Phylogeny 4 Flashcards
lineage sorting (2)
- the accidental and gradual reduction in genetic diversity due to drift
- lineage sorting is said to have gone to “completion” when one of the original copies becomes fixated
what determines how likely fixations happens under genetic drift
- population size
- number of generations
how does population size affect how likely fixations happens under genetic drift
- the smaller the population size, the faster drift happens
how does number of generations affect how likely fixations happens under genetic drift
- the more generations that pass, the more likely drift is to lead to fixation
what happens with genetic drift if the population is divided into two isolated populations
- initially, both daughter populations inherit similar frequencies of the different alleles
- as time continues, drift happens independently in the two populations and luck may favour different alleles in the separate populations
- eventually, fixation will occur in both populations, but they might fix to different alleles by random chance
Fst (3)
- measure of how much allele frequencies differ between two populations
- goes from ~0 (allele frequencies the same) to ~1 (fixed differences)
- can be measured for a single locus or for the average of many loci to show how populations are different across a genome
gene tree (2)
- lines of a gene tree represent copies of a gene locus descending from parent to offspring
- the nodes of a gene tree represent a single copy being passed to multiple children
species tree (2)
- lines of species tree represent species or populations descending through time
- nodes of a species tree represent speciation (isolation of populations)
gene and species trees
- gene tress flow, through time, inside species trees
incomplete lineage sorting (ILS) (2)
- lineage sorting was incomplete: no copy reached complete fixation
- also called deep coalescence in a backwards looking perspective
what raises the probability that a locus has incomplete lineage sorting along a branch
- the population size is larger: more variability
- the branch is shorter: fewer number of generations
when will two nearby locus have different gene trees (3)
- when recombinations happens between the loci
- the more recombination, the more different the gene trees
- if recombination occurs between loci, the linkage is momentarily broken and ancestry may follow different lines
why do two nearby loci share the same gene tree even if mutation occurs in one of the locus
- same gene tree even if there may be new mutations in different places
why do two nearby loci share the same gene tree even if selection happens at one locus
- if this changes the gene tree of one locus, it will also change it for the other locus (because they are linked)
what happens in a gene tree if there is recombination vs no recombination (2)
- no recombination: gamete gets copies of both loci from the same parent
- recombination: gamete has a mix of copies from both parents
linked loci (2)
- when loci are close together and recombination is infrequent
- these loci tend to be inherited together
linkage and recombination in gene trees (2)
- linkage binds adjacent sections of the genome to have the same gene tree
- recombination breaks this linkage up and can be within a gene so that the first half of a gene can have a different tree than the second half
how does distance between two loci affect gene trees
- the further apart two loci, the more recombination, and the more different the resulting gene trees will be
looking forward and backward with linkage (3)
- if genes are nearby on the same chromosome, their alleles tend to be passed down together as a unit
- looking forward in time: this means if an allele in one gene gets selected, the linked allele of the other gets dragged along (hitchhiking)
- looking backward in time: this means alleles at both loci tend to have come from the same parent, following the same lines of ancestry
who is the person that was the MCRA for a certain allele in the ancestry of a certain gene tree for everyone alive (2)
- they were the only person whose copy of this gene survived to the present
- they were NOT the only person who was alive at the time or the only person whose descendants survived to the present
what do we observe when looking forwards through time in a gene tree
- drift and fixation
what do we observe when looking backwards through time in a gene tree
- coalescence
for any locus, what will happen if you look back far enough (2)
- the ancestors of all of the living gene copies will coalesce to a single common ancestral copy
- the living copies will represent the lucky fixation of a single ancestral copy
what is the expected time to fixation/coalescence
4Ne generations for nuclear genes in diploids
2Ne generations in haploids
where Ne = effective population size
what are some reasons why a species tree may differ from a gene tree at a certain loci (3)
- incomplete lineage sorting
- hybridization introducing “foreign” alleles
- error in inferring the gene tree
why may there be errors in inferring the gene tree
- an inferred gene tree could be discordant with the species tree because convergent ,mutations can lead us to infer incorrectly
what prediction is associated with ILS
- equal frequencies of the two discordant types: ancestral polymorphisms would sort either way with equal probability, so the two shapes of discordant gene trees should occur in equal frequencies among different loci
what prediction is associated with hybridization
- unequal frequencies: each event of hybridization generates specific discordant trees so one discordant tree will likely be more common than the other
what prediction is associated with errors in inferring the gene tree
- equal frequencies: error because of convergent mutations should be unbiased, and so both errors should be equally frequent
introgression
- the introduction of gene copies from one species to another through hybridization
how did hybridization occur between Neanderthals and Humans (2)
- Neanderthals were Eurasian
- hybridization with Neanderthals happened in Eurasia, only with human lineages that had left Africa
when did the node that gave rise to neanderthals and denisovans occurs
- 450K years ago
when was the first bottleneck event in humans
- humans almost went extinct 200,000 years ago: human bottleneck to about 9000 individuals
- this means that ALL humans are extremely closely related due to being from a very small population 200K years ago
human diversity (3)
- we are divided into temporary subpopulations that mix occasionally; most of the variability is shared
- generally there are two main groups: Africa and Outside Africa
- Africa holds more of our species’ genetic diversity than the rest of the world
why do non-Africans have less diversity
- founder effect on those leaving Africa: a bottleneck to about 1000 individuals only
