crucial

# CH1 # definitions

better-to-know

Why we don't see aging (t) mutations in mile but see in elephants ?
= The +
effect cannot be seen because mice is dead because of external reasons

before we saw the +

effect of mutation

·
population size of mice is higher then humans. Thus , they are
adapting faster

& Haplotype =
group of genes tend to
be inherited from single parent

* Some neutral mutations can

genetically hitchike with positively selected

genes.
Selections lower
polymorphism and lowers
genetic diversity
.

& Admixture :
genetic mixture of guetically different populations
short
Microevolution :
changes in
range

↑
*oute
e

How selection affects gene expression ?

* mutations
*
-
change protein structure
-

change gene expression

self-domestication -
eg .

pigs approaching humans and at their meal

becomes not afraid of them .

- Balancing
Selection

what makes us human ?

mating type differences
-

gene expression changes -stis high divergea

# CH3#

① common garden experimentsE different types of species are grown under some

environmental conditions

① standing genetic variation : mutation/variation already present in ancestral

population

Change/Evolution >
on
population level vs natural selection -
on individual level
-

① Norms of Reaction :
Range of phenotypes that a specific genotype can
produce under varying
(Phenotypic Plasticity) environmental conditions.

to soil richness
1 Eg . Short-tall plants with some
genotype due differences

& Pleiotropy : One allele affecting multiple phenotypes - a factor limiting adaptation

& Exaptation : Old

adaptation gaining new function depending on fitness - feathers
1) insulation
2) flight
Grandmother Hypothesis =>
Menapause paradox is a

"Why in whales ? Grandma's raising young affect

population size.

Grandmas lead to

fish resources for nutrition for youngs

K life history strategies

offting
vs r

Trade-off e body size ↑ neededa

resources

Plastic response
Antogonistic pleiotropy
Opsins Y

-Phenotypea
allele
* this is also on

& adaptation

life history traits :

17 development

2)fecundity (fertilita

- cause either new genes or

pseudogenes
 # CH4 : PHYLOGENIES #

species that
:
Group of organisms can interbreed

have ? - 2
5 gens ago, how
many ancestors would
you

To construct phylogenies
>
-
use neutral traits

convergent evolution :
independent evolution of same
phenotype in different lineages
(paralel evolution

Which one evolved first ? -

Mitochondra or Chloroplast Mito
.

① Outgroup
eg .
:

humans
A taxon

are
equally
outgroup
distant
to
to

chimpanzees
all others

ana bonobos
manuman
bonobos gorina

Bifurcation : nodes
separate into two (not more than 2)

Polytomy
·
: Branch splitting into more than 2 subbranches

&Topology : who shares more recent common ancestor wh whom

clade ~
Monophyletic Group) Accurate classification

# >
-

Monophyletic
Polyphyletic
Paraphyletic

- homoplasy =
analogous traits
↓
traits emerged
as a result

of convergent
evolution
-

not homologous !
E

no common
ancestor

DNA sea and

phenotype
 # CH5 :
Interferring Phylogenies #

Exhaustive/ heuristic algorithm

sequence aligners Distance /Similarity Matrix

choosing characters >

fast-evolving vs slow evolving
-

& Maximum Parsimony : Tree w/ least changes happen to be most

likely

Consensus Tree -
equally
as
parsimonis

* Long Branch
Attraction

& UPGMA ,
MLS Algorithms

# Bootstrap
~noise , bootstrap replicates
How many times/trees I found mice and human are close ?

# Phylogeography

& Evolution of nocturnal life w/lemurs

-
>
* independence doesn't exist
* contrasts
independent
&
 CH1
Evolution : All organisms are related through the natural selection.
Genetic changes in gene pools over generations.
Speciation and extinction can be understood via both evidence and lab experiments
Adaptation can be observed directly via historical data and indirectly via lab experiments .

Mad Adaptation

How to study evolution ?

• comparative studies
• Extinct an extant (still existing)
• Experiments
• modeling via computer

Even in 6 or 7 generation evolutionary change can be observed.

Polymorphism example : skin pigmentation

Microevolution: Changes in short range

Macroevolution: in long run, creates adaptation and/or speciation

Hypermutations in immune cells can be caused by organism itself

Genetic change leads to evolution by
• natural selection
• natural processes, such as genetic drift.
Non-genetic changes are not evolution, eg. phenotypic plasticity.

Darwin -> blending inheritance

evolution accepted + synthesized with Mendelian genetics = "modern synthesis"

Point mutations are more frequent. Most mutations are natural.
Larger organisms have lower mutation rate in somatic cells and have more advantage in damage control.
Father have mutation in gametes, due to constant mitosis.

Mutations can affect

1) protein structure
2) gene expression *

Genetic drift depends on population size. Mainly affects neutral alleles, with no effect on fitness.
stochastic: random admixture
>
-

- Balancing
Selection

heterozygote advantage

outgroup: a taxa equally distant to another taxa

 Stabilizing Sel .

microevolution mechanisms:
1) migration and admixture
Directional Sel

2) non-random mating
3) sex & recombination
>
-
Disruptive Sel .

what makes us human ?

mating type differences
-

gene expression changes -stis high divergea

 CH5

Homoplasy (analogous traits) : same traits developed in different species without common ancestry.

Discrete characters :
• phenotypes (presence or absence) or protein or DNA sequence
• Can include character change models and their probabilities
eg. Probability of cytosine to thymine conversion
eg. Probability of cytosine to adenine conversion.

Distances : summaries of character differences between taxa

e.g. total number of nuc. substitutions between taxa
• or, quantitative measures of phenotypes

Choosing optimal tree:

1) evaluate differences among taxa

2a) non model-based methods

– maximum parsimony – on characters – least squares – on distances
Tree with least number of changes is most likely
– clustering (UPGMA, NJ) – on distances

2b) model-based methods

– computationally demanding, use more info – exhaustive or heuristic (trial & error)
– maximum likelihood
– Bayesian inference
Account the probability of multiple changes at the same position

3) rooting trees (using outgroup lineages)

4) calculating confidence
• bootstrap
• jackknife
• odds ratio testing vs

Sequence alignments suggest homology, but if misaligned, wrong tree can be found . If alignments is established we can
compare sequences.

Fast evolving characteristics: to study close relations,

• neutral is better
• avoid loci involved in rapid adaptation eg. immune loci

Slow evolving characteristics: for distant relations

• conserved genes
• lower risk of homoplasy
• finding homology among the taxa.

parsimony score: sum of minimum changes per tree

consensus tree: equally parsimonious trees possible will include polytomies
distance methods
1. calculate pairwise distances among taxa
– e.g. number of differences in DNA or protein alignments
– e.g. Euclidean distance if using quantitative characters
2. Create a distance matrix.
3. Summarize the matrix in a tree.
– find the best fitting topology
– branch lengths in the tree should be closest to original distances

In which conditions are the distance method are used?

1. Which topology is best?
>
-

2. What branch lengths to infer?

distance methods
1) Least squares
• Find a tree with the smallest difference to the distance matrix
• Minimize (tree branches - observed distances) 2
• Minimizing the differences between the observed data and the estimated relationships in the tree
• as number of the tips increases heuristic algorithms are needed

search algorithms can be

-
exhaustive or heuristic !

2) UPGMA
• Cluster pairs starting from closest pairs. Hierarchical clustering.
• Simplest method

caveats of some distance methods

1) Traits treated equally
– assumed equally homologous
2) all branches assumed to evolve at the same rate- risk of long branch attraction
– applies to UPGMA and WLS
– neighbor joining can overcome long branch attraction
– model-based approaches more flexible than distance methods,
but may take more time and complicated to understand

Outgroup : equally distant to all other taxa

Bootstrap

Evolution of nocturnal life with lemurs