Evolutionary Genetics Flashcards
Wrong assumptions
Genetic diversity in humans is large compared to other great apes
Disease-causing alleles are specific to certain continental groups
Human phenotypes correlate with human genotypes
Biases in records
Archaeological => stone tools, no wooden tools
Paleontological => bones, no soft tissue
Genetic => survival is selective
Oldest fossil (primates)
Mid eocene
Last common ancestor of primates
80 MYA
Darwin and Huxley
Similarities btw humans and great apes
Humans should share genus homo with chimps and bonobos at least
=> subfamily
Chromosomal analyses
late prophase G-banding => stain
Human chromosome 2: fusion of 2 primate chromosomes
Orang Utans: pericentric inversion
Y chromosomes change faster bc no recombination => badly resolved
Common ancestor of humans and chimpanzees
5 to 6 Ma
Chimps and humans
High behavioral similarity
Group agression
Culture
Tool use
Differences
Bipedality
Brain size
Complex language
Are differences btw humans and chimps genetically canalized?
Similarity 96-98%
DNA-DNA hybridisation
Low melting temperature = not clearly related => low association
High mt = clearly rel.
Are genome differences functional?
If in coding regions or regulatory sequences
Whole genome shotgun
Create snippets of sequences, align them to known genome
Divergence in Y chromosome
Rapid evolution
Genes novel to humans
About 60 novel genes
Cerebral cortex => large brains and testes
Gene duplication: leads to more geene product
=> humans have much higher copy number of many genes
Important gene in diff chimps/humans
FOXP2 (forkhead domain genes)
=> TF
mutations => KE family => phenotype: language impairment => autosomal inheritance
Activation of neurons not concentrated to Broca’s area
Mutations could contribute to language => but does not have to be cause
FOXP2 knock out mice
Non-vocal Behavior not affected, only vocalizations
Microarray analysis
Blood amd liver expression patterns closer in humans and chimps than to macaques
But brain: chimps closer to macaques
Time shift in expression patterns
Delayed expression pattern in humans causes delayed development of brain
Handedness
Humans 9:1 prefer right hand
Chimps and other g. apes: no preference
Handedness mirrored in lateral asymmetry of sensory and motor regions of forebrain
=> neanderthals thought to be right handed => tools, art etc.
=> last common ancestor probably too
Asymmetric gene expression
Allelic expression of genes involved in hemispheric asymmetry
=> 27 genes with consistently hemispheric differences
What genetic changes have made us human?
• 1-2% sequence divergence
Heterochromatin changes
Retrotransposons
Duplications, deletions, point mutations
• most changes regulatory levels and expression patterns
• few gene function alterations
Divergence chimps and bonobos
River Kongo
Highest diversity in humans
In african populations => longer time of evolution
The further away from east africa, the lower the diversity
Time to MRCA
~ 120 ka => but not certain
Orang Utans
Extremely philopatric => females basically never move => stay where they are born
Fst value
Measure for genetic differentiation btw populations
=> high in chimps
=> low in humans
Multiregional model
H. erectus dispersed from africa => at similar time settled in europe and asia => constant geneflow btw all thre groups
Anatomically modern H. sapiens genes arose in many populations
Assimilation of H.erectus
Genetic divergence
If isolation => no geneflow
Out of Africa model
Modern H.sapiens evolved in africa and replaced H.erectus populations by spreading to europe and asia => extinction of H.erectus
Genetically most likely model of human evolution
Best demographic model is out of africa exponential replacement model
Homoplasy
Feature that has been gained/lost independently in diff lineages over the course of the evolution
Bottleneck/ founder event
Reduced genetic diversity
Only small part of population left africa
Also with mating => but sexual selection? Well certainly not natural selection
Hyper variable regions
Due to homoplasy
=> fast occurring evolution
=> underestimation of difference
Mainly conquering males mated with neanderthal women => mtDNA no overlap in current humans, nuclear DNA looks different
Denisovans
Distal phalanx of finger => genetic legacy
Problem with DNA sequencing
Half life => jurassic parc completely wrong, DNA doesn’t survive that long
Contamination by other organisms
Geneflow btw neanderthals and modern humans
More from neanderthals to humans
Phylogenies
Always show only part of the picture => gene trees! Mt DNA might be different from nuclear DNA
Racist view
Hierarchy and falsification of skull shape
Linnaeus
Diurnus americanus, europaeus, asiaticus und afer
Nocturnus
Concept of race
Imaginary categories that mix physical, intellectual and cultural characteristics
Taxonomic definition of race
Subspecies that are biologically distinct groups
Phenotypic plasticity
Same organism might have different phenotype in different environments
Hight difference between classes
Malnutrition
Short evolutionary time
Not enough generations to cause significant change in genes
Skin pigmentation
Dark skin
Adaptation to UV radiation
Eumelanin
Light skin
Pheomelanin => Vitamin D production => deficit leads to bone deformations
Single base pair mutations
Might be enough to disrupt signal cascadebresponsible for eumelanosome production
=> one single mutation can have drastic effects on phenotype
Genetic Variation
In humans highest within populations
In other GAs btw populations
=> two europeans can genetically be more diff from each other than a european and an african
Effect size vs sample size
At large enough sample size, any difference can be significance
But biologically relevant?
‘Structure’ algorithm analysis
K2 = Africans, Europ, mid east, south asia more vs east asia, america, oceania
K3 = Africa vs Europe, mid east, south asia vs east asia, america, oceania
Etc.
=> even at high K europe, mid east, south asians are still in same cluster
Fst
0 = no genetic diversity btw pop
1 = completely gebetically diff
Genetic diversity in humans
Recent founder event => multiple events
Diversity in humans is a gradient
Selective sweep
Fixation of a beneficial allele (frequency = 1) leads to reduction in genetic variation
Genetic surfing
Spatial spread of alleles that have not been lost by genetic drift
FOXP2
Already in Neanderthals
Nuclear DNA/full genome
Suggests common ancestor of Denisovans and Neanderthals to exclusion of humans
MtDNA
Suggests MRCA of humans and neanderthals to exclusion of denisovans
4 human population explosions
100’000 years: first expansion
11’000-5’000 years: agriculture
5’000-500 years: domestication of horse and military inventions
500 years: industrialization
Pheomelanin
More abundant in Light skin
Clusters in organelles
