two main sub patterns of Phylogeny

anagenesis

cladogenesis

anagenesis

what type of selection?

evolution of species involving an entire population

replacement of ancestral variants by descendent variants

directional selection

cladogenesis

what type of selection?

splitting event that leads to development of greater variety among sister organisms

coexistence of noncompeting variants

diversifying selections (more diff they are more able to coexist)

can phylogeny pattern occur without selection?

yes

fitness

two components

survivor ship

fecundity

Natural selection

three components

variants that effect fitness tend to be inherited

variation in traits that affect fitness

heritability of these traits/variants

logistic model of density-dependent population group

actual population are (at some point) density-dependent

as pop size approaches carrying capacity, the rate of growth decreases

no competition results in ____

competition results in ____

no competition results in coexistence

competition results in replacement (if diff carrying capacities or diff rates of growth)

different kinds of results of selection (coexistence or replacement) are responsible for 2 diff kinds of patterns of phylogeny

what are the two patterns and which associates with which result of selection?

coexistence

cladogenesis

replacement

anagenesis

in L.E. Orgel's Selection in vitro experiments,

how did they measure for fitness

fitness reflected by rate of replication

r-selection

looking for variants that grow faster than others

characteristics of selection algorithm

what type of process

result of

stepwise process (ea step leads to greater fitness)

result of genetics

it is not random

tests for selection

correspondence btw structure and engineering design

experimental tests (e.g. paint colors on butterfly wings)

tests at the molecular level

comparative method

K_A/K_S test for selection versus neutrality

a measurement for the pace by which the protein product of a gene has evolved compared with that expected under selective neutrality.

look at gene sequence

is KA/KS ratio 1, <1, >1

if no selection, ratio = 1

if purifying or stabilizing selection, ratio = <1

if directional/diversifying/positive selection, ratio = >1

purifying or stabilizing selection

diversity decreases as population stabilizes in terms of a certain trait

McDonald-Kreitman test

three steps

examine interspecies polymorphism pattern in coding region of gene

examine interspecies divergence pattern in same gene

compare KA/KS ratios between species and within species

McDonald-Kreitman test

if K_A/K_S ratios between species and within species are the same

amino acid differences are due to neutral change (drift)

McDonald-Kreitman test

if K_A/K_S ratio between species > K_A/K_S ratio within species

amino acid differences are due to positive selection

McDonald-Kreitman assumptions

only non-synon muts adaptive

syn muts always neutral

advantageous muts fix more rapidly than neutral

*adaptive mutations within a species will fix and lead to fixed differences between the species

linkage disequilibrium test

uses 1. allele's frequency

2. extent of linkage disequilibrium surrounding it

to detect recent selection

linkage disequilibrium

how used to detect recent selection?

assoc btw single allele at one locus with multiple loci at various distances

the LD test uses LD as a clock for estimating the ages of alleles

Linkage disequilibrium test

if neutral evolution, what do you expect

if positive selection, what do you expect

if neutral

new mut--rare freq; high LD

old mut--rare freq; low LD

common freq; low LD

if positive

new mut--common; high LD

unusually rapid rise in allele freq

advantage of Linkage disequilibrium over Ka/KS and McDonald Kreiger tests

good for detecting recent selection

use phylogeny to test for selection using what method

testing correlations

and how

comparative method

if all share a common ancestor, partic feature they share occurred in common ancestor and was not the result of selection

if different ancestor, does suggest selection

concentrated changes test

asks what

what does it tell you

asks if there is an influence of one character on another

asks if the correlation is significant or not by looking at the phylogeny (depends on distribution of traits along the phylogeny)

if the correlation is significant, it is likely that selection is involved

monophyletic taxa

or clade

 refers to any group of organisms that includes the most recent common ancestor of all those organisms and all the descendants of that common ancestor

cladogram

way to depict phylogenic data

depicts relationships of all species from common ancestor

does not depict time

phylogram

way to depict phylogenic data

phylogenetic tree that explicitly represents number of character changes through its branch lengths.

length of branch proportional to amt of change

homologous

similarities due to common ancestry

analagous

similarities (in diff or same species) sharing common form or function but not common ancestry

independently evolved

non homologous

diff characters sharing neither function nor ancestry

test of homology

that they have common ancestry

not that they have common function

 two diff types of molecular homologies

orthologous vs paralagous

orthologous genes

common ancestry shared through speciation events

paralogous genes

common ancestry shared through gene duplication events

molecular sequence alignments are what type of hypotheses

homology hypotheses

Symplesiomorphy

A character shared by a number of groups, but inherited from ancestors older than the last common ancestor.

Synapomorphy

An apomorphy (derived or specialised character) shared by two or more groups which originated in their last common ancestor.

important of synapomorphic characters

only synapomorphic character states can be used as evidence that taxa are related.

Phylogenetic trees are built by discovering groups united by synapomorphies.

parsimony

what is it

what is the assumption

method

method for inferring phylogeny

assumption: indentities shared more often by common descent than by independent changes

collect alternative phylogenetic hypothesis

evaluate number of evolut. steps

choose most parsimonious tree

outgroup

The chosen outgroup is hypothesized to be rather closely related to the other groups, but less closely than any single one of the other groups is to each other.

The evolutionary conclusion from this is that the outgroup branched from the parent group before the other groups branched from each other.

outgroup representative(s) define the branch containing

the root

need rooted tree to infer what

directionality

Eisen's method of using phylogeny to make predictions about gene function

1. define all homologs

2. hypothesize homologous residues (alignment)

3. infer phylogenic relationships (gene tree)

4. distinguish orthologs from paralogs

5. map known functions to phylogeny

6. reconstruct evolutionary changes

7. predict functions for unknowns by parsimony

identification of different types of homology allows the detection of what

detection of the particular evolutionary event that led to the divergence of homologs

to id these events you need to integrate the gene tree with other info such as gene function, species phenotype, or species phylogeny

Eisen's assumptions in using phylogenomic analysis to make predictions on gene function

that function of uncharacterized proteins can be predicted by position the MutS family tree

1. all orthologs should have the same function

2. paralogs probably have different functions--that's why they coexist (divergence has occurred)

Eisen's phylogenomic analysis to give insights about MutS protein family

used phylogenetic reconstructions

& analysis of complete genome sequences

Eisen's phylogenomic analysis of MutS protein family gave insights into what three areas

1. evolution of MutS protein family
2. diversity of functions within and between species
3. predictions of functions of uncharacterized genes

which variant has the advantage depends on what?

the environment

fitness is context dependent

depends on what give two examples

environment

based on other variations in the genome