Midterm 2

Question 1

Maximum Parisomy

Answer 1

When building a genetic tree the least number of steps is the most likely option.

Question 2

What type of data should be used in building phylogeny trees?

Answer 2

1)Homologous traits
2)Discreet traits
3)Variable Traits
4)In dependant traits

Question 3

Two assumptions of Kimura theory

Answer 3

Variable Base frequencies and variable substitutions

Question 4

Bootstrapping

Answer 4

Random align sequence sampling to construct hundreds of possible trees, the more time a branch or node appears via this generation the higher boot strap value is produced.

Question 5

What increases boot strap value?

Answer 5

The more change a sequence has the higher bootstrap value as each time you sample its more likely that that branch will not align with another.

Question 6

Factors that affect our ability to build a tree based on maximum parisomy

Answer 6

1)Horizontal gene transfer
2)Analogy looks like homology
3)Characters are dependant
4)Changes do not occur at a standard rate
5)Missing taxa data
6)Contamination in sampling.

Question 7

Ultra-metric tree

Answer 7

A phylogentic tree where the length of branches equals the amount of time that has passed since a species diverged from a node.

Question 8

Additive tree

Answer 8

A phylogentic tree where each branch represents the amount of genetic change a species has undergone since the last divergence.

Question 9

synapomorphy

Answer 9

a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants.

Question 10

Homoplasy

Answer 10

the development of organs or other bodily structures within different species, which resemble each other and have the same functions, but did not have a common ancestral origin.

Question 11

Apomorphy/ Autapomorphy

Answer 11

a specialized trait or character that is unique to a group or species

Question 12

pleisomorphy/ synapomorphy

Answer 12

The ancestral character state for a particular clade

Question 13

Polytomy

Answer 13

A node on a phylogeny where more than two lineages descend from a single ancestral lineage

Question 14

Challenges of synapomorphies used to build trees

Answer 14

1)Lack of fossil evidence
2)Analogy
3)Reversals

Question 15

Paraphylectic group

Answer 15

A group that includes the common ancestor and some but not all its descendants ex. reptiles that do not include birds

Question 16

Polyphletic group

Answer 16

A group that includes a few descendants but no common ancestor ex. warm blooded creatures

Question 17

Unrooted Phylogentic tree

Answer 17

illustrate the relatedness of the leaf nodes without making assumptions about ancestry

Question 18

Dn

Answer 18

Rate of non synonymous mutations

Question 19

Ds

Answer 19

Rate of synonymous mutations

Question 20

What does it mean when Dn/Ds is =1, >1, <1

Answer 20

<1= Advantageous mutations are being selected for
=1 means equal or no selection
>1 Purifying selection on deleterious mutations

Question 21

Purifying selection

Answer 21

selection to remain the same, aka reduces genetic diversity, both at sites under direct selection and at linked neutral sites.

Question 22

Directional selection

Answer 22

a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction

Question 23

Codon Bias

Answer 23

Genes which are heavily transcribed have very low rates of synonymous mutations because of transnational efficiency.

Question 24

Tipping point for selection and drift

Answer 24

s ~ (1/2Ne)

Question 25

Relation between animal size and selection and drift

Answer 25

Small animals are governed by selection, large animals by drift

Question 26

Neutral Theory

Answer 26

Most changes we see are neutral so drift is the primary driver of evolutionary change on a genetic level.

Question 27

Difference between the neutral and nearly neutral theory

Answer 27

In the Neutral theory drift and selection are in equilibrium in the nearly neutral theory drift and selection are in direct competition with one another.

Question 28

The two branches of evolutionary genetics

Answer 28

Population genetics:the study of genetic variation within and among populations and the evolutionary factors that explain this variation and Quantitative Genetics: the study of the genetic basis underlying phenotypic variation among individuals.

Question 29

4 ways alleles and phenotypes interact

Answer 29

1)Dominance: Interaction at a singular locus 2)Epistasis: the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes 3)Pleiotrophy:a single gene affects two or more characters 4)Plasticity: Traits are dependant on the enviroment

Question 30

Stipulations of Hardy Weinberg Equilibrium

Answer 30

1)No selection 2)No migration 3)No mutation 4)Random mating 5)Large population

Question 31

Viability selection

Answer 31

Selection resulting from differences in survival rate

Question 32

Fecundity selection

Answer 32

Selection resulting from differences in reproductive success

Question 33

Change in allele frequency of one allele

Answer 33

ΔP= (p^2W11+pqW12)/ŵ

Question 34

what does ŵ represent

Answer 34

mean fitness or p^2W11+2pqW12+q^2W22

Question 35

Selection with a dominant allele is

Answer 35

fast but takes very long to reach fixation as recessive alleles are hard to weed out

Question 36

Selection with a recessive allele is

Answer 36

Slow but once common reaches fixation quickly

Question 37

four ways genetic diversity is maintained

Answer 37

1) Recessive alleles are hard to get rid of 2)Via selection 3)recurrent mutation 4)Drift

Question 38

Three ways selection helps maintain diversity

Answer 38

1)Hetero zygote advantage :the mix is better than its parts 2)Frequency dependant selection:The success of a trait depends on its frequency 3)Local adaptation: Each region has different fitness for the same allele

Question 39

Formula for determining the chance of a negative selection allele to arise

Answer 39

q=sqrt(mutation rate(u)/selection(s))

Question 40

What is purging

Answer 40

the reduction of the frequency of a deleterious allele, caused by an increased efficiency of natural selection prompted by inbreeding

Question 41

Inbreeding depression

Answer 41

reduced survival and fertility of offspring of related individuals due to the exposure of deleterious mutations to natural selection

Question 42

What causes inbreeding?

Answer 42

small population size or use of breeding systems

Question 43

Assortative vs Disassortative mating

Answer 43

Assortative mating is when individuals breed with those similar to them phenotypically, Disassortative is the opposite where individuals breed with those that are phenotypically different

Question 44

Gene flow

Answer 44

The movement of individuals followed by mating or movement of gameetes

Question 45

What is the main effect of geneflow?

Answer 45

Causes single generation allele frequency shifts

Question 46

What is the effect of migration?

Answer 46

1)homogenization of populations where the island ends up becoming the mainland frequency 2)Depress fitness/ affect local adaptation

Question 47

Genetic drift

Answer 47

A random process that results in change of allele frequency between generations

Question 48

The causes of drift

Answer 48

1)Background drift, populations work through cycles 2)Founder effect 3)Population bottle necks

Question 49

Probability of an allele going to fixation

Answer 49

x/2n

Question 50

Formula for effective population size

Answer 50

Question 51

Loss of heterozygosity per generation

Answer 51

Question 52

What effects the size of Effective population size

Answer 52

1)Variation in regular population 2)Sex ratio 3)Variation in family size

Question 53

Vge

Answer 53

Variation of phenotype due to interaction between genes and enviroment

Question 54

Vg

Answer 54

Genetic variance

Question 55

Ve

Answer 55

Environmental variance (not heritable)