BIOL3045 Study Guide - Final Guide: Strong Inference, Atlantic Cod, Variance
14 Jun 2018
School
Department
Course
Professor
Animal Ecological Physiology BIOL3045 460381099
Lecture 1: Introduction.
Environmental change
• Correlation is not sufficient enough to explain cause and effect.
• Need to understand physiology, evolution and ecology to determine how an organism will
respond to an environmental change. Too simple to assume only one possible explanation.
• Correlations of animal population shifts with increasing temperature can suggest climate change
is the cause, however this may be due to other factors such as fishing, hunting, introduced
species, etc.
• Need to use experimental manipulation to explain cause and effect (experimental biology).
• Example: Atlantic cod moved north and disappeared from the south, correlated with increase in
north sea temperature however, was actually due to removal of fish from humans; English
butterfly moved north, correlated with them chasing the climate they evolved in however, was
actually due to them escaping the urbanisation (soot created from coalmines) during the
industrial revolution.
Reading: Platt, J. R. 1964. Strong inference. Science 146, 347-353.
• What is strong inference? The designing of experiments and the suggestion of alternate
hypotheses. They need to be rational and based on the hypothesis you have accepted or
excluded.
• What are its advantages? Based on strong intellectual basis, process is sped up and is more
specific. A method for reaching firm inductive conclusions one after the other, as rapidly as
possible to limit bias and erratic behaviour.
• Does that fat that o to ells ae alike peet ifeee? No, can be used to discover
something great and unknown, just like how other simplified models have been used to uncover
ground breaking information.
• Do ou agee ith the idea that: If ou have a hypothesis and I have enough hypothesis,
eidetl oe ust e eliiated? No, disproving something is very hard to do. There can be
multiple reasons for one explanation. It is too simplistic to assume that there can be only a single
explanation, most processes have multiple causes and their interactions.
Lecture 2: Phenotypic variance.
Sources of variation
Individuals Principal target for selection, differences in individuals allows those with
more preferable traits to be selected for. Association of traits can be used to
explain function. Example: Rats with faster muscle activation have lower
ryanodine receptor mRNA.
Populations Population variance = genetic effects + environmental effects + interaction
between genetic effects and environment + error.
Genetic effects: populations are different in the same environment.
Environmental effects: same populations change in different environments.
Gene-environment effects: different populations have different responses in
different environments. Some increase of decrease more than others.
find more resources at oneclass.com
find more resources at oneclass.com
Animal Ecological Physiology BIOL3045 460381099
Phenotypic plasticity
• Environmentally sensitive production of alternate phenotypes by a given genotype. Every
individual inherits the genetic capability to produce each of the different phenotypes, however
the actual phenotype depends on the particular environment it experiences.
• Reaction norm: phenotypic expression of a single genotype exposed to different acute
environmental conditions. Phenotypic plasticity causes a shift in a reaction norm due to a
chronic change in environment.
Mechanisms underlying phenotypic plasticity
Development Genotype stays the same but access to different gene altered. Genetic
capability maintained across generations. Developmental modifiers selected
for.
Acclimation Physiological change in response to an environmental factor. Reversible
change within adult phenotypes. Genetic capability not altered.
Selection Changes in genotype, genetic capability to produce phenotypes may also
change. Selection for phenotypes that are suited to those conditions, or
maintain performance across a broad range of conditions.
Reading: Huey and Hertz 1984. Is a jack-of all-temperatures a master of none? Evolution 38, 441-444.
• What is the principal of allocation? If an organism allocated energy to one function, it reduces
the amount of energy available to other functions. Partitioning of resources to maximize fitness.
• How would individual plasticity influence selection and the generalist specialist trade-off?
Weaken selection because phenotypes can change independently from sequence changes.
Lecture 3: Experimental design.
Generalist-specialist trade-off
If phenotypes are heritable, then specialization to that
environment occurs.
Variable environments favour performance of generalists.
The trade-off is: maximum performance of generalists is
lower than that of specialists, their reaction norm is wider
but the peak is not as tall as specialists.
Similar to reaction rate vs. temperature where: specialists
have small changes in temp with large changes in reaction
rates; generalists have small change in temp with small
change in reaction rate.
Reading: Drummond, G. B. and Vowler, S. L. 2012. Different tests for a difference: how do we do
research? J. Physiol 590.2, 235-238.
• What is frequentist statistics? Statistics that determines how frequently would a result like this
be observed. Calculates false discovery rates using confidence intervals, effect size, power
analysis.
• What is the sta a i feuetist statistis? Set-up experiments to test for an effect, but
the logic behind the tests is to look for lack of support. Ho will never be true, because there will
always be some differences.
find more resources at oneclass.com
find more resources at oneclass.com
Animal Ecological Physiology BIOL3045 460381099
• What is the Bayesian logic? Bayesian approaches use experimental data to update this prior
knowledge (from experiments and theory).
• What are the strengths of Bayesian logic? Use of data, not the underlying distributions.
• What are permutation tests? Randomization of data to test how frequently one would get a
result as extreme or more extreme as the experimental results, relative to the total number of
permutations. Advantageous because most studies have relatively small sample sizes
• that cannot represent assumed distributions, also has no assumptions.
Lecture 4: Experimental design.
Reading: Altman, N. and Krzywinski 2017. Interpreting P values. Nature Methods 14, 213-214.
• What does the P-value actually signify? The p-value is a probability statement about the
observed sample not about the hypothesis. probability that a difference in means at least as
large as that observed can be generated from random samples if the treatment does not have
an effect.
• Should the P-value be the only and absolute decision making criterion for inferences about
hypotheses? No, it can be quite arbitrary.
• Should one do anything else? Bayesian analysis to help interpretation of P-values, calculation of
false discovery rates, employ confidence intervals and effect size in combination with P-values.
Lecture 5: Adaptation.
• Heritable changes in phenotype that results from natural selection and increase fitness of an
organism in a particular environment.
• It is one response to environmental variation.
• Adaptation can be attributed to : fitness of an individual, through reproductive output and
passing on of an allele; natural selection where there is a change in genetic variability. This can
either be stabilizing or directional.
• There is o eatio o fo a hole speies as idiiduals ithi the a diffe. These
differences are attributed to the following:
Adaptation of reaction norms Selection
• Animals distributed across different climate gradients. Different selection pressures in each
different environment.
• Creates new reaction norms, with optimum temperatures moving up or down.
• Eventually, if one population is separated into a different climate, reproduction isolation with
occur and form two different species (speciation).
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Environmental change: correlation is not sufficient enough to explain cause and effect, need to understand physiology, evolution and ecology to determine how an organism will respond to an environmental change. The designing of experiments and the suggestion of alternate hypotheses. Based on strong intellectual basis, process is sped up and is more specific. No, disproving something is very hard to do. There can be multiple reasons for one explanation. It is too simplistic to assume that there can be only a single explanation, most processes have multiple causes and their interactions. Principal target for selection, differences in individuals allows those with more preferable traits to be selected for. Association of traits can be used to explain function. Example: rats with faster muscle activation have lower ryanodine receptor mrna. Population variance = genetic effects + environmental effects + interaction between genetic effects and environment + error. Genetic effects: populations are different in the same environment.
