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Genetics Flashcards

1
Q

briefly outline previous findings on genetic evidence for human diversity

A
  • Evidence for Out of Africa through mtDNA (Cann, Stoneking, Wilson 1987)
  • Dating of human/chimpanzee divergence time (first Sarich and Wilson 1967)
  • Identifying new ancient hominins and resolving our relationships with them (e.g. Denisovan full genome, Meyer et al 2012)
  • ‘Seeing’ genetic evolution through selection studies
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2
Q

Outline Darwins contributions to genetics

A
  • Evolution by natural selection in The
    Origin of Species (1859)
  • Requires- heritable variation in reproductive success
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3
Q

Outline historical models on how inheritance occurs

A
  • Preformatism, 17th-18th century- ovists vs spermatists
  • Blending, 19th century – mix of maternal and paternal
  • Darwin- Pangenesis (1868)- gemmules generated by body parts continuously- migrate to gonads, develop into cells/organs they were from
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4
Q

Outline Mendel’s contribution to genetics

A
  • Experimental, breeding peas, from 1856-1863 (>30k plants)
  • Published in 1866
  • Suggested discrete units of inheritance. ‘Particulate inheritance’ where discrete units (genes) control for discrete traits
  • genes come in different forms (alleles)- not blended inheritance (as would have semi wrinkled rather than wrinkled or smooth)
  • principle of segregation- One pair of genes per individual (diploid), the two gene copies in the parent segregate during reproduction, with one random copy being passed on by each parent
  • idea of dominant and reccessive traits
  • law of independent assortment- Traits are inherited independently of one another (but sometimes linkage)
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5
Q

Outline Galton’s/Fishers contributions to genetics

A
  • Conflict (?) between ‘complex’ traits like height – individuals follow the average parental height, blending
  • Fisher (1918) showed that Mendelian inheritance consistent with biometric observations
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6
Q

List ‘classic’ results in population genetics

A
  • Hardy-Weinberg equilibrium (1908)
  • R. A. Fisher on Mendelian traits (1918)
  • J. B. S. Haldane (A Mathematical Theory of Natural and Artificial Selection, 1924-1934)
  • S. Wright (e.g. Evolution in Mendellian Populations, 1931)
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7
Q

Outline the catch up of cell biology with Mendelian genetics

A
  • 1869: Miescher named a
    chemical found in nuclei of cells - nucleic acid
  • 1880s: Weismann proposed that bodies in cell nuclei called chromosomes were the basis of Heredity
  • 1953: Watson, Crick, Franklin, Wilkins elucidated structure of one of Miescher’s nucleic acids, DNA
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8
Q

Outline the basic elements of DNA

A
  • DNA: deoxyribonucleic acid Nucleotides: A, C, G, T
  • Base pairing = purine (adenine or guanine) + pyrimidine (thymine or cytosine)
  • Semi-conservative replication – after replication, each new double helix is formed of one original strand and one new one
  • Mistakes can happen during replication, leading to variation
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9
Q

Outline the genome

A
  • definition- total DNA content of a cell
  • ~3.2bn base pairs per genome copy
  • Two genome copies in most human cells (‘diploid’ = two copies of each chromosome, ‘haploid’ = one copy)- exceptions are germline cells (sperm, egg; haploid), some somatic cells e.g. hepatocytes in the liver can by polyploid (>2 genome copies/cell)
  • Split into 22 pairs of autosomes and 1 pair of sex chromosomes
  • Haploid n = 23, diploid 2n = 46.
  • Also many mitochondria in cells (1-2.5k per cell, ‘power plants’ of the cell), each with several copies of mtDNA (mitochondrial DNA)
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10
Q

Outline the chromosomes

A

Autosomal chromosomes (22 pairs):
* Vary in length (47-249 Mb)
* Inherit one copy from each parent

Sex chromosomes (1 pair):
* X and Y, genetic sex determination
* XX (genetically female) and XY (genetically male);
rarely, other karyotypes, often with health impacts
* Y = paternal inheritance, passed from father to son
* X = female-biased inheritance, mother passes on one
and father does to XX females

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11
Q

Outline mitochondrial DNA

A
  • Short, 16,569 bp circular chromosome
  • 1000s of near-identical copies per cell
  • Maternal inheritance ~only
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12
Q

Outline the function of the genome

A
  • carries ~20,000 protein- coding genes.
    These are transcribed into mRNA and then translated into proteins, with some intermediate steps (e.g. splicing, which determines which exons are translated, can lead to alternative protein isoforms; protein folding)
  • The Central Dogma (Crick 1958) states that information (here, the sequence code) cannot be passed on by proteins. Simplified to DNA -> RNA -> proteins
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13
Q

outline translation/coding

A
  • Translation occurs amino-acid by amino-acid, with each DNA triplet (codon) coding for an amino acid
  • The coding is redundant – multiple codons code for the same amino acid
  • The universality of this code among living organisms is proof of the common ancestry of all life
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14
Q

Outline the composition of the human genome

A
  • Only 1.5% of the human genome is protein- coding (exons)
  • introns make up rest- thought to be under evolutionary constraint (biological role), some can affect gene regulation
  • E.g. the ENCODE 2012 project estimated that 80% of the genome is biochemically active and therefore might have some impact on gene regulation
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15
Q

Outline the link between genome size/complexity and organisms

A
  • Human do not have particularly big genomes, but there are broader trends – e.g. eukaryotes, and especially vertebrates, have larger genomes.
  • more ‘complex’ organisms have relatively more non-coding DNA- complex regulation may be especially important
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16
Q

Outline genetic mutations, including types

A
  • ‘Random’ – but the rate of mutation varies along the genome (1.25e-8 / bp / generation)
  • somatic (not carried in germ cells- rusk varies on when ind development occur, cancer is risk) and germline (all tissues and in half of gametes)
  • Allows novelty in evolution, divergence between species, variation among individuals
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17
Q

Outline types of genetic mutations

A
  • indel- insertion/deletion
  • point- creates SNP (single nucleotide polymorphism)- can be synonymous or missence), or nonsense (stop)
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18
Q

Outline a particular area of new diversity due to mutations

A
  • short tandem repeats- STRs (micro satellites)- short repeats of DNA motif that occur sequentially
  • These mutate quickly by adding or losing repeats due to ‘slippage’ during meiosis
  • Due to the high mutation rate they are very diverse, and are used extensively in forensics and for paternity testing
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19
Q

Outline structural genetic mutations

A
  • can remove, or duplicate, many genes at once
  • can have profound phenotypic impacts
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20
Q

Outliene 2 examples of effects of genetic mutations

A
  • MC1R gene: switch from dark to red melanin- Recessive inheritance, several different non-synonymous variants in Europe causing varied degrees of loss of function,
  • Caspase 12 gene: various immune functions, e.g. truncated form increases risk of mild bacterial infections but decreases risk of sepsis, truncated form at high frequency, especially
    outside Africa
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21
Q

Outline regulation (mutations)

A
  • Changes can also be how much protein you make; when the protein is made (in utero, childhood, adulthood; certa times of day or year); and where the protein is made (e.g. brain and gut but not lungs)
  • Cis regulation: variation impacting regulation in nearby genes
  • Trans regulation: variation impacting expression/function of protein products that in turn regulate other usually distant genes
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22
Q

Outline recombination

A
  • refers to when a segment of a chromosome is swapped between the two chromosome copies of an individual
  • Occurs during meiosis
  • Quite frequent (e.g. over the genome, average 41.1 in mothers and 26.4 in fathers / meiosis, Chowdhury et al 2009)
  • Average rate ~1/100Mb, but huge variation creating ‘recombination hotspots’ – sometimes with 1000x the average genome-wide rate
  • mtDNA and the majority of the Y chromosome don’t recombine
  • less frequent between genes that are nearby on a chromosome (linked)
  • Distant genes are inherited more independently (more like genes on different chromosomes)
  • non-random association of alleles at different loci is called ‘linkage disequilibrium’ (LD)- High LD suggests genes are close each other on a chromosome
  • Recombination mixes up the code on copies of a chromosome creating new combinations of variants – new haplotypes. But not new variants (in itself)
  • considered a major evolutionary advantage of sex because it breaks up associations e.g. if a chromosome has one gene version that is very bad for survival and a different gene that is very advantageous, recombination breaks up the association so selection can act independently
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23
Q

Outlien diversity in the human genome

A
  • approximately 20 million base pairs will differ between ones 2 human genomes copies
    These are caused by 3.5-4.5 million single nucleotide polymorphisms (SNPs), which impact one base pair; 5-600k indels; and significant numbers of larger deletions
  • each carry more than 100 ‘dead gene’ copies. Most LoFs are heterozygote, i.e. with one good copy intact, but some that impact non-essential genes are homozygous (brackets)
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24
Q

When is a gene called essential, how many instances of this are there in the human genome

A
  • when the loss of its function compromises viability of the individual (for example, embryonic lethality) or results in profound loss of fitness
  • ~ 3,000 human genes cannot tolerate loss of even one of the two gene copies (haploinsufficiency) (Bartha et al. 2018)
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25
Q

Outline the nature/history of data regarding human genome sequencing

A
  • Human genome project – started sequencing 1990, main publications in 2001, ran until 2003- cost approx 3b fr one genome
  • then cost rapidly decreased- in 2022, average of $525
  • lead to massive fats increase- ENA – European Nucleotide Archive
    21.3 trillion bases, equivalent to ~6.7k human genomes, SRA – Sequence Read Archive
    ~73,700 trillion bases, equivalent to >23m human genomes
  • if stored UK population, would be 13 exabytes
  • Huge challenges – physical storage, data sharing, bioinformatic processing, data analysis.
  • also issue with Privacy and ethics: who can access, for what? Who ‘owns’ the data? Security?
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26
Q

What is a holotype

A

a set of linked variants

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27
Q

diagram of what genome data looks like

A
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28
Q

Ape phylogeny diagram

A
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29
Q

outline genetic divergence in the great ape phylogeny

A
  • Humans and chimpanzees/bonobos: 98.8% sequence identity =120 differences/10,000 base pair
  • Humans and Neanderthals: 99.87% =13 differences/10,000 base pair
  • Two Yoruba individuals (West Africa): 99.9% =10 differences/10,000 base pairs
  • Two French individuals (W-Europe): 99.93% =7 diffferences/10,000 base pair
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30
Q

Outline genetic divergence in the great ape phylogeny in relation to time

A
  • Mutations build up over time- suggests greater average genetic divergence = more time- Split dates estimated from
    genetic divergence
  • However, ‘Molecular clock’ assumption – not always valid- assumes mutation rate is the same, generation time is the same, selection (e.g. removing damaging variants) is the same
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31
Q

Outline the link between genetic diversity and genetic divergence

A
  • Genetic diversity and genetic divergence are connected – greater divergence within group means it has greater diversity
  • Average divergence between individuals from same human population. E.g. French ancestry individuals differ at ~0.07% of the genome while Yoruban (from Nigeria) ancestry individuals differ at ~0.10% of the genome
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32
Q

outline Human-chimp functional divergence

A
  • Humans and chimpanzees show ~98.8% sequence identity
  • share >99% of our ~20,000 genes.
    Human and chimps have –
  • ~35m SNP differences
  • only 100k exome differences
  • only 40k amino-acid changing
  • another ~3% structural variations (deletions, insertions, inversions)
  • Half on the human lineage, identify using an outgroup (orang-utan or gorilla)
  • Most of the genome can be aligned (coloured regions on right), but some is hard to sequence (white) or align (colour mismatches)
  • Human Chromosome 2 is the result of the fusion of two chimpanzee chromosomes (usually called 2A and 2B) that happened millions of years ago
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33
Q

Outline a study into the effects of Human-chimpanzee functional genetic divergence

A

Nielsen et al, 2005:
- comparison of 13,731 human genes with their chimpanzee orthologs (genes with common ancestry through speciation), 35 showed excess of non- synonymous changes
- many mutations don’t change the amino acid (synonymous), calculate the proportion of n.s. and s. differences, ask if high relative to expectations
- Biological process categories (e.g. Gene Ontology/GO Term enrichment) with an excess of putatively positively selected genes were immunity and defence, Gametogenesis / fertilization / sperm motility, and Chemosensory perception / olfaction

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33
Q

outline suggestions for explanations of Human-chimpanzee functional genetic divergence

A
  • may be that more protein changes suggest positive selection e.g. in testes for fertility/sperm competition
  • or, could just indicate less purifying selection- e.g. sex-specific genes only expressed in one sex, so invisible to evolution half the time and less selection?
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34
Q

Outline a common location of human-specific mutations in the genome

A

Pollard et al (2006):
- many short DNA regions that are conserved in other animals with many derived mutations
- human accelerated regions (HARs)
- most HARs not in exon - suggests functional roles may be in gene regulation
- many in genomic regions with many genes involved in neurodevelopment.
- Positively selected regulatory roles?
- But many HARs in regions with high recombination rate, bias toward A/T to G/C mutations- could suggest runaway feedback in a specific mutational processes (‘GC-biased gene conversion’), causing many mutations

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35
Q

Outline recent work on HARs

A

Keough et al, 2023:
- ~30% of HARs are nearby human-specific structural variants that change local gene regulation interactions
- pressure for these HARs to adapt to new regulatory interactions may drive rapid divergence.
Note: HARs are by definition ‘unsual’ genomic regions, and different HARs may have different explanations (adaptive regulatory effects vs neutral mutation properties)

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36
Q

Outline examples of Genes involved in human-chimp phenotypic divergence, aside from language and neurodevelopment related ones

A
  • HACNS1 (a HAR)- involved in limb and digit development, precise phenotypic impacts not fully clear
  • Human-specific growth hormone receptor 3rd exon deletion (GHRd3) associated with birth weight, life history traits – hypothesized also enabled ancestors to survive extreme malnutrition
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37
Q

Name an example of a involved in human-chimp phenotypic divergence- LANGUAGE

A

FOXP2

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38
Q

Outline research into FOXP2

A
  • Lai et al, 2001- FOXP2 mutations in a family with language disorders
  • Enard et al, 2002- FOXP2 has human- specific non-synonymous mutations (but long gene- 603kb (vs 24 median)- suggests strong likelihood of mutations
  • Enard et al, 2009- FOXP2-humanized mice show specific changes in dopamine levels, neuronal morphology, synaptic plasticity in the striatum, and pup vocalizations
  • Fontenot, 2014- accelerated FOXp2 evolution in the human lineage - hub gene in a human coexpression module
  • involved in regulation of hundereds of other genes, including foetal brain development (Spiteri et al. 2007), and the lungs (Shu et al, 2007)
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39
Q

Outline dating of FOXP2 variants

A
  • variants are mostly old- Neanderthals had ‘human’ derived amino acid changing variants
  • limited evidence of recent selection in different human populations, despite possible recent additional intronic regulatory changes (Atkinson et al 2018)
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40
Q

Outline other language-gene associations

A
  • Specific language impairment loci SLI1 and SLI2 related to a child’s ability to repeat nonsense words
  • CYP19A1 mutations in humans have been found in association with dyslexia, while in other vertebrates (fish and birds) orthologs are known to be involved in sexual differentiation of the brain and the regulation of vocalization
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41
Q

Summarise fundings on language related genes involved in human-chimp phenotypic divergence

A

Human language may have qualitative differences from nonhuman primate communication, but genetic and biological basis is complex, including genes with continuity with other animals

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42
Q

List evidence for neurological-developmental Genes involved in human-chimp phenotypic divergence

A
  • micorcephaly (MCPH)
  • Brain size – DUF1220 domain
  • Brain size – NOTCH2
  • SRGAP2 and slower development
  • Neoteny and human cranial development
  • differences in expression of synaptic genes in the prefrontal cortex
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43
Q

Outline microcephaly

A
  • Small (~430 cc v ~1,400 cc) but otherwise ~normal brain, some mental impairment
  • Due to loss of activity of the ASPM gene or MCPH1 gene (among others)
  • Doesn’t imply that these genes were involved in our evolution; but genetic disorders demonstrate breadth of potential genetic impacts
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44
Q

Outline the DUF1220 domain

A
  • Many more copies in humans than other apes, association with brain size and various mental health disorders (Dumas et al, 2007)
  • Neanderthals have most copies (~350, and biggest brains
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45
Q

outline NOTCH2

A

Suzuki et al 2018-
- Human/Denisovan/Neanderthals – duplications in NOTCH2 gene
* 1q21.1 distal deletion/duplication syndrome- micro/macrocephaly
* Evolutionary duplications
* Cellular mechanisms

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46
Q

outline SRGAP2

A
  • Charrier et al (2012)- involved in delayed maturation, and therefore increased density on dendrites
  • other such examples include HYDIN2 – 3.2 MYA and BOLA2 – 0.5 MYA
47
Q

Outline overall delayed genetic development (human-chimp phenotypic divergence)

A
  • Different peak expression of synaptic genes in the prefrontal cortex- Chimpanzee and macaque, before year 1 of postnatal development; Humans, end of childhood, year 5
  • Many genes expressed later in the human brain than in chimpanzee, but this is pattern specific to the prefrontal cortex, not in the cerebellum (Liu et al, 2012)
48
Q

Outline recent research developments regarding human-chimp phenotypic divergence

A

The scale of functional work studying regulation and development is massively increasing:
* Regulation differences during brain development at single-cell scale (e.g. Khrameeva et al 2020)
* Cerebral organoid induced pluripotent stem cells (IPSCs) as model system (Kanton et al 2019)
* ‘Fusion’ IPSC organoids composed of human/chimp cells (Agoglia et al 2021)

49
Q

Summarise the integration of evidence regarding human-chimp phenotypic divergence

A

Somel, 2013:
- Likely that many genetic variants associated with individual traits (complex traits) and many genetic variants impact multiple traits (pleitropy)

50
Q

Outline heterozygosity rates in humans

A
  • humans have low genetic diversity
  • much less heterozygosity than chimps- 0.001- 1 in every 1000 sites heterozygous
51
Q

List potential factors for low heterozygosity in humans

A
  • selection effects
  • mutations
  • population size (and effect on genetic drift)
  • bottlenecks
52
Q

Outline potential impacts of selection on uniquely low human heterozygosity

A
  • if genome were under intense selective constraint as only one genetic way of being human, could reduce diversity
  • would have to apply to whole genome to impact average heterozygosity, and would need to explain low diversity in some other animals
  • most mutations selectively neutral (Kimura, 1968), as have no/very limited on phenotype- therefore not under selection
  • overall not plausible- not that unique
53
Q

Outline the rationale for the influence of population size on low human heterozygosity

A
  • frequency of variants in a population fluctuate over time
  • ultimately, all variants with eliminated, or reach extinction
  • if one heterozygous individual, 50% chance that allele lost after one generation due to random loss of diversity
  • heterozygosity lost because variants are lost/become rare
  • Bigger populations can retain more diversity as there is less genetic drift
  • alleles fixed/lost faster if smaller population size- rate of drift related to population size
54
Q

Outline the influence of mutation rate on genetic diversity

A
  • Mutation adds to diversity
  • more individuals means more new mutations per generation
  • Bigger population scan retain more diversity as there is less genetic drift
55
Q

Outline how population size can be estimated, and implications for this

A
  • can use genetic diversity to infer past population size, and compare this between species and human populations
  • assumption- all groups have same mutation rate
56
Q

Outline split dates and genetic divergence in humans compared to other apes

A
  • humans low heterozygosity- can analyse what population size required to result in this
  • split date- ~7mil ya- estimated from genetic divergence
57
Q

Outline genetic bottlenecks

A
  • period of intense genetic drift
  • sudden drastic decrease in population
  • survivors have low genetic diversity
  • leads to less diversity in next population
  • Hard to recover- need migration or new mutations
  • suggests short period of low population may be enough to loose diversity
58
Q

List possibilities for the occurrence of low population size causing low heterozygosity

A
  • long term or recent
  • all people (e.g. speciation), or just one (e.g. out of Africa)
59
Q

Outline estimations of an occurrence of a speciation bottleneck

A

Hublin et al, 2017:
- Jebel Irhoud (Morocco)
* ~300kya
* Modern facial morphology, archaic neurocranium
* Links to South African Florisbad Skull (~260ky)

Vidal et al, 2022:
- Omo Kibish
* ~233kya
* ‘Fully modern’

  • suggests signal of speciation bottleneck between 200kya and 350kya
  • upper bound- Neanderthal/human split at 500-600kya based on genetic dates (high uncertainties/hard to interpret)
60
Q

Outline if there is evidence of a speciation bottleneck

A

Prüfer et al, 2014:
- No obvious signal of speciation bottleneck
- No collapse in population size between 200-300ky where speciation ‘should’ be
- non-African bottleneck 50-150kya, but pre-dates human speciation
- Long-term low population size sometime ~0.5- 2mya- debated theory of a dramatic bottleneck 900kya (Hu et al 2023)- but predates human speciation

  • summary- some signals of low population size, but for extended period (not bottleneck)
61
Q

Outline out of Africa (genetics)

A
  • argue for a Recent African Origin of the human species followed by dispersal(s) to Eurasia that entirely or largely entirely replaced more divergent Eurasian hominins already living there
62
Q

Different out of Africa theories

A
  • Human species origin in Africa, with non-African populations originating from a dispersal <100kya
  • As above, but with introgression from local Eurasian hominins (Neanderthals, Denisovans, H. erectus?)
  • Ancient dispersal from Africa followed by gradual evolution of humans through partially differentiated but interconnected regional groups (e.g. Weidenreich 1946; some proponents in 1980s e.g. Wolpoff)
  • Ancient dispersal from Africa followed by isolation and parallel evolution of human-like traits (Coon 1962, ‘candelarbra’)
63
Q

Outline a likely possibility of explaining the occurrence of the low population size causing low human heterozygosity

A

Rosenberg & Kang, 2015:
- layered bottlenecks
- serial founder effect

64
Q

List evidence for the suggestion of serial bottlenecks

A
  • mtDNA
  • Y chromosome
  • autosomal diversity
  • full genome data
65
Q

Outline mtDNA evidence for serial bottlenecks

A
  • inherited through the female line only (mother to daughter)- short genetic locus but fast mutation rate
  • Cann, Stoneking & Wilson 1987- Non-African mtDNA diversity is a subset of African mtDNA
  • Root of the tree dated to 140-290kya based on limited data (Cann et
    al 1987)- although depends on sampling on drift
  • Full mtDNA gave root estimate of 172ky +- 50ky and expansion time
    of non-African lineages of 48ky (Ingman et al 2000)
66
Q

Outline Y-chromosome evidence for serial bottlenecks

A

Karmin et al, 2015:
- Non-African Y-chromosome diversity is a subset of African Y-chromosome on the tree
- lower genetic diversity further from Africa- autosomal DNA and Y chromosome

67
Q

Outlier evidence for serial bottlenecks from autosomal diversity

A
  • provides samples from all of our ancestry rather than just two lineages (mt = maternal and Y = paternal)
  • Analysis of trees from tightly linked autosomal loci placed 9/10 with roots in Africa (Takahata et al 2001)
  • Analysis of autosomal STR diversity showed linear decrease with ‘land bridge’ distance from Addis Ababa (Prugnolle et al 2005)- strongly consistent with serial founder effects
  • Linkage disequilibrium is low in Africa and high outside Africa (Jakobsen et al 2008) (LD higher in populations with low diversity)
68
Q

Outline linkage disequilibrium

A
  • correlation between alleles at nearby loci, broken up by recombination
  • If LD is high between loci, if observe the allele at one then, can guess the other
  • In a population with no diversity, LD is 100% between all loci
  • At maximum genetic diversity (everyone is different at every site) LD would be 0% between all loci
69
Q

Outline dull genome data support for out of Africa/serial bottlenecks

A
  • Low non-African diversity replicated in whole genomes
  • Ne inference supports non-African specific bottleneck
70
Q

Outline evidence beyond out of Africa/serial bottlenecks

A
  • Multiple archaic introgression events
  • new finds with early dates of modern humans in Greece (>210ky) and Israel (~180ky) may indicate failed and plausibly successful - China (>80ky) – early OOA dispersals
71
Q

Outline evidence of complexity within African genetic history

A
  • introgression signals in Africa (Hammer et al, 201; Lachance et al, 2012)
  • question id there are ancient Hominins, or deep African structure (Ragsdale et al, 2023), or both
  • Prufer et al, 2014- signals of population increase could reflect population growth within Africa and/or increasing connectivity of African subpopulations
  • these archaic introgression signals suggest strictest OOA models not supported- Both Neanderthals and Denisovans (and perhaps other groups) interbred with modern humans after they left Africa
72
Q

Outline the extent to which the presence of a genetic switch for being human is plausible in sight of data on diversity and timeframes

A
  • individual gene couldn’t have caused speciation bottleneck in genome-wide diversity (as evidence supports several bottlenecks)
  • Time-frame of 200-300kya if switch for modern anatomy, perhaps 50-100ky if modern behaviour
  • Any ‘switch’ genes would have undergone strong selection and become fixed in people- everyone similar vision (no diveristy)
  • recombination- diversity only low near to gene
  • population size reconstructions- based on diversity across the genomes may not detect switch signal
  • proposed models- Upper Paleolithic (e.g. Klein 2002)
73
Q

Outline if there is evidence of a genetic candidate for a genetic switch

A

Mallick et al, 2016:
- ‘time to the most recent common ancestor’ (TMRCA) of mtDNA dated to ~172kya
- Average TMRCA based on a sample of 40 diverse people is 1.5-2mya
- No genes with TMRCA <100ky- genetic diversity can be older than our species- speciation doesn’t ‘reset’ diversity
- mtDNA has an unusually recent root

74
Q

Outline the first ancient DNA sample

A
  • Higuchi et al, 1984- ~140yo museum specimen, dried muscle- 229bp of mtDNA retrieved- sequence closely related to zebra
75
Q

Outline decay/limits of ancient DNA

A
  • decay associated with humidity/thermal fluctuations (Kistler et al, 2017)
  • older DNA garder to analyse due to DNA molecule diffusion
  • affected by sample type- e.g. petrous vs cochlea
76
Q

Outline the human genetic tree

A
  • Neanderthals and Denisovans- sister taxa- diverged from modern humans ~450- 750 kya; interbred with humans (Meyer et al, 2012)
  • Serre et al, 2004 – can’t rule out up to 25% admixture- Neanderthal mtDNA could have entered human pool, but drifted to extinction
  • strong evidence for introgression from neanderthal draft genome (Green et al, 2010)
  • Europeans are genetically closer to Neanderthal than Africans, consistent with ~2% introgression (Prufer et al, 2014)
76
Q

Outline analysis of ancient hominin DNA

A
  • Meyer et al, 2016- from 430kya- nuclear DNA sequences from middle pliestocene Sima de los Huesos homininst al, 2017- neanderthal and denisovan DNA from Pleistocene sediments
77
Q

Outline denisovan ancient DNA

A

Reich et al, 2010; Meyer et al, 2012:
- Fragmentary bones- found from 1984 on in a cave in Siberia- robust
-divergent mtDNA- different to autosomal data on neanderthal clase
- Only Denisova cave and Xianhe jaw from Tibettan Plateau, but more widely dispersed in the pas
- Papuans are more similar to Denisovan than non- Papuans- may suggest introgression

78
Q

Outline Sima de los Huesos

A

Meyer et al, 2014:
- assemblage in spain- 28 hominin individual, attributed to Homo heidelbergensis, but also shared distinct neanderthal/derived traits- dental, mandibular and aspects of facial morphology
- low coverage autosomal DNA, but identifies as Neanderthal-related but divergent

79
Q

Outline maps of introgression

A
  • signals of Neanderthal introgression- excess similarity to Neanderthals compared to Africans
  • peak in New Guinea (~3%) , 2z2% east Asia, 1.8% Europe (Prufer et al, 2017)
  • Signals of Denisovan introgression peak in New Guinea (~4-6%), with limited additional signals in East Asia and South Asia (<0.5%) (Sankararaman et al, 2016)
  • also suggestions of introgression in Africa, but don’t have ancient DNA representing any possible source
  • introgression also supported by long archaic chunks (Racimo et al, 2015)
80
Q

Outline an alternative explanation to archaic introgression

A
  • gene flow (<100,000 ya) mainstream interpretation- however ancient structure been suggested- 230,000 ya
  • e.g. the African population that originally founded Neanderthals going on to found the first Out of Africa dispersals (Sankararaman et al, 2012)
  • Also suggestions that introgression signals could be false positives due to correlation between mutation rate and heterozygosity driving a higher mut rate in Africans who diverged a bit further away from Neanderthals as a result (Bill Amos)
  • The strongest evidence- introgressed haplotypes are ‘too long’ for ancient structure and; found ancient humans with recent Neanderthal ancestors
81
Q

Outline mixing between neanderthals and Denisovans

A

Slon et al, 2018-
- ‘Denny’ had a Neanderthal mother and Denisovan father- suggests mixing may be common
- Dennis father had ancient signals off mixing with Neanderthals (7.5-15kya)

82
Q

Summarise findings on the hominin tree

A
  • complex- more like phylogenetic network
  • statistical reconstructions- finding simplest model that fits genetic data (principle of parsimony)
  • possible that some were discrete pulses (e.g. first waves of people Out of Africa meeting Neanderthals), but equally probable that they were rather complex interactions occurring in various places at various times
83
Q

Outline functional significance of archaic introgression

A
  • Cases of archaic haplotypes in humans amplified by positive selection
  • Some genes may have facilitated adaptation to OOA environments e.g. Immunity, pigmentation, hypoxia (Racimo et al, 2015)
84
Q

Outline deleterious genetic evidence of introgression

A
  • Neanderthal ancestry not uniformly distributed over the genome
  • less ancestry on X chromosome- could imply sex-spexific admixture (Neanderthal males, human females), X chromosome rich in male hybrid sterility genes in other animals
  • Genes that are only expressed in testes have 5x lower Neanderthal ancestry, exons strongly depleted for neanderthal ancestry
  • suggests ancient selection against admixed individuals (Sankararaman et al, 2014)
  • Modern human genomes have large regions where no archaic introgression is , some show depleted neanderthal and denisovan introgression e.g. FOXP2, amylase gene cluster (Vermot et al, 2016)
85
Q

Outline the relation between archaic genetics and human uniqueness

A
  • Neanderthals and Denisovans diverged from modern humans over 450kya
  • 12,027 base pair positions where all humans carry a derived allele and Neanderthals and Denisovans carry the ancestral allele- most likely to be neutral- only 42 fixed amino acid changes in 36 genes
  • Including high frequency alleles (>90% frequency in humans) yields 648 amino acid changes over 560 genes- many more differences are in regions potentially involved in regulation (Kuhlwilm & Boeckx, 2019)
  • several genes identified with human-specific changes, or that have been inferred to be under selection and have high frequency non-synonymous differences- related to brain growth trajectory, cellular features of neurones, craniofacial phenotype and life history traits- suggests human modernity related to network of changes (Kuhlwilm & Boeckx, 2019)
  • Somel et al (2013)- question of how may fixed mutations can be exected- depends on assumed selection strength, population size, but estimated 700 relevant mutations for cognitive ability could arise over 200ky but only a few would reach fixation (similar arguments could be made for other complex phenotypes- many variants with relevant effects, together leading to consistent phenotypic differences, but few fixed genetic differences)
86
Q

Summary view on human uniqueness

A

Somel et al (2013)- cognitive ability-700 relevant mutations for cognitive ability could arise over 200ky but only a few would reach fixation- for complex phenotypes, many variants with relevant effects, together leading to consistent phenotypic differences, but few fixed genetic differences

87
Q

Online causes of genetic divergence between populations, and how the changes over time

A
  • immediately after population splits into 2 large populations, allele frequencies similar in both daughter populations
  • Over time, frequency drifts independently
  • This drift may be apart
  • if each population undergoes bottleneck, the bottleneck would mean alley frequencies drift independently ion each daughter population
  • overtime, populations may be linked through migration- causes them to become genetically more similar- homogenising- allele frequencies subsequently drift together
  • if diversity lost in both, cant resurrect
88
Q

Outline patterns of human population divergence

A
  • low genetic diversity- reflects low long term population size
  • suggests rapid drift, and potentially rapid divergence
  • OOA and serial bottlenecks- may have been rapid drift and local divergence, particularly between African and non-African populations
  • Populations show phenotypic differences, and local adaptation- may suggest significant genetic divergence
  • However, lots of historical and ancient migration- may limit divergence
89
Q

Outline statistics on shared an unique variants across human populations

A

Biddanda et al, 2020:
- 1000 Genome Project data (whole genomes: from Africa, Europe, South Asia, East Asia, Americas)
- Partition SNPs into unobserved (u), rare (R; minor allele <5%) and common (C; minor allele >5%) and assess sharing
* About 50% of variants are observed just once (‘singletons’)’ most other variants rare
* Many are observed in just one
sub-population (~60%; most singletons)- other 40% show regional or global sharing.
* Only about 3% are globally common

90
Q

Outline how genetic divergence is measured

A
  • calculated based on allele or haplotype frequency differences between populations
  • Fst- how much genetic variance eis between subpopulations (S), relative to within the total population (T)
91
Q

Outline human Fst

A
  • Lewotin (1972)- 17 classical genetic loci- -.15 (15% variation between and 85% within populations)
  • low compared to large mammals- grey wolf 0.8- low genetic differentiation given the wide geographic range of the species
  • ancestry testing companies can predict ‘origins’ or group membership- however ancestry weak as which present day populatiosmn cluster with (affected by divergence, drift and migration)
  • while 60% variants were rare + regional, almost all singletons so not contributing to Fst
92
Q

Outline the global structuring of limited human genetic divergence

A
  • likely reflects our recent common origin (Piazza et al, 1994)
  • argues strongly against ‘race’ as a genetically meaningful classification
  • Metspalu et al, 2011- Average Fst estimates among populations of >500,000 SNPs genome wide- ‘Intercontinental’ Fst is usually around 0.1 to 0.2, Additional bottleneck(s) increase divergence e.g. Melanesia, slightly reduced in non-African pairs (likely reflects OOA bottlenecks), Regional FST generally < 7.5% (hierarchically structured- multiple ways to define regions)
  • Ramachandran et al, 2005- geographic trends- isolation by distance (genetic distance increases with geographic)- correlation improves when distance is calculated using waypoints avoiding large seas where possible- correlation is consistent with serial bottlenecks as populations left Africa however persists within continents and hence likely substantially also reflects recent migration/‘gene flow
93
Q

Outline genetic divergence clusters, and if they are meaningful

A
  • e.g. regional patterns of SNP sharing, assignment of genetic ancestry- but also increases with distance- questions whether genetic variation clinal or clustered
  • Metspalu et al, 2011- variation among South Asian populations- principle component and admixture analysis to investigate lack of genetic variation and divergence and identify major axes of variation/ancestry clusters- found clustering- wide signals of positive selection in South Asia
  • however, sampling on clines makes clusters appear- geographical barriers lead to some clustering (Pagani et al, 2016)
  • Overall, human genetic divergence is low, and reflects a combination of background diversity, serial bottlenecks, and substantial post-OOA and recent gene flow, structured by geographic barriers
  • Appearance of clusters largely result of analysis methods/sampling strategies, but can also reflect environmental boundaries
94
Q

Outline the relationship between genetic and phenotypic divergence in humans

A
  • genetic coding for proteins and phenotype impact is complex process- via development, subject to gene-environment interactions
  • can predict phenotypes from genetic data (‘Polygenic Risk Scores’), but complicated and not always accurate
  • some if same patterns seen in genotypes occur in phenotypes (e.g. divergence with distance)- partly why possible to predict ethnicity based on phenotypes- but some of most profound phenotypic differences likely arisen due to natural selection
  • Relethford, 2009- correlation between geographic distance and phenotypic distance over 18 craniometric traits
95
Q

Outline links between genetic divergence and health

A
  • Population specific patterns of genetic disease are common (e.g. Tay-Sachs disease, caused by variation in the HEXA gene is 100 times more common among people of Ashkenazi Jewish ancestry; ‘Finnish heritage diseases’- 36 rare genetic disorders more common among people of Finnish heritage)
  • Higher frequencies often caused by population-specific bottlenecks
  • most genetic diseases caused by rare SNPs- selection stops reaching high frequency, often recessive as selection removes dominant genetic diseases
  • Rare variants tend to be recent (all variants start at 1/2N frequency with the first mutation)- tend to be highly local- suggests the genetic causes of many genetic disorders will also be population specific (Fu et al, 2013)
  • strong patterns of regional variation in drug response (pharmacogenetics)- common differences are often associated with founder effects or population isolation/endogamy- e.g. Vysya caste in India have a 100-fold increased incidence of butyrylcholinesterase deficiency, which impacts response to muscle relaxants and can be dangerous (Jobling, 2013)
96
Q

Outline selective sweeps

A
  • If a variant increases number of offspring an individual contributes to the gene pool it is advantageous it is expected to increase in frequency- whereas deleterious variants reduce the contribution to the gene pool and are expected to fall in frequency
  • selection coefficient describes a relative modification to fitness due to an allele- 0.01 is strong positive selection, 1% greater contribution to gene pool than a neutral allele; -0.01 is strong negative selection (deleterious)
  • drift (the fluctuating element) can overpower selection leading to fixation of deleterious alleles, particularly if population size is small
  • Rate of increase depends on the selection coefficient, s, and whether the allele is recessive, dominant or additive
  • in additive model, would take 925 generations (23ky) for allele at 0.01 s to go from 1-99% frequency
  • selective sweep is rapid fixation of an advantageous mutation by positive selection (Choudhuri, 2014)
97
Q

List examples of individual selected genes relating to health/disease (local adaptation)

A
  • ACKR1- Malaria
  • HBB- Malaria
  • loci for skin pigmentation
  • EPAS1- high attitude
  • MCM6/LCT- lactase persistence
98
Q

Malaria causes background

A
  • Most malaria in sub-Saharan Africa is caused by the parasite Plasmodium falciparum
  • However, recently improves diagnostics revealing evidence of P.vivax
  • questions why P.vivax uncommon in sub-saharan Africa (Sabeti et al, 2006)
99
Q

Outline selection on the ACKE1 gene and malaria

A

Sabeti et al, 2006:
- encodes the Duffy blood antigen system, involved in P. vivax erythrocyte invasion
- Duffy negative individuals have a T- > C mutation in ACKR1 promotor (FYO)- prevents extpression- gives resistance to P. vivax
- High frequency in Africa thought to reflect past selection for resistance
- However, recently Duffy negative poe[;e heyyomg P.vivax infection in some areas- may be due to P.vivax evolving (arms race)- or observation bias (limited expression of ACKR1 even with mutation
- Other health effects of Duffy negative allele e.g. FYO individuals are more susceptible to HIV

100
Q

Outline election on HBB gene and malaria

A
  • sickle-cell phenotype in Africa- caused by non-synonymous point mutation in the HBB gene- HbS allele
  • Homozygotes for the HbS allele have sickle shaped blood cells and sickle cell disease, while heterozygotes generally have normal blood
  • Globally, ~43 million people are heterozygote carriers of the sickle cell allele while 4.4 million have sickle cell disease, which can lead to sickle cell anaemia and has significant negative health effects
  • HbS is at high frequency in regions with high levels of Plasmodium falciparum in sub-Saharan Africa
  • correlation between blood dissorders observed (Haldane, 1949) and confirmed (Allison, 1954)
  • morality curves in infancy in Kenya (malaria most dangerous)- Homozygote HbS mortality is highest, while heterozygote HbS mortality is lowest, leading to balancing selection (Aidoo et al 2002)
101
Q

Outline global variation in skin pigmentation, including genetic basis

A
  • high variation- continuous distribution- not obvious clusters given a global samples of populations
  • tanning can effect, but overall under genetic control (~80% heritability)
  • polygenic complex trait- many genetic variants affect pigmentation
  • Hernandez-Pachero et al, 2017- GWAS- genetic loci associated with pigmentation in Puerto Rico- 82 loci with suggestive associations
102
Q

Selective/adaptive advantages of darker skin pigmentation

A
  • Protection against folate photodegradataion
  • Protection from sunburn
  • Protection against skin cancer
  • Shielding of sweat glands
  • Immunological function of pigment,
    eumelanin
103
Q

Selective/adaptive advantage of lighter skin pigmentation

A

Avoiding vitamin D deficiency

104
Q

Outline sexual dimorphism in skin pigmentation

A
  • women often have lighter skin pigmentation
  • may be due to greater vitamin D requirements during pregnancy
  • sexual selection for lighter women and darker men may occur in some cultures
105
Q

Outline the effects of UV for selection on skin pigmentation

A
  • Modern skin cancer rates are elevated at extreme latitudes- but unlikely to become selection pressure as occurs after longer term exposure
  • Association of pigmentation levels with UVA intensity, and tanning with UVB variance (Jablonski & Chaplin, 2010)
106
Q

Outline an example of a gene with major effect for skin pigmentation

A

SLC24A5:
- Zebrafish phenotype golden reflects fewer, smaller melanophores, caused by variants in Zebrafish SLC24A5
- non-synonymous variants (rs1426654) in SLC24A5 was under selection and explains 25- 38% of melanin index difference between Europeans and Africans (Lamason et al 2005)
- Variant is high frequency in Europe/Middle East and parts of South Asia, made it to the Khoi San in southern Africa through migration (Mallick et al, 2013)

107
Q

Outline the complexity of the genetic basis of skin pigmentation

A
  • African populations have most variable pigmentation globally
  • genetic heritability high (0.55-0.95), however, less than 20% of heritability is explained by the top 50 previously identified pigmentation associated genes, a small number of known and newly identified genes are important - overall 4 loci explain 29% of variance in Africa (SLC24A5, MFSD12, DDB1/TMEM138 and OCA2/HERC2)- considerable missing heritability (Martin et al, 2017)
  • Some of this signal is due to ancient European to Africa gene- flow, e.g. introduction of SLC24A5 variants to KhoeSan groups- many other genes/variants involved (Crawford et al, 2017)
108
Q

Outline phenotype convergence in skin pigmentation

A
  • chimpanzee have light skin pigmentation under hair- doesn’t necessarily mean common ancestor did, nut raises possibility of multiple changes over evolutionary time
  • found that sets of genes determining light skin colour in East Asia and Europe are different (Crawford et al, 2017)
  • e.g. KITLG common between East Asian and north European
109
Q

Outline ancient DNA findings regarding skin pigmentation

A
  • SLC24A5 is low frequency in European HGs, and shows a rapid increase with early Neolithic migrations
  • Mathieson et al, 2015- Study of 230 ancient European samples; frequency trajectory evidence is very helpful, but still largely biased to European samples
110
Q

Summarise population genetics of high altitude adaptation

A
  • Beall et al (2002)- population variance- 15.4% of Andean highlanders suffer from chronic mountain sickness (Monge’s disease)- high haemoglobin concentration is similar to what happens to lowlanders who live for extended periods at high altitude
  • Gene showing signals of adaptation (e.g. higher than normal differentiation between nearby high and low altitude populations) may either be unique to individual regions or convergent- Convergence is often at the gene level rather than variants – i.e. different variants in different populations but impacting the same genes, selection on the same genes does not always imply convergent physiological response (Azad et al, 2017)
  • EPAS1- under strong selection in Tibetans, liked to low hemoglobin concentration at high altitude and high blood capillary density- also under selection in Andeans, the physiological adaptation is different (Yang et al, 2020; Eichstaedt et al, 2017)
  • Unusually
    different allele frequencies between nearby groups is a possible indicator of selection
  • EPAS1 introgression- selected EPAS1 haplotype in Tibetans is very similar to the Altai Denisovan haplotype- adaptive introgression (Huerta-Sanchez et al, 2014)
  • Introgression likely occurred >40kya- Ancient DNA shows that the haplotype was at a moderate frequency at least 5.1kya, with a sharp increase in frequency over the last 700 years (Wang et al, 2023)
  • Ancient proteomics identified a 160ky old Tibetan plateau (3280m) jaw-bone as Denisovan – so populations in broad region (Chen et al, 2019)
  • Agriculture in Tibetan Plateau may be drier of genetic selection as facilitated year round occupation more recently
111
Q

Outline lactase persistence

A
  • lactose is sugar in milk- digested by enzyme lactase
  • most mammals (including humans historically) only consume milk as dependent offspring, and lactase isn’t produced in adulthood
  • in some human groups with a history of dairying, lactase produced into adulthood (Gerbault et al, 2011)
  • no lactase produced in adulthood may lead to lactose intolerance symptoms (e.g. (including humans historically) only consume milk as dependent offspring, and lactase isn’t produced in adulthood)
112
Q

Outline association between lactase persistence and ancient dispersals

A
  • question whether persistence spread into Europe with first herders, or if occurred later
  • question of role of milk processing in reducing lactose content (yoghurt, cheese, kefir, butter etc)
  • question o driver of selection- dietary e.g. carbohydrates, calcium in high latitudes; or if to do with sterile water source availability and immunity/microorganisms
  • milk processing origination in neolithic culture ~11kya (Salque et al, 2012)- but aDNA suggests lactase persistence arose later
  • aDNA- lactase persistence only appears ~4kya, associated with apparent migrations from Asian steppes- suggest people; were herding and consuming milk/processed dairy long before persistence- milk fat residues in potsherds show weak correlation with rate of frequency increase in aDNA (Bon et al, 2017)
  • Lactose intolerant people can still gain considerable nutrients from milk and fermented dairy products, microbiome may have buffered symptoms
112
Q

Outline the genetic basis of lactase persistence

A
  • involved MCM6 and LCT genes
  • SNP identified as associated with lactose intolerance in Finnish families (Ennatah et al, 2002)
  • Also found in 236 cases from 4 different populations, including Finnish, Korean, Italian and German individuals (Gerbault et al, 2011)
  • Strong genetic signal of selection- highFst, long haplotype (Bersaglieri et al 2004)
113
Q

Outline convergent evolution of lactase persistence

A
  • found 3 new lactase persistence alleles in East Africa (Tishkoff et al, 2007)
  • 2 interacting variants in the Middle East (Enattah et al, 2008)
  • effect of recent movements- different variants that are very close to each other in the genome and cause lactase persistence have independently been subject to positive selection in different places (Jobling)
114
Q

Outline local adaptation in terms of gene-culture co-evolution

A
  • lactase persistence may be example- cultural practice of limited milk consumption may have driven genetic selection- which in turn drove emore cultural adaptation (more milk reliance)
  • or, cultural practices (milk processing) may have buffered genetic maladaptation
  • e.g. HbS Duffy- influence of pathogen exposure in farming, SLC24AS in skin pigemntation- role of sexual selection
  • Gene-culture co-evolution- major force in human adaptation (Laland et al, 2010)
  • Adaptation via cultural behaviour and genes occurs in humans, and these interact
  • Relationships can be complex

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