Phylogeny 4

Question 1

lineage sorting (2)

Answer 1

• 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

Question 2

what determines how likely fixations happens under genetic drift

Answer 2

• population size

- number of generations

Question 3

how does population size affect how likely fixations happens under genetic drift

Answer 3

• the smaller the population size, the faster drift happens

Question 4

how does number of generations affect how likely fixations happens under genetic drift

Answer 4

• the more generations that pass, the more likely drift is to lead to fixation

Question 5

what happens with genetic drift if the population is divided into two isolated populations

Answer 5

• 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

Question 6

Fst (3)

Answer 6

• 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

Question 7

gene tree (2)

Answer 7

• 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

Question 8

species tree (2)

Answer 8

• lines of species tree represent species or populations descending through time
• nodes of a species tree represent speciation (isolation of populations)

Question 9

gene and species trees

Answer 9

• gene tress flow, through time, inside species trees

Question 10

incomplete lineage sorting (ILS) (2)

Answer 10

• lineage sorting was incomplete: no copy reached complete fixation
• also called deep coalescence in a backwards looking perspective

Question 11

what raises the probability that a locus has incomplete lineage sorting along a branch

Answer 11

• the population size is larger: more variability

- the branch is shorter: fewer number of generations

Question 12

when will two nearby locus have different gene trees (3)

Answer 12

• 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

Question 13

why do two nearby loci share the same gene tree even if mutation occurs in one of the locus

Answer 13

• same gene tree even if there may be new mutations in different places

Question 14

why do two nearby loci share the same gene tree even if selection happens at one locus

Answer 14

• if this changes the gene tree of one locus, it will also change it for the other locus (because they are linked)

Question 15

what happens in a gene tree if there is recombination vs no recombination (2)

Answer 15

• no recombination: gamete gets copies of both loci from the same parent
• recombination: gamete has a mix of copies from both parents

Question 16

linked loci (2)

Answer 16

• when loci are close together and recombination is infrequent
• these loci tend to be inherited together

Question 17

linkage and recombination in gene trees (2)

Answer 17

• 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

Question 18

how does distance between two loci affect gene trees

Answer 18

• the further apart two loci, the more recombination, and the more different the resulting gene trees will be

Question 19

looking forward and backward with linkage (3)

Answer 19

• 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

Question 20

who is the person that was the MCRA for a certain allele in the ancestry of a certain gene tree for everyone alive (2)

Answer 20

• 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

Question 21

what do we observe when looking forwards through time in a gene tree

Answer 21

• drift and fixation

Question 22

what do we observe when looking backwards through time in a gene tree

Answer 22

• coalescence

Question 23

for any locus, what will happen if you look back far enough (2)

Answer 23

• 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

Question 24

what is the expected time to fixation/coalescence

Answer 24

4Ne generations for nuclear genes in diploids
2Ne generations in haploids
where Ne = effective population size

Question 25

what are some reasons why a species tree may differ from a gene tree at a certain loci (3)

Answer 25

• incomplete lineage sorting
• hybridization introducing “foreign” alleles
• error in inferring the gene tree

Question 26

why may there be errors in inferring the gene tree

Answer 26

• an inferred gene tree could be discordant with the species tree because convergent ,mutations can lead us to infer incorrectly

Question 27

what prediction is associated with ILS

Answer 27

• 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

Question 28

what prediction is associated with hybridization

Answer 28

• unequal frequencies: each event of hybridization generates specific discordant trees so one discordant tree will likely be more common than the other

Question 29

what prediction is associated with errors in inferring the gene tree

Answer 29

• equal frequencies: error because of convergent mutations should be unbiased, and so both errors should be equally frequent

Question 30

introgression

Answer 30

• the introduction of gene copies from one species to another through hybridization

Question 31

how did hybridization occur between Neanderthals and Humans (2)

Answer 31

• Neanderthals were Eurasian

- hybridization with Neanderthals happened in Eurasia, only with human lineages that had left Africa

Question 32

when did the node that gave rise to neanderthals and denisovans occurs

Answer 32

• 450K years ago

Question 33

when was the first bottleneck event in humans

Answer 33

• 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

Question 34

human diversity (3)

Answer 34

• 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

Question 35

why do non-Africans have less diversity

Answer 35

• founder effect on those leaving Africa: a bottleneck to about 1000 individuals only