Quant Bio Exam 2

Question 1

Coalescent

Answer 1

theoretical model used in population genetics to describe the evolutionary relationships within a sample of alleles or sequences

Question 2

Goal of Coalescent Theory

Answer 2

model of the distribution of gene divergence in a genealogy. It is used to estimate population genetic parameters (like population size, migration rates, and recombination rates) and to perform hypothesis testing

Question 3

Total Branch Length in a Coalescent Tree

Answer 3

Total Branch Length (TBL) measures how much history genes share. It is usually calculated by weighting time intervals by the number of lineages in the epoch

Question 4

Genetic Drift

Answer 4

Evolution without selection or mutation

Question 5

Nearly Neutral Theory

Answer 5

explains how genetic drift (random chance) can be the dominant factor in evolution, even for nearly neutral mutations (have a slight effect on fitness) but are so weak that they behave essentially as neutral mutation

Question 6

Genetic Drift and Beneficial Mutations

Answer 6

Even with a selective advantage, most beneficial mutations do not fix in the population

Question 7

Key Prediction about Coding Regions

Answer 7

Synonymous (silent) sites should evolve faster than non-synonymous (replacement) sites because synonymous mutations are less likely to alter function and are therefore more likely to be neutral

Question 8

Non-degenerate sites

Answer 8

All possible changes at this site are nonsynoymous

Question 9

Two-fold degenerate

Answer 9

If one of the three ends changes the code can be one of two things

Question 10

four-fold degenerate

Answer 10

all possible changes are synonymous

Question 11

Neutral Theory

Answer 11

much of th egenetic variation present in populations are. a reflection of mutation and drift, two interacting processes

Question 12

at a molecular level…

Answer 12

most evolution is nuetral

Question 13

the coalecent is a model which

Answer 13

describes the relationship within a sample from the present

Question 14

selection for benificial mutation is less common than

Answer 14

removal of harmful mutation and the fixation of nuetral mutations

Question 15

EAF

Answer 15

ecosystem approach to fisheries

Question 16

Why do we need an EAF management system?

Answer 16

• Because of previous failures in ‘traditional’ fisheries management
• fisheries must include management in peoples actions surrounding fish and Not just fish
• concerns over global fish stock
• EAF helps to manage the negative affects on ecosystems, non-target species, habitats and biodiversity
• (broadly) EAF helps to consider the broader aspects surrounding fishing

Question 17

What is ecosystem modeling?

Answer 17

a qualitative and quantitative representation of ecological interactions (e.g.,
predator-prey interactions, anthropogenic disturbances and natural disturbances)
between various ecosystem components (e.g., species or functional grou

Question 18

Core purposes of ecosystem model

Answer 18

• describing and understanding the current ecosystem
• forecasting and hindcasting scenarios (e.g., climate change, fishing)
• support management decision

Question 19

Purpose of Ecosim

Answer 19

Ecosim is the temporally-dynamic model component of the EwE suite. It is used to explore changes in policy and environmental stressor impacts on the ecosystem over time

Question 20

matrix population model

Answer 20

linear, deterministic model that produces exponential growth

Question 21

core recursion equation

Answer 21

n_t+1 = A * n_t

Question 22

A is called the projection matrix because

Answer 22

it projects the number of individuals in each age class at time t + 1 from the number of individuals in each age class at time t

Question 23

Population vector

Answer 23

column vector, represents the number of individuals in each life stage (e.g., age, size, or other categories) of a population at a specific time

Question 24

seven steps to modeling a biological problem

Answer 24

Formulating the question, determining ingredients, qualitative and quantitative description, analysis, checks, relating results

Question 25

matrix (A) position: Fecundity (F)

Answer 25

first row

Question 26

matrix (A) position: Stasis (S) (self loops)

Answer 26

on the diagonal

Question 27

matrix (A) position: Progression

Answer 27

below the diagonal

Question 28

Sensitivity

Answer 28

absolute change in λ resulting from a small absolute change in a matrix element (a_ij)

Question 29

Elasticity

Answer 29

proportional change in λ resulting from a small proportional change in a matrix element (a_ij)

Question 30

Elasticities across all matrix elements sum to

Answer 30

1

Question 31

Stochastic Population Growth Rate

Answer 31

for stochastic models, λ is typically calculated numerically as the mean of the log() of population ratios over a long simulation run

Question 32

Environmental stochasticity

Answer 32

a concept within population dynamics that describes random environmental events that result in variation of population size

Question 33

demographic stochasticity

Answer 33

the random fluctuation in population size caused by chance events in births and deaths

Question 34

demographic stochasticity is typically (what?) in large populations

Answer 34

unimportant

Question 35

hitchhiking effect

Answer 35

rapidly spreading beneficial mutation, which results in local removal of standing genetic variation (still, this is LESS COMMON than removal of harmful mutation and the fixation of nuetral mutations)

Question 36

1 / 2 N_e (where N_e is the effective population size)

Answer 36

the probability that two randomly chosen alleles are copies of the same allele in the previous generation

Question 37

N_e

Answer 37

effective population size

Question 38

coalecence trees help us to understand

Answer 38

a populations history

Question 39

Coalescent Trees

Answer 39

models trace the ancestry of sampled alleles/sequences backward in time to their common ancestor. They model the gene genealogy within a population or species

Question 40

Phylogenetic Trees

Answer 40

trace the evolutionary history of species, populations, or divergent taxa (phylogeny) (they are tree reconstruction methods)

Question 41

Coalescent Trees are driven by

Answer 41

stochastic processes, specifically genetic drift and population size (). They are often used for simulations to repeatedly draw samples under specific population parameters and are usually not inferred from data in the same way as phylogenies

Question 42

Phylogenetic Trees construction

Answer 42

tree reconstruction methods inferred from the observed sequence divergence between taxa

Question 43

Phylogenetic Trees: Branches

Answer 43

represent evolutionary time or the number of substitutions separating taxa.

Question 44

Coalescent Trees: Branching

Answer 44

the point in the past where two ancestral lineages merge, branch lengths represent time epochs (usually in generations, scaled by N(sub_e) during which a specific number of lineages existed

Question 45

effective population size (N e )

Answer 45

is the number of breeding individuals

Question 46

census size

Answer 46

the actual count of individuals (N_c)

Question 47

original Neutral Theory

Answer 47

most mutations that fix are either neutral (having no effect on fitness) or highly deleterious (and quickly removed)

Question 48

The Vulnerability Parameter

Answer 48

expresses a prey's control in the food web

Question 49

Low vulnerability rates

Answer 49

imply bottom-up control (predation rate is limited by how fast prey become vulnerable)

Question 50

High vulnerability rates

Answer 50

imply top-down control (predator is in control of prey population)

Question 51

Statistical Criteria for Best Fit: The best fit model is determined using two primary criteria:

Answer 51

Weighted Sum of Squared Residuals (SS): Measures the discrepancy between observed and predicted data and Akaike’s Information Criterion (AICc): AICc is a measure of model fit penalized by model complexity () (the number of parameters estimated). A lower AICc value indicates a 'better' fit of the model

Question 52

flux

Answer 52

a flow rate of mass or energy

Question 53

Four modes of energy exchange

Answer 53

1. Conduction 2. Convection 3. Radiation 4. Latent Heat Flux

Question 54

Conduction

Answer 54

Heat transfer by direct contact between two bodies

Question 55

Convection

Answer 55

Heat or mass transport by fluid (air) flow

Question 56

Radiation

Answer 56

Transfer of energy by electromagnetic energy * No molecular contact * eg. sun vs shade

Question 57

Latent heat flux

Answer 57

Movement of heat by water change phase (liquid to vapour) - Huge amount of E involved (sanity check)

Question 58

Ohm’s Law

Answer 58

Describes flow of current through an electric circuit

Question 59

W =

Answer 59

J/s