evolution exam 4

gene flow

transfer of genetic material between pops

migration, pollen, horizontal gene transfer

gene flow/migration allele frequencies

1. calculate initial (pre-migration) genotype/allele frequencies

2. calculate post migration genotype/allele frequencies based on # of migrants and their genotype frequencies

continent-island model

assume one way movement from a large population to a smaller population on an island

continent-island migration equation

frequency of A1 on island = p

frequency of A1 on continent = p_m

proportion of island pop who are migrants from the continent (migration rate) = m

frequency of A1 on the island after migration = p^*

p^*= mp_m + (1-m)p

change on island from one generation to the next

Δp = p^* - p = mp_m + (1-m)p-p

Δp = m(p_m-p)

equilibrium

allele frequency on the island will be the same as it is on the continent

p = p_m

clines

continuous change in allele frequency in space 

hardy-weinberg principle

allele/genotype frequencies in a population will remain the same from one gen to gen in the absence of other evolutionary influences

gene flow homogenizing populations

1. gene flow includes exchange of alleles

2. equalization of frequencies across different populations

3. counteracting divergence like genetic drift and natural selection

F_ST , allele frequencies and variance

F_ST = 0 means no genetic differentiation between populations (interbreeding and share genetic material)

F_ST = 1 means complete genetic differentiation (pops are completely isolated, share no genetic diversity) 

dispersal reasons

ephemeral (TW) habitat

get away from relatives (competition or inbreeding)

no dispersal

not possible

no suitable habitat

energetic costs

random factors in evolution

1. mass extinction

2. mutation

3. genetic drift

mass extinction

results from random occurrences (asteroid and volcanoes)

mutation

random process that gives rise to new alleles each generation at constant rate

adds allelic diversity; affects alleles frequencies at a given locus

genetic drift

random changes in allele frequencies or genotypes within a population due to sampling from a limited population

reduces allelic diversity; affects allele frequencies at all loci in the genome 

why does a genetic drift happen?

population are not infinite, sampling error randomly changes allele frequencies

does genetic drift work better in small or larger pops?

it is faster, more efficient small pops

with more time, it can be drastic in large pops

can genetic drift fix/lose alleles

in the absence of other evolutionary forces, drift causes the eventual fixation or loss of allele

the probability that an allele will eventually go to fixation is the same as the frequency of that allele in the current pop

allele fixation probability equation

N = pop size

2N = number of alleles at locus A 

x = initial number of copies of A1

what is the probability any 1 copy of these alleles will go to fixation? = 1/2N

what is the probability that allele A1 will go to fixation? = x(1/2N) = x/2N

equations for proportion of frequencies after generations

H_g+1 = H_g (1-(1/2N))

H_g+1 = expected heterozygosity in next gen

H_g = observed heterozygosity in current gen

H_t = H₀ (1-(1/2N))^t

effective population size (N_e)

smaller than census size

fewer individuals contribute to next generation’s genes than could

bottleneck effect

drastic reduction in the pop size due to random event, leaving a small sample of alleles left

founder effects

if a pop is founded by a smaller group of individuals, chance alone causes different allele frequencies in the new  population

gene flow vs genetic drift

opposite effects on allele frequencies: drift lowers diversity and gene flow increases diversity

gene flow makes pops more similar to one another; drift makes them different

estimate allele frequency variation across populations

F_ST = (H_et - H_es)/H_et

H_et is expected total heterozygotes

H_es expected heterozygotes from combined subpops

understand the balance between migration and drift

F_ST = 1/(4N_em+1)

N_em = ((1/F_ST) -1)/4

discrete genetics

traits with a limited number of phenotypes that fall into distinct categories

ex one gene with 2 alleles 

quantitative traits

combined effects of many loci produce quantitative traits and a continuous distribution

standard quantitative genetic model

framework for understanding complex traits influenced by many genes and the environment

quantitative genetics

statistical analysis of traits controlled by many loci

S, selection differential

trait mean of pop after selection - trait mean of pop before selection

quantifies how trait distribution of the current population is affected by selection

R, response to selection

R=S x H²

quantifies the difference between the phenotypic distribution of the original population and the next generation

how to measure heritability?

1. common garden experiment

2. parent offspring regression and slope line

heritability range

H²=0 means no heritability

H²=0.5 means little heritability 

H²=1 means strong heritability 

quantitative trait loci (QTL)

regions of the genome that affect a quantitative trait

finding QTL’s

1. identify 2 pops with differing traits

2. cross the pops, then cross F1 offsprings to get F2 hybrids 

3. genotype individuals at molecular markers along the chromosomes, correlate genotypes with phenotype

4. QTL’s have a strong correlation with the trait of interest

genome-wide association study (GWAS)

similar to QTL, but looks at variation within a population and requires a large sample size

hardy-weinberg assumptions

no selection

effects of natural selection on allele/genotype frequencies

advantageous alleles become more common

disadvantageous alleles are less common

how do heterozygotes impede evolution?

natural selection, recessive deleterious alleles hide in heterozygotes

slows as fixation approaches

mutation-selection balance

conditions under which the mutation rate at a given locus = the strength of selection against deleterious alleles at that locus

majority of new mutations are weakly deleterious

natural selection in large populations will remove deleterious mutations

equilibrium frequency

state of allele and genotype frequencies in a population that remain constant from one gen to gen

equilibrium frequency of a deleterious allele, q

q=Mu/s

Mu is mutation rate (directly proportional)

s is selection (inversely proportional)

gene flow and selection

gene flow can hinder local adaptation by swamping a pop with alleles that are beneficial in other environments but not the current one. If selection isn’t strong enough, gene flow prevents good alleles from reaching high frequencies

genetic drift and selection

when genetic drift is the stronger force, alleles are eventually lost/fixed (s<1/4Ne)

when selection is stronger, beneficial alleles rise to high frequency and deleterious stay low (s>1/4Ne)

primates:

most recent common ancestor of all primates lived 80MYA

stereoscopic color vision, large brain

new world monkeys

platyrrhine

prehensile tail, flat nosed

old world monkeys

catarrhine

non grasping tail, downward facing nose

hominoidea (apes)

split from the old world monkeys 28-30 MYA

no tail

large brains

erect posture

hominidea (great apes)

elongated skulls

short canine

enlarged ovaries/mammary glands

orangutans (Pongo)

bornean, sumatran, tapanuli

gorillas (Gorilla)

western, eastern

lives in small groups led by male silverback

males 2x size of females

chimpanzees (Pan troglodyte)

extensive tool use

extended child care

prolonged adolescence

poly (promiscuity) and highly social

Bonobos (Pan paniscus)

less violent than chimps

female form hierarchy

tool use

which apes are most closely related to humans?

chimps and bonobos

split 5.5 million years ago

human -like history

bipedal (evolved to walk and run)

large brains

language, culture 

evolution of human features

1. bipedal

2. larger brains and smaller teeth

homo evolution

1. australopithecus

2. homo habilis

3. homo erectus

4. homo sapiens

hominin

any species more closely related to humans than to chimps

progressive evolution

linear path and directional process of evolution

evolutionary radiation

taxonomic diversity of a lineage from common ancestors and new species, ecological niches

ardipithecus ramidus

chimp-like traits: long arms and fingers, grasping feet, long snout

human-like traits: open pelvis, small canines, neck attached to bottom of skulls 

adapted for bipedal walking and arboreal life

early hominin species

australopithecus africanus, australopithecus afarensis, kenyathropus platyops

Lucy

Australopithecus afarensis

3 MYA

lack of splayed big toe

mix of traits for walking and climbing 

appearance of Homo

2.5 million years ago, transitional hominins in Africa

larger braincase, flatter face, stone tools, greater height, longer legs

migration out of Africa

migration out of Africa 1.7 mya

first migration out of Africa did not include the modern human lineage 

the wanderers

fossils of first human ancestors to trek out of africa reveal primitive features and brutal way of life

Homo erectus

built for walking and endurance running

first hominin to leave Africa and colonize Europe/Asia

how long ago did modern humans exist

0.2 million years ago

two hypotheses for transition from archaic to modern humans

1. african replacement

2. multiregional evolution

african replacement

“out-of-africa”

-Homo sapiens evolved in africa

-replaced all other congeners worldwide without gene flow 

multiregional evolution

-homo sapiens evolved concurrently in africa, europe, asia, oceania from populations of homo erectus

-gene flow among archaic and modern humans within regions 

neanderthals

found from 400,000 to 30,000 years ago

prominent brow ridge, larger bulbous nose, powerful build

denisovans

group of hominids first detected by DNA analyses

denisovan and neanderthal

all modern humans are more closely related to each other than neanderthals or denisovans

BUT ancestors of modern humans hybridized with both neanderthals and denisovans after initial expansion out of africa

is there more human genetic diversity within or across populations?

there is more diversity within pops than across

do deleterious mutation occur more often closer or farther from Africa?

deleterious mutation occurs more often the further from Southern Africa you go