of synonymous substitutions, mostly neutral, reflects mutation rate and time

dN

rate of nonsynonymous substitutions, subject to selection, can be accelerated or slowed

neutral evolution

dN/dS ratio, w=1, nonsynonymous and synonymous accumulate at same rate

purifying selection

dN/dS ratio, w<1, protein is constrained, nonsynonymous changes removed

positive selection

dN/dS ratio, w>1, protein is adapting, nonsynoymous changes favored

allozymes

only detect nonsynonymous mutations (they change protein), they miss synonymous mutations

saturation

when the mutation rate is high enough to lead to homoplasy, worse in portions of the genome with higher levels of mutation

orthologs

shared by speciation, not duplication (A1, A2)

paralogs

copies of genes that happen in the same genome (A1, B1)

homologs

gene inherited in two species by a common ancestor (orthologs, paralogs)

selectionists

all variation maintained by natural selection, balancing selection, frequency-dependent selection, etc.

neutralists

most variation is selectively neutral, persists because drift hasn’t eliminated it yet

molecular clock

if neutral substitutions accumulate at a roughly constant rate, the number of differences between two species is proportional to the time since they diverged

cladogram

a branching diagram that depicts species divergence from common ancestors

clade

a group of organisms that include the most recent common ancestor of all its members and descendants

transposable elements

majority of the human genome (about 44%)

pseudogenes

disabled former genes, evolve at the neutral rate (w=1)

c-value paradox

amount of DNA in a haploid genome, genome size does not correlate with organismal complexity

large genomes

larger cells, slower development, replicate slower, negative metabolic rate correlation with size

TEs (transposable elements)

DNA sequences that can move from one location to another. Single largest component of most large eukaryotic genomes.

Class I Retrotransposons

TEs: copy and paste, original stays; new copy added, can only increase in number, genome expander

class II DNA transposons

TEs: cut and paste, copy number stays about same, more mutagenic but don’t expand genomes as much

LINEs

autonomous (encode own proteins), use copy paste method, move on their own

SINEs

non autonomous (can’t move on own), hijack enzymes produced by LINEs

exaptation

a feature originally for one function is co-opted for a new function

TEs insertions cause

gene disruption, altered gene regulation (sometimes beneficial)

ectopic recombination

deletions, duplications, inversions, translocations

redundancy

gene duplication provides a safety net that allows evolutionary experimentation

tandem duplication

unequal crossing over, adjacent copies (hemoglobin)

segmental duplication

large segments duplicated elsewhere, hotspots of copy number variation and gene innovation, most duplicated genes are epigenetically silenced

retro duplication

mRNA reverse transcribed by LINE-1 and reinserted, no introns, often no promoter

nonfunctionalization

one copy accumulates disabling mutations and becomes a pseudo gene, other copy retains the original function, default expectation under neutral evolution

neofunctionalization

one copy gains mutations and new beneficial function while the other maintains ancestral function

subfunctionalization

ancestral functions are split between copies, both become essential and preserved by drift, original gene had multiple functions or expression domains, each copy loses some subset of those functions through mutations

gene families

globin superfamily, hox gene clusters, olfactory receptors, opsins

polyploidy

more than two complete chromosome sets. every gene duplicated simultaneously

autopolyploidy

genome duplication within a species

allopolyploidy

hybridization between species + genome doubling. hybrid gets both genes

gene balance hypothesis

selection preserves duplicates when losing one would disrupt stoichiometry

prokaryotes

horizontal gene transfer: transformation, transduction, conjugation, 80% of bacterial genes transferred at some point

eukaryotes

horizontal gene transfer: TEs transfer between distant species, bdelloid rotifers, parasitic plants

transformation

free DNA in environment → DNA uptake → into bacterial cell

transduction

DNA transfer via virus → into bacterial cell

conjugation

donor cell with plasmid DNA → conjugation pilus → recipient cell

genome evolution framework

TEs. duplication, HGT, deletion

qualitative

one or few genes with large effects (blood type)

quantitative

many genes with small effects + environment (body size, thermal tolerance, disease resistance)

central limit theorem

when many genes each contribute a small effect, the sum produces a normal distribution (bell shaped curve)

threshold traits

traits appear qualitative but are quantitative underneath, still respond to selection on the underlying quantitative liability, discrete outcome

genetic architecture

the full set of genetic properties underlying a trait, how many genes, how large each effect is, how alleles interact

oligogenic

few genes, large effects, qualitative traits, can evolve quickly via large effect alleles

polygenic

many genes, small effects, quantitative traits, evolves via many small allelic shifts

dominance

same locus, complete: Aa=AA, incomplete: Aa intermediate, over dominance: Aa>both

epistasis

different loci, effect of one gene depends on genotype at another (labrador coat color)

additive alleles

when two copies are present at a locus and this yields twice the phenotypic effect

pleiotrophy

one gene → multiple traits, a gene affecting body size may also affect metabolic rate, fecundity, longevity, creates genetic correlations

polygenic inheritance

many genes → one trait, ex. human height

Vp

phenotypic variance, total spread of phenotypes in the population

Vg

genetic variance, due to genetic differences among individuals

Ve

environmental variance, due to environmental differences experienced by individuals

Vg= Va + Vd + Vi

genetic variance = additive + dominance + epistatic

Va

additive, predicts parent-offspring resemblance, fuel for natural selections response

Vd

dominance, within locus allelic interactions, reshuffled each generation

Vi

between locus interactions, reshuffled by recombination

H2=Vg/Vp

broad sense heritability, useful for clonal organisms or inbred lines

h2=Va/Vp

narrow sense heritability, predicts response to selection in sexually reproducing organisms

Va changes

h2 changes when: new mutations, migration, drift, selection alter additive variance

Ve changes

more variable environment: Ve increases → h2 decreases, more uniform environment: Ve decreases → h2 increases

R=h2 x S

breeders equations

R

response to selection, change in population mean phenotype across one generation

h2

narrow sense heritability, proportion of Vp that is additive genetic

S

selection differential, mean of selected parents minus overall population mean