Phylogeny

Question 1

define Population

Answer 1

individuals living together that interbreed with each other

Question 2

define Species

Answer 2

usually made up of multiple populations, that are capable of interbreeding and exchanging genes with each other.

Question 3

define Common Ancestor

Answer 3

an ancestral species from which multiple current species diverged from.
the last ancestor that two species shared genetic identity with

Question 4

define Phylogeny

Answer 4

the genetic history of life, encompassing the history of genes, genomes and species.
it is typically explained through a tree of branching lineages, showing a map of genetic history

Question 5

what does a branching point (node) on a phylogenetic tree represent?

Answer 5

A speciation event!
- species divide into two new species

Question 6

how is time represented on a phylogenetic tree?

Answer 6

root = farthest point in the past being referenced
tips = present time/species
** time is not represented linearly. length of branches has no indication for actual amount of time passed

Question 7

define Most Recent Common Ancestor

Answer 7

On a phylogenetic tree, the most recent node (ancestor) shared between two species.

Question 8

define Monophyletic Group (Clade)

Answer 8

an ancestor and all of its descendants on a phylogenetic tree.

Question 9

define Sister Groups

Answer 9

a pair of closest relatives (relative to the tree being looked at)
- move back 1 step to the mother (node), and look at its other children/descendants.

Question 10

define Synapomorphy

Answer 10

a trait that is shared AND derived (heritable by all species that have the trait).
- the derived trait is shared by all descendants from when the trait/mutation arose, indicating that those species that share the trait are part of a monophyletic group.

Question 11

define Parsimony

Answer 11

the simplest explanation, that minimizes changes, based on the data presented

Question 12

define Likelihood

Answer 12

used in constructing phylogenetic trees, determines conclusions based on data presented that makes the most logical sense while also being the least complex.
- The probability of the data given the tree

Question 13

define Bootstrapping

Answer 13

allows us to measure variance in phylogenetic data by randomly sampling the data repeatedly and constructing phylogenetic trees each time, finally comparing them to see how similar the trees are.
- if the data’s variance is low, the same tree will repeatedly be constructed, therefore resulting in higher confidence for that tree.
Low variance = higher confidence

Question 14

define Convergence (not homologous traits)

Answer 14

when the same mutations/traits arise independently in different lineages i.e. they do NOT share a common ancestor with that trait

Question 15

define Homologous (traits)

Answer 15

traits that are inherited from a common ancestor

Question 16

what is the method of “sister clade comparison”?

Answer 16

Find a pair of sister clades that different in a trait and see which clade has more species. If many pairs show the same pattern, like there being one clade with more species than the other in every pair, then this is evidence that the trait affects diversification.

Question 17

define Character(s) and Character States

Answer 17

Character(s) = the variable or parameter being referenced (ex. eye colour)
Character state = the value or quality of the character (ex. blue vs brown vs green eyes)

Question 18

how do we determine phylogenetic correlations between traits?

Answer 18

we look at the relevant sample size, being the number of evolutionary events (NOT the number of species with the traits)
like if two different traits are passed down a lineage together, did they arise multiple times together?
or if there’s correlation between a certain trait and diversification of a species?

Question 19

how many species have been described by scientists?

Answer 19

about 2 million so far

Question 20

define Systematics

Answer 20

the field that reconstructs phylogenetic relationships

Question 21

define Taxonomy

Answer 21

the science of discovering and distinguishing/characterizing species

Question 22

how many estimates species live on earth?

Answer 22

current estimate : 8.7 million
but there are probably more

Question 23

what is the order of geological periods?

Answer 23

Precambrian -> Paleozoic -> Mesozoic -> Cenozoic

Question 24

when was the Precambrian Period + Major events that happened in it?

Answer 24

4.6 billion - 540 million years ago.
Origin of Life ~4 billion years ago
Oxygenation Catastrophe ~2.4 billion years ago
Origin of Animals ~0.7-1 billion years ago

Question 25

when was the Paleozoic Period + Major events that happened in it?

Answer 25

540 - 252 million years ago
First tetrapods & Land plants ~450-395 million years ago

Question 26

when was the Mesozoic Period + Major events that happened in it?

Answer 26

252 - 66 million years ago
Origin of mammals & dinosaurs

Question 27

when was the Cenozoic Period + Major events that happened in it?

Answer 27

66 million years ago - 0
Origin of hominids

Question 28

how much of human DNA is from Neanderthals?

Answer 28

~2.6% of human DNA is derived from the Neanderthal genome

Question 29

define Hybridization

Answer 29

occurs when two divergent lineages (species) with independent evolutionary histories come into contact and interbreed, sometimes causing a speciation event or just introducing new alleles.

Question 30

define Lineage Sorting

Answer 30

the gradual reduction in genetic diversity due to drift. Lineage Sorting that has gone to completion is when genetic drift leads to fixation of only 1 of the original alleles.

Question 31

what determines how likely fixation happens under genetic drift?

Answer 31

Population size - the smaller the population, the faster drift happens.
Number of generations - the more generations that pass, it’s more likely drift will lead to fixation.

Question 32

how does drift affect different isolated populations?

Answer 32

isolated populations will be affected by drift separately, and tend to diverge more and more in gene frequency as time passes. Eventually, if an allele fixes it will likely be to different alleles.

Question 33

define Fst

Answer 33

a measure of how much allele frequencies differ between two isolated populations.
Fst = 0 - same allele frequencies.
Fst = 1 - fixed alleles that are different.
It can be measured by a single locus, the average of many loci, or for entire genomes.

Question 34

what is a Gene Tree and how does it different from a species tree?

Answer 34

a gene tree shows the lines of descent of gene copies passed from parents to offspring, and the nodes represent a single copy of a gene passed to multiple children.
a species tree represent lineages of species or populations descending through time, and the nodes represent speciation events.

Question 35

define Incomplete Lineage Sorting (ILS)

Answer 35

when lineage sorting does not reach fixation of a single allele.

Question 36

how does the gene tree look for two genes at nearby loci?

Answer 36

two genes at nearby loci should have the same gene tree unless recombination happens between the loci, then they will have different gene trees.

Question 37

define Linkage (of genes)

Answer 37

when two adjacent sections of the genome are “linked” (close together), thus having the same gene tree.
- they are inherited together
recombination breaks this up.

Question 38

define Coalescence

Answer 38

• looking back in time to find a common ancestor.
• ancestors of all current living gene copies will coalesce to a single common ancestral copy.

Question 39

define Introgression

Answer 39

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

Question 40

why are humans so closely related to each other?

Answer 40

about 200,000 years ago, there was a bottleneck in the human population in Africa with ~9000 individuals left.
this means all humans today came from that small population only 200k years ago.