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Genetics > Johnno Martini - Human evolution and pop genetics > Flashcards

Johnno Martini - Human evolution and pop genetics Flashcards

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Biology 101 flashcards
1
Q

What is population genetics?

A

A component of genetics that describes and measures genetic variation within and between population

  • Studies how variation arises - new variation from mutation, recombination and migration
  • Studies patterns of differential reproduction of genotypes from mating patterns, fertility and survival of individuals of different genotypes
  • Then proposes mechanisms and derives models to explain these processe
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2
Q

What are the assumptions of HW principle

A
  1. No selection
  2. No mutation
  3. Closed population - no migration
  4. Large population - random events play no part
  5. Random mating - zygotes formed by random union of gametes

Consequences:

  1. Allele frequencies don’t change over time
  2. p2+ 2pq+q2 = 1
  3. Genotype frequencies don’t change over time
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3
Q

HW equilibrium

A

H (heterozygote) must always be greater than at least D (dominant) or R (recessive)

p = D +1/2H

q=R +1/2H

Can only be assumed with codominance or heterozygoes can be recognised another way

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4
Q

Calculating allele frequencies

A

= homozygote frequency plus half the sum of the appropriate heterozygous genotypes (may be more than 1 in the case of multiple alleles)

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5
Q

Inbreeding definition

A

A greater frequency of mating between relatives than expected on the basis of random mating

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6
Q

What is ‘Identity by descent’?

A

Allele inherited from the same parent is passed on by both F1 offspring to the homozygous F2 individual

Probability of this occurring = Inbreeding coefficient = F

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7
Q

What is copy number variations (CNVs)?

A

Form of structural variation of DNA of a genome that results in the cell having an abnormal or normal variation in the number of copies of one or more sections of DNA

CNV accounts for 13% of human genomic DNA

Ranges from 1kb to several megabases

CNVs contrast with SNPs which only affect 1 nucleotide base

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8
Q

What is the Histocompatability leucocyte antigen (HLA) complex?

A

Series of loci that determine antigens on cell surface of white blood cells

Group of gene on Ch. 6

3 major classes:

  1. Class I: HLA-A, HLA-B, HLA-C
  2. Class II: HLA-D - with variants, relevant to Insulin dependent diabetes mellitus
  3. Class III: encode components of complement system
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9
Q

Autosomal dominant disease - Huntington

A

Assume A2 = disease allele

A2 allele would be rare so frequency of homozygous A2A2 is extremely low. Most affected individuals will be heterozygotes

Affected = a = 2pq + q2

Unaffected = 1-a = p2

Frequency of A2 =1/2a

Frequency of affected indivudals = 5x10^-5

Frequency of q= 2.5 x 10^-5

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10
Q

Autosomal recessive - cystic fibrosis allele calculations

A

Homozygous recessives A2A2 affected (a)

Heterozygotes + homozygous A1A1 = 1-a

Assume q2=qa, q=square root of a

100x more mutant CF alleles in heterozygotes than present in affecteds

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11
Q

Sex-linked recessive disease - allele calculations

A

Only look at males - hemizygous for normal and affected

a= affected

1-a= normal

Disease allele= A2=q=a

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12
Q

Why do populations deviate from HW equilibrium?

A
  1. Mutation
  2. Non-random mating
  3. Selection
  4. Population size
  5. Modern medicine
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13
Q

Mutation in HW

A
  • Recurrent mutations are most important - alleles of a gene aare in selection/mutation balance
  • Many human diseases are result of recent mutations in human lineage, but may be shared with primates
  • Most newly arising mutations are recessive
  • 1200 recessive disease genes, 1/3 CNV related
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14
Q

Non-random mating/inbreeding in HW

A
  • D=p2 + Fpq
  • H=2pq-2Fpq
  • R=q2 + Fpq
  • Inbreeding alone does not change p and q - it only affects genotype frequences of D, H and R
  • F=0 = HW frequencies, no inbreeding
  • F=1: H=0
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15
Q

Selection in HW

A
  1. Mutation/selection balance: frequency of affected individuals reflects the relative rates of introduction of new mutant alleles by mutation and their removal by selection
  2. If heterozygotes have normal fitness –> deleterious alleles shielded by selection and slows loss of allele from population
  3. Heterozygote advantage: maintain both alleles even though 1 homozygote may be deleterious
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16
Q

Population size in HW

A

Effect comes from random events in small populations

e.g. founder effect or bottleneck - by chance an abnormal allele is present more commonly in founders/survivors than it would be in larger population

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17
Q

Modern medicine in HW

A

Affected individuals treated successfully to reach reproductive age- mutant allele seen at higher frequency

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18
Q

Reasons for frequencies of deleterious alleles - mutation/selection balance

A

e. g. Achondroplastic dwarfism
* Homozygous AD is lethal

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19
Q

What are the 2 categories of mutations that confer an advantage?

A
  1. Confer prenatal advantage
  2. Confer a mating advantage
20
Q

Prenatal advantage

A

50% of conceptions result in miscarraige

e.g. Insulin-dependent diabetes mellitus (IDDM/juvenile diabetes)

5-6% of offspring with diabetic fathers developed IDDM, only 1-2% from mothers

21
Q

Risk factors for IDDM

A
  • Most important risk factor is DQ allele
  • Effect on intra-uterine survival demonstrated using DR alleles - haplotypes DR3 and DR4
  • Mothers preferentially transmitted DR3, fathers preferentially transmitted DR4
  • Embryos carrying Dr3 or DR4 were more likely to be carried to term

OTHER ADVANTAGES:

  • Interactions between cell surface antigens in placental wall and embryo cause dilation of uterine blood vessels to provide better blood flow to embryo
22
Q

Genes involved in premature birth - follice stimulating hormoen receptor gene

A

Potentially: having smaller fetus was more advantageous when transiting birth canal

23
Q

Mutations conferring mating advantage

A

e.g. Huntington disease

Not affected until after reproductive stage

Frequnecy of HD actually increasing

Advantage: they produce more offspring than their normal siblings

  • Initially thought to be more sexually promiscous
  • Recently suggested HD elevates carrier’s immune activity
24
Q

Heterozygote advantage - CF

A

Mutations in cystic fibrosis transmembrnae conductance regulator (CFTR) gene = chloride channel

  • Most common lethal genetic disease - 1/2000 live births
  • Most mtuant alleles are deltaF508 (70%)
  • Allele arose once and dispersed - polymorphism

Theoretical advantage of 2%

Advantages need to account for why heterozygotes would not be equally advantageous in non-Caucasian population

  • Non-caucasian populations are largely tropical - need sweat production
  1. E.coli heat-stable eneterotoxin - diarrhoea related diseases
  2. Heterozygotes for deltaF508 less prone to asthma
  3. Favoured = resistance to typhoid fever, bacterium cannot enter cells except if at 26C (lack of advantage in tropical areas)

BUT CHOLERA NOR TYPHOID KILLED enough to account for maintenance of the allele

  1. TB - deaths in Europe only, carriers do not produce nutrient required by tuberculin bacillus
  2. CF heterozygous males may have higher fertility –> more offspring and more male offspring
25
Q

Founder effect - amish in USA

A

e.g. Pennsylvania Amish - established by 3 couples

Disease= Ellis-van Crevald dwarfism: extra digits

Initial frequency: 1/12

Frequency falling but not yet normal frequency

26
Q

What are the 2 groups of monkeys?

A
  1. Platyrrhine monkeys (New World): forward facing nostrils, 3 premolars, strong prehensile tails (used to hold objects)
  2. Catarrhine monkeys (Old World): downward pointing nostril, reduced teeth, weak tail
  • Separation of groups occurred in Early Cretaceous period
27
Q

Ardipithecus ramidus

A

Common features with chimpanzees, but ancestral to humans rather than all hominids

  • Showed adaptations for bipedalism
28
Q

Possible phylogeny of humans/bonobos/chimps

A

a) trichotomy - all 3 genera arose at same time
b) chimpanzees arose from common line with gorilla
c) champanzees could be on common line with humans

29
Q

Australopithecus species

A
  1. A.anamensis: upright walking but spent much time in trees
  2. A.afarensis: Lucy - definitely bipedal
  • Ancestor of robus Australopithecines = Parnthropus (3 species)=side branch of hominid evolution
    3. A. africanus: human-like pelvis, bipedal, upper body was ape-like (more time in trees than afarensis), reduced tooth size, increased cranial capacity
    4. A.sediba: some claim should be Homo
30
Q

Homo genus

A
  1. H.habilis: reduced tooth size, increase cranial capacity
  2. H. rudolfensis: existed alongside habilis (variant of habilis based on jawline?)
  3. H. erecturs: taller, small teath, increased brain size, sexes are same size, travelled into Europe and Asia
  4. H. sapiens -1370cc, reduction in skeletal robusticity

H. antecessor: early European fossils

H. rhodesiensis: African material

31
Q

Molecular phylogenies

A
  • Mt DNA: humans intermediate betweenn 2 great ape genera
  • Y-linked or non coding: human and chimp lineages more recent than gorilla
32
Q

Problem of allele-sorting

A

Gene tree not necessarily same as species tree

  • Minimise problem by using several sequences for each taxon
  • When a population is polymorphic for diff alleles, alleles will show phylogenetic relationships
  • Instances of incomplete lineage sorting –> wrong phylogenetic analysis
33
Q

Reasons for controversy with human evolution

A
  1. Fossils are fragmentary - difficult to determine what species and age
  2. Research not often carried out in unbiased manner - manufactured evidence e.g. Piltdown Man in England
    • Similarities between Neanderthals/denisovans and humans can be explained by incomplete lineage sorting, rather than matings, but not appealing to public and granting authorities
34
Q

Origin of modern humans

A

H.erectus migrated out of Africa - possible originated in Asia and migrated back to Africa

3 possible models

  1. African replacement
  2. Hybridization/assimilation
  3. Multiregional evolution
35
Q
  1. African replacement hypothesis
A

= Out of Africa

  • Previously existing populations in Europe/Asia were replaced by migration of Homo sapiens from Africa
  • H.erectus was REPLACED by humans
  • Arose from analysis of mtDNA haplotypes
  • Expect all modern humans to have characteristics more similar to archaic African specimens than to archaic specimens from other parts of the world
  • Measurement of skulls supports AR model
36
Q
  1. Hybrdization/assimilation model
A

Modern humans migrated out of Africa subsequent to sprad of H. erectus and neanderhtalensis but there was HYBRIDIZATION between the species

37
Q
  1. Multiregional model
A
  • Preexisting populations descended from H.erectus evolved into H.sapiens independently in various region
  • Interbreeding between individuals from various regions gives uniformity to modern Homo sapiens
  • Expect modern skulls to resemble archaic specimens from same local area
38
Q

Tests for hypotheses (mt DNA)

A

Deepest branch is in African populations - supporting AR

Mitochondrial eve? - simplistic if even true

  • mtDNA is haploid - ancestral lines will have been lost, only seeing those that survived
39
Q

Mitochondrial selection

A
  • Populations in cooler climates have lower mitochdonrial diversity
  • Greater the difference in minimum temperature - the greater the genetic differentiation
  • Differentiation only shown for mtDNA not nuclear
  • Non-synonymous point mutations in ND3 and ATP6 genes show correlation with temperature - haplotypes with these mutations are selected where temperature is lower
40
Q

Y chromosome sequences

A

Migrated out of Africa and then BACK to Africa e.g. Khoe-San distribution

41
Q

Neanderthal

A

150-30 000 years ago

  • Lived in Denisova caves
  • Side branch of human evolution that separated 400,000 years ago
  • Disappeared 30-40,000 years ago
  • Hybridization between Neanderthals and modern humans, but after H. sapiens had left Africa
  • 1-4% Eurasian genomes come from Neandertals (incomplete lineage sorting?)
  • 40% higher in East Asians
42
Q

Perry’s Y chromosome

A
  • Haplotype older than existence of modern humans
  • Hybridization brought it into human lineage in Cameroon?
43
Q

Denisovans

A
  • May have existed same time as Neadnertals - distribution narrowly overlapped, may have occupied Denisova at same time
  • Denisova - Southern Siberia
  • Unique upon completion of mtDNA sequencing
  • Descendant of early Homo species that had survived to be contemporaneous with humans and neandertals
  • Not formally described
  • Traces of Denisovans in some human populations e.g. Indonesia, New Guinea
44
Q

MUNGO MAN - Australia

A
  • 40,000 year old skeleton of gracile human
  • Some aboriginals are direct descendants of earliest arrivals
  • Had a sequence not found in mtDNA - but relatd to insert of mtDNA into nuclear DNA (nuclear mt sequence) of Ch. 11
  • No genomic data available
45
Q

Where in Africa did humans originate?

A
  • Originally thought to be Southern Africa
  • Later found to be East and central Africa - South Africa is sink of variation from later migrations
46
Q

Bantu farmers

A

Moved east and south from their original homeland

47
Q

MtDNA of prehistoric hunter-gatherers and farmers

Did hunter-gather populations gradually take up agriculture or was it early farmers themselves that migrated?

A

Most of ancient hunter-gatherers share mt types taht are rare in central europeans today

Modern Europeans show mix of:

  1. farmers of near Eastern origin
  2. West-European hunter-gatherers
  3. Ancient north Eurasians
  • Most likely first farmers migrated into area

Genetics (3 decks)

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