Population genomic and the future Flashcards
What different elements of populations of genomics are questions asked around?
- Population structure and demographic history
- Admixture detection
- Identification of genes/traits under selection genome wide: +ve/-ve selection, convergent evolution, GWAS for disease loci and OTLs
- Genetics of speciation
What is one method for generating cheap and quick genome wide polymorphism data?
RAD-sequencing:
- To identify large number of SNPs from individual genomes
- Using this individual genotype data - to look answer questions about history of populations and selection etc
Explain the convergent evolution in the mechanism for echo location
- Echo location - in bats and in cetaceans (marine mammals) - how did this occur
- Prestin - protein in mammalian outer hair cells (OHCs) - and is thought to confer high frequency sensitivity and selectivity in the mammalian auditory system
- AA from cetaceans is much more similar to with echolocating bats than to other marine mammals - in Prestin gene
- Parker et al., 2013 - genome wide convergent evolution - significant evidence for convergence among bats and bottlenose dolphin - also found convergence in many genes linked to vision (200+ genes)
- E.g., some of these genes are are associated with mutations in these genes that cause deafness in humans
Give an example of a study about genomics of speciation
Marine stickleback fish:
- Have colonized and adapted to thousands of streams and lakes formed since the last ice age
- Compare genome sequences from different ecological systems of stickleback - freshwater and marine
- Using measure analagous to Fst - bigger spike on histogram - difference in alleles - e.g., EDA gene
- Inversion - ‘crossover suppressor’ - stops recombination breaking up the relationships between groups of genes that are contributing to fitness within an ecological forms
- Is common to find cluster of genes in inversions related to adaptations
How is studying dogs helpful?
- As dogs are all one species, but have very different morpholgies and wide phenotypic variation - then it is great to study what genes may be affecting which morphology
- As these genes are likely to affect morphology in other species too
What study with mosquitos could tell us about the paleogeographic environment drivers within a population?
- Phylogeography of the pitcher plant mosquito
- RAD-seq - revealed genetic structure and direction of evolution from a southern Appalachian refugium following recession of the Laurentide Ice Sheet - similar to snails in Queensland example
- Emerson et al., 2010
What was the range of Neanderthals?
- Protot neanderthal traits appear in europe 600k-350k ya
- Last definite foxxils ~30000 ya
- Archaeological finds suggest presence in Gibraltar until 24000 ya
- Hybrid skeleton - Portugal - 24500 ya?
What questions can be asked about the interaction between humans and neanderthals?
- There may have been a small overlap between neanderthals and modern humans
- But did they ever interbreed? Did humans out compete them?
What evidence suggests that there may have been admixture between humans and neanderthals?
MCPH1 gene - regulates brain size during development
- 70% of human pop carries D haplotype
- Genealogy suggests entered population ~37,000 ya and swept to high freq
- Interhaplotype divergence analysis suggests D arose 1.1 million ya in separate lineage from humans and introgressed into humans ~37,000 ya
- Evidence of limited admixture between humans and neanderthals
- Evans et al., 2006
From sequencing neanderthal genome, what was found about admixture between humans and neanderthals?
- 2010 - results indicate admixture between non-African populations and these archaic hominin species
- Not present in African pops
- 1.9-3.1% of Eurasian genome derived from Neanderthals
- Melanesians: 4-6% of genome dervied from Denisovans (other archaic human species)
- Suggests admixture while modern humans were on their way out of Africa 47-65,000 ya and interacted with Denisovans in Eurasia
How much hybridisation is likely to have taken place between modern humans and neanderthals?
How much hybridisation took place?
- Probably low rate <2% rate of successful interbreeding for Neanderthals
When and where are modern human pops and neanderthals likely to have admixed?
When and where?
- 47-65k ya - at the front of the wave of expanding modern humans into Europe and Asia from Africa
- Hybridisation between ancestors of Melanesians and Denisovans throughout South East Asia
- Evidence of early modern human introgression into Denisovans 100k ya
What was the fate of introgressed DNA determined by selection or drift?
Mostly drift ? But could vary among loci, consistency of Neanderthal fragments present mostly low
Did Neanderthal traits/DNA give a selective advantage to modern humans?
Possibly…
- Some evidence that some MHC alleles may be derived from Neanderthals (resistant to non-African diseases)
- Or even allele in Tibetans - for hypoxia at high altitudes - evidence suggests this allele can from Denisovans
What things come out of studies about the advantages and disadvantages neanderthals provide modern humans?
- Genes associated with function in brain and testes - less likely to be represented in modern humans - suggests might be selection pressure against these alleles because neanderthal alleles are mismatched against alleles in modern humans
- So heterozygote individual would have reduced fitness
