Download Lab 2 - Variation Lab Website Introduction To Variation Goals

Lab 2 - Variation
Lab Website
• Laboratory notes,
schedule, etc. now
available on web.
• Notes in pdf format.
http://biology.queensu.ca/~brownjw/Biol206/Lab
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Monday January 13, 2003
Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Introduction To Variation
Goals
• Fundamental to comparative biology
• Raw material and product of
evolution (i.e. the stuff)
• Traits include morphological,
physiological, biochemical,
behavioural, genetic, etc.
• Enables researchers to answer many
different kinds of questions
• To appreciate the importance and uses of
variation in biological investigations
• To be able to distinguish different types of
variation, and understand the distribution of
variation across different scales *
– What types are evolutionarily significant?
• To become familiar with the various
methods for assaying genetic variation
– E.g. phylogenetic affinities, population
history, migration, behavioural, mating
systems, etc.
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Genotype vs. Phenotype
Genotype vs. Phenotype
Genotype:
Phenotype:
• The detectable outward manifestations of a
specific genotype
• ‘Detectable’ how?
• The genetic makeup of an individual
• A representation of the alleles in an individual *
• The nucleotide sequence of an individual’s DNA
– Idea of phenotype has changed drastically over
past 50 years
TGCTACACGATAGAATGTATCT
• E.g. morphological, protein, DNA?
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Genotype vs. Phenotype
Genotype vs. Phenotype
Phenotype:
• Functional definition may be better:
Æ
– ‘Seen’ by natural (or unnatural) selection
– Can be morphological, physiological,
biochemical, behavioural, etc.
Æ
• E.g. size, resistance, fecundity, metabolic rate, etc.
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Genotype vs. Phenotype
Genotype Æ Phenotype
• It is often easier to determine the relationship
between genotype and phenotype when you
consider one trait at a time (e.g. colour, etc.)
• Trait is influenced by alleles at relevant
genetic loci (= genotype)
• Translation into phenotype is complicated by
environmental and developmental conditions
Phenotype:
• Problems with the functional definition:
– We may not be able to determine
the functional role of many traits
– Some traits are vestigial
• E.g. eyes in cave fish, appendix in humans
• Underlies idea of ‘phenotypic plasticity’
• May depend on fundamental processes
– Different environmental conditions
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Genotype Æ Phenotype
Discrete vs. Continuous
Variation
• Discrete (polymorphic) variation:
• Number of loci influencing trait often
determines relationship between genotype
and phenotype
– Can affect how fast trait will evolve
– Determines appropriate analyses (e.g. statistics)
– Often determines distribution of variation *
– Usually controlled by few loci (1 or 2)
– Individuals can be assigned to a small number
of phenotypic categories
• Consider a trait controlled by one locus:
– If dominance is present, there will be two
phenotypic classes (E.g. tall, short)
– If codominant, there will be three classes
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Discrete vs. Continuous
Variation
• Discrete (polymorphic) variation:
– Usually controlled by few loci (1 or 2)
– Individuals can be assigned to a small number
of phenotypic categories
• Consider a trait controlled by one locus:
– If dominance is present, there will be two
phenotypic classes (E.g. tall, short)
– If codominant, there will be three classes
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Discrete vs. Continuous
Variation
Discrete vs. Continuous
Variation
• Continuous (polygenic) variation:
– Also called ‘quantitative genetic control’
• Simple example – Mendel’s peas
– Controlled by one locus
– Smooth is dominant to wrinkled
– Peas are either smooth (SS or Ss) or wrinkled (ss)
– Controlled by many (> 3) loci
– No discrete phenotypic classes – full range of
phenotypic expression (E.g. human height)
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Discrete vs. Continuous
Variation
• Continuous (polygenic) variation:
• Additive model – each locus has an equal
effect on the trait in question
– However, may involve major gene control and
modifier genes
• Threshold model – requires a certain number
of alleles to affect trait at all
– results in a discontinuous distribution
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Additive Model
Additive Model
Individual #1
Individual #2
Individual #1
Individual #2
++-+-+++-+
++++++-+++
+-+--+-+--+-+---+-+
++-+-+++-+
++++++-+++
+-+--+-+--+-+---+-+
* + adds 5 grams to body size, - does nothing
* + adds 5 grams to body size, - does nothing
How much more does individual 1 weigh?
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Discrete vs. Continuous
Variation
Major Gene Control
• Continuous (polygenic) variation:
• Additive model – each locus has an equal
effect on the trait in question
– However, may involve major gene control and
modifier genes
• Threshold model – requires a certain number
of alleles to affect trait at all
– results in a discontinuous distribution
Individual #1
Individual #2
++-+-+++-+
++++++--++
+-+--+-+--+-+---+-+
* + adds 5 grams to body size, - does nothing
+ adds 50 grams to body size
- other loci are “modifier genes”
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Discrete vs. Continuous
Variation
• Continuous (polygenic) variation:
Body Size
• Additive model – each locus has an equal
effect on the trait in question
– However, may involve major gene control and
modifier genes
• Threshold model – requires a certain number
of alleles to affect trait at all
Number of + alleles
– results in a discontinuous distribution
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Discrete vs. Continuous
Variation
• Distinguishing between polymorphic
and polygenic traits
Body Size
– Complicated by genotype by environment
interactions
– Introduces ‘random noise’ into phenotype
• E.g. a polymorphic trait may appear
polygenic
Number of + alleles
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Discrete vs. Continuous
Variation
Levels Of Variation
*Know this COLD! Phenotypic variation
Polymorphic
Polygenic
Genotypic variation
Discrete
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
• Variation (both phenotypic and genotypic)
can occur at different scales
Continuous
– Individual Æ Population Æ Species
USUALLY
- Modifiers
- Thresholds
- Supergenes
- Environmental
variance
• The distribution of variation across these
different scales has importance for both the
process of evolution and the types of
questions we can ask
USUALLY
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Variation Within Individuals
Variation Among Individuals
Within Populations
• Phenotypic:
• This is the level at which evolution operates *
– ‘Developmental variation’ - has no genetic basis
• Genotypic:
– Only if phenotypic variation comes about because
of underlying genetic variation
• Amount of variation present can indicate
mating system, population history, etc.
– Heterozygotes have ‘allelic variation’
– Important for both fitness and measuring
migration
– E.g. selfing vs. outcrossing
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
Variation Among Populations
Within A Species
Frequencies
• Defining a ‘population’ can often be tricky
– But ignore this for now
• Question: Are populations genetically identical?
• Must be able to calculate allele and
genotype frequencies (simple proportions)
for populations and species
– Diverging evolutionary forces tend to cause
population differentiation, while homogenizing
forces tend to counter this
• May indicate species history, migration, etc.
Allele Frequency
=
# Ax alleles
Total # of all alleles
Genotype Frequency
=
# AxAy individuals
Total # of all individuals
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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Next Week
• Quiz #1 on Lab #2 material * * *
• Read lab manual before you come
to lab next week
– Mating Systems
• Very important/difficult topic
• Will be tested directly on this
(Quizzes/Exams)
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Biology 206 Lab #2 – Variation
Joseph W. Brown - January 13, 2003
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