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Genetics 101: Genetic differentiation in the age
of ecological restoration
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Susan J. Mazer
Department of Ecology, Evolution & Marine Biology
University of California, Santa Barbara
[email protected]
Genetics 101: Genetic differentiation in the age
of ecological restoration
Q
T I F F
a r e
u ic k T im
( U n c o m
n e e d e d
e ™
a n d
a
p r e s s e d )
d e c o m p r e s s o r
t o
s e e
t h is
p ic t u r e .
Susan J. Mazer
Department of Ecology, Evolution & Marine Biology
University of California, Santa Barbara
[email protected]
Genetic concepts to be considered
• Rules of inheritance
• Genetic processes
• Consequences of mismatches between sources
of material for restoration and
(a) the environment of the restoration site or
(b) the genotypes resident at the restoration site
Up and running: common vocabulary
Population
genetic
processes
Genetic
phenomena
Ecological
considerations
Up and running: common vocabulary
Population
genetic
processes
Inheritance in a nutshell
Local adaptation
Genetic differentiation
Genetic drift
Founder effect
Genetic swamping
Genetic
phenomena
Ecological
considerations
Up and running: common vocabulary
Population
genetic
processes
Genetic
phenomena
Inheritance in a nutshell
Ecotype
Local adaptation
Heterosis & “hybrid vigor”
Genetic differentiation
Inbreeding depression
Genetic drift
Outbreeding depression
Founder effect
Hybrid breakdown
Genetic swamping
Ecological
considerations
Up and running: common vocabulary
Population
genetic
processes
Genetic
phenomena
Ecological
considerations
Inheritance in a nutshell
Ecotype
Phenology
Local adaptation
Heterosis & “hybrid vigor”
Pollen limitation
Genetic differentiation
Inbreeding depression
Climate change
Genetic drift
Outbreeding depression
Founder effect
Hybrid breakdown
Genetic swamping
Inheritance in a tiny nutshell
• Gene: The sequence of DNA that determines the expression
of a given trait.
Inheritance in a tiny nutshell
• Gene: The sequence of DNA that determines the expression
of a given trait.
• Most species are diploid: Each gene is present in two
copies or alleles, one on each member of a chromosome
pair. Each allele is inherited from one parent.
Inheritance in a tiny nutshell
• Gene: The sequence of DNA that determines the expression
of a given trait.
• Most species are diploid: Each gene is present in two
copies or alleles, one on each member of a chromosome
pair. Each allele is inherited from one parent.
• One or more genes determine the appearance or
performance of an individual for a given trait (e.g., drought
tolerance, flower color, seed size, timing of flowering).
Inheritance in a tiny nutshell
• Gene: The sequence of DNA that determines the expression
of a given trait.
• Most species are diploid: Each gene is present in two
copies or alleles, one on each member of a chromosome
pair. Each allele is inherited from one parent.
• One or more genes determine the appearance or
performance of an individual for a given trait (e.g., drought
tolerance, flower color, seed size, timing of flowering).
• When the two alleles of a gene are identical, an individual is
homozygous for this gene or trait.
Inheritance in a tiny nutshell
• Gene: The sequence of DNA that determines the expression
of a given trait.
• Most species are diploid: Each gene is present in two
copies or alleles, one on each member of a chromosome
pair. Each allele is inherited from one parent.
• One or more genes determine the appearance or
performance of an individual for a given trait (e.g., drought
tolerance, flower color, seed size, timing of flowering).
• When the two alleles of a gene are identical, an individual is
homozygous for this gene or trait.
• When the two alleles of a gene differ, the individual is
heterozygous for this gene or trait.
Up and running: common vocabulary
• Local adaptation:
The process in which natural selection favors different
alleles or genetic types (genotypes) in different
environments.
Up and running: common vocabulary
• Local adaptation:
The process in which natural selection favors different
alleles or genetic types (genotypes) in different
environments.
Up and running: common vocabulary
• Local adaptation:
The process in which natural selection favors different
alleles or genetic types (genotypes) in different
environments.
Result: genetic differences between plant populations in
locations that differ in attributes such as…
soil quality
climate (temperature, rainfall, date of first frost)
identity of pollinators
presence and composition of competing species
presence of predators
presence and identity of diseases
Up and running: common vocabulary
• Genetic differentiation
The process and the outcome of genetic
divergence among populations, resulting from
natural selection.
Up and running: common vocabulary
• Genetic differentiation
The process and the outcome of genetic
divergence among populations, resulting from
natural selection.
Genetic differentiation among populations can
also result from random processes such as
genetic drift and founder effects.
Genetic differentiation: example
• Broadleaf lupine, Lupinus latifolius (D. L. Doede, 2005)
84 populations sampled; 4 distinct seed zones detected
associated with watershed, topography, and climate
Populations differ
in plant size and
flowering time
when raised in a
common
environment
Genetic differentiation: example
• Broadleaf lupine, Lupinus latifolius
84 populations sampled; 4 distinct seed zones detected
associated with watershed, topography, and climate
Populations differ in
growth form or habit
Genetic differentiation: example
• Broadleaf lupine, Lupinus latifolius
84 populations sampled; 4 distinct seed zones detected
associated with watershed, topography, and climate
Populations differ in
flower color
Up and running: common vocabulary
• Genetic drift
Random fluctuations in the frequency of a
specific gene in a small isolated population due to
chance.
The process by which gene frequencies change at
random from generation to generation in small
populations due to the chance sampling of
different genes among the successful egg and
sperm.
Up and running: common vocabulary
• Genetic drift
Random fluctuations in the frequency of a
specific gene in a small isolated population due to
chance.
The process by which gene frequencies change at
random from generation to generation in small
populations due to the chance sampling of
different genes among the successful egg and
sperm.
Over time, there is a net loss of heterozygosity
and an increase in homozygosity until some
alleles are lost forever…..
Up and running: common vocabulary
• Genetic drift
Start with 10 alleles
Several generations of random sampling
Only 6 of the original alleles
have left descendants
Several generations of random sampling
Only 2 of the original alleles
(and their descendants)
remain.
Up and running: common vocabulary
• Founder effect
Genetic drift observed in a population founded by a
small, non-representative sample of a larger
population. Rare alleles may become common by
chance.
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Up and running: common vocabulary
• Founder effect
Genetic drift observed in a population founded by a
small, non-representative sample of a larger
population. Rare alleles may become common by
chance.
Example: A small group of seeds collected from a
large population may contain genotypes that do not
fully represent the population.
Small samples from large populations typically
include less genetic variation than the original
population.
This reduced genetic variation can limit the
population’s ability to survive and to persist in a novel
environment.
Founder effect: example
• Hawaiian silverswords
Surviving populations of silverswords (Argyroxiphium
sandwicense and A. kaunense: Asteraceae) have experienced
severe bottlenecks and are genetically depauperate.
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A restored population of the Mauna Kea silversword, A. sandwicense,
consists of 1500 individuals all derived from a two or three original
parents.
Up and running: common vocabulary
• Genetic swamping or Dilution
Rapid increase in the frequency of an introduced
genotype that may lead to the replacement of
local genotypes.
Up and running: common vocabulary
• Genetic swamping or Dilution
Rapid increase in the frequency of an introduced
genotype that may lead to the replacement of
local genotypes.
Cause: a short-term or long-term fitness
advantage of the introduced genotype.
Up and running: common vocabulary
• Genetic swamping or Dilution
Rapid increase in the frequency of an introduced
genotype that may lead to the replacement of
local genotypes.
Cause: a short-term or long-term fitness
advantage of the introduced genotype.
Consequence: a reduction in genetic variation
relative to the initial mixture of resident and
introduced genotypes.
Up and running: common vocabulary
Population
genetic
processes
Genetic
phenomena
Inheritance in a nutshell
Ecotype
Local adaptation
Heterosis & “hybrid vigor”
Genetic differentiation
Inbreeding depression
Genetic drift
Outbreeding depression
Founder effect
Hybrid breakdown
Genetic swamping
Ecological
considerations
Up and running: common vocabulary
• Ecotype:
The smallest subdivision of a species, consisting
of populations adapted to a particular set of
environmental conditions. These populations may
be infertile when crossed with other ecotypes of
the same species.
Up and running: common vocabulary
• Ecotype:
The smallest subdivision of a species, consisting
of populations adapted to a particular set of
environmental conditions. These populations may
be infertile when crossed with other ecotypes of
the same species.
In other words, ecotypes are genetically distinct
populations within a species, resulting from
adaptation to local environmental conditions.
Up and running: common vocabulary
• Ecotype:
The smallest subdivision of a species, consisting
of populations adapted to a particular set of
environmental conditions. These populations may
be infertile when crossed with other ecotypes of
the same species.
In other words, ecotypes are genetically distinct
populations within a species, resulting from
adaptation to local environmental conditions.
G. Turesson. 1922. The species and variety as
ecological units.
Ecotypes: example
Beach ecotype,
prostrate habit
with pubescent
leaves
Mountain
ecotype, erect
shrub with
hairless leaves
Hybrid leaves
Beach
ecotype
Mountain
ecotype
Ecotypes of Sida fallax and their hybrids in Hawai’i. A. Beach ecotype. B. Mountain ecotype.
C, D, and E: hybrid leaves. F: Beach flower. G. Hybrid flower. H. Mountain flower.
Up and running: common vocabulary
• Heterosis
Where heterozygotes within a species or within a
population have higher fitness than homozygotes.
Hybrid varieties of maize are
often prized for their
consistently high performance
Up and running: common vocabulary
• Hybrid vigor (“interspecific heterosis”)
Where the hybrids between two species perform
better than either of the parent species.
Loganberry is a highperforming hybrid
between raspberry and
blackberry
Up and running: common vocabulary
• Heterosis and “hybrid vigor”
Where heterozygotes within a species or the
hybrids between species have a higher fitness
than either of their parents.
Heterozygotes often grow better, are better able to
survive, and/or are more fertile than the
homozygotes.
Up and running: common vocabulary
• Heterosis and “hybrid vigor”
Where heterozygotes within a species or the
hybrids between species have a higher fitness
than either of their parents.
Heterozygotes often grow better, are better able to
survive, and/or are more fertile than the
homozygotes.
This observation often causes people to think that
mixing genotypes from two or more populations
is always good.
Up and running: common vocabulary
• Inbreeding depression
Reduction in performance following mating
between very closely related individuals of the
same species.
Up and running: common vocabulary
• Inbreeding depression
Reduction in performance following mating
between very closely related individuals of the
same species.
The union of gametes produced by very close
relatives can generate offspring with high
frequencies of (recessive) genetic diseases in
homozygous form.
Up and running: common vocabulary
• Inbreeding depression
Reduction in performance following mating
between very closely related individuals of the
same species.
The union of gametes produced by very close
relatives can generate offspring with high
frequencies of (recessive) genetic diseases in
homozygous form.
This observation often reinforces the assumption
that mixing genotypes from multiple populations
will improve the performance of the resulting
population.
Up and running: common vocabulary
• Inbreeding depression
Inbreeding depression: example
• Port Orford Cedar (Scott E. Kolpak, Richard A.
Sniezko, and Christine F. Hayot)
Ovules fertilized by self-pollination are less
likely to mature successfully than those
fertilized with outcross pollen
Seedings derived from self-pollination are
shorter than those produced by outcrossing
Seedling height by cross type
Height (cm)
% Filled seed
% filled seed by cross type
Outcross
Cross type
Self
Outcross
Open
Cross type
Self
Up and running: common vocabulary
• Outbreeding depression
Reduction in population performance following
hybridization between genetically distinct
individuals of the same species.
Mating between genotypes adapted to different
environmental conditions can generate offspring
that are poorly adapted to the home environments
of either parent.
Up and running: common vocabulary
• Outbreeding depression
Reduction in population performance following
hybridization between genetically distinct
individuals of the same species.
Mating between genotypes adapted to different
environmental conditions can generate offspring
that are poorly adapted to the home environments
of either parent.
Outbreeding depression: example
• Lotus scoparius (Fabaceae: deerweed)
Mean number of seeds per
flower
The success of crosses between populations
decreases with the genetic distance between the
populations (Montalvo & Ellstrand, 2001).
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Genetic Distance between
crossed plants
Up and running: common vocabulary
• Hybrid breakdown
Up and running: common vocabulary
• Hybrid breakdown
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Up and running: common vocabulary
• Hybrid breakdown
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QuickTime™ and a
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Up and running: common vocabulary
• Hybrid breakdown
“Classic” definition: Where the first-generation
hybrid offspring between two species are healthy,
but subsequent generations resulting from the
matings between these hybrids perform poorly.
Up and running: common vocabulary
• Hybrid breakdown
“Classic” definition: Where the first-generation
hybrid offspring between two species are healthy,
but subsequent generations resulting from the
matings between these hybrids perform poorly.
Updated definition: Where the first-generation
hybrid offspring between two ecotypes or
genotypes within a species are healthy, but
subsequent generations resulting from the
matings between these hybrids are unhealthy and
decrease in frequency.
Hybrid breakdown: examples
• Agrostemma githago & Silene alba (Caryophyllaceae): The F2
generation has poorer performance than either of the original parental
resident and foreign genotypes.
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Agrostemma lithago
Silene alba
Hufford & Mazer, TREE, 2003
Hybrid breakdown: examples
• Agrostemma githago & Silene alba (Caryophyllaceae): The F2
generation has poorer performance than either of the original parental
resident and foreign genotypes.
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QuickTime™ and a
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Agrostemma lithago
Silene alba
Hufford & Mazer, TREE, 2003
Mechanism of Hybrid Breakdown beteen
Genotypes Participating in Restoration Effort
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Resident
Population
Under
Restoration
Source
Population of
Introduced
Genotypes
If local adaptation has occurred, resident and
source populations will be genetically distinct
and homozygous for alternative alleles of the
same gene
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Resident
Population
Under
Restoration
Source
Population of
Introduced
Genotypes
Restoration Phase I: Introduction of genotypes from
a chosen “source” population
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Resident
Population
Under
Restoration
Source
Population of
Introduced
Genotypes
Restoration Step II: Mating between genotypes of
resident and source populations….What is the fate
of these hybrids?
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Resident
Population
Under
Restoration
F1 Hybrids
produced
Following
Introduction
Source
Population of
Introduced
Genotypes
Genotypes Participating in Restoration Effort:
What is the fate of these hybrids?
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Bb
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Resident
Population
Under
Restoration
F1 Hybrids
produced
Following
Introduction
Source
Population of
Introduced
Genotypes
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
aa
BB
CC
dd
EE
X
aA
Bb
Cc
dD
Ee
F2 generation
following
recombination
Parent 2
AA
bb
cc
DD
ee
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
Parent 2
aa
BB
CC
dd
EE
aA
Bb
Cc
Assume: Parent
dD at
is a resident
Ee
X
1
restoration site or
adapted to its
F2environment.
generation
following
recombination
AA
bb
cc
DD
ee
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
Parent 2
aa
BB
CC
dd
EE
aA
Bb
Cc
Assume: Parent
dD at
is a resident
Ee
X
1
restoration site or
adapted to its
F2environment.
generation
following
recombination
AA
bb
cc
DD
ee
Assume: Parent 2
is adapted to an
alternative
environment and
genetically distinct
from Parent 1.
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
F1
hybrid
aa
BB
CC
dd
EE
Parent 2
X
AA
bb
cc
DD
ee
aA
Bb
Cc
dD
Ee
F1
hybrids will have a full complement of
F2 generation
alleles
followingfrom each parent, so they may
recombination
function well at restoration site
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
aa
BB
CC
dd
EE
Parent 2
X
AA
bb
cc
DD
ee
aA
Bb
Cc
dD
Ee
F1
hybrid
F2 generation
following
recombination
Following sexual
reproduction, F2
hybrid offspring will
regain homozygosity
at many loci
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
aa
BB
CC
dd
EE
Parent 2
X
AA
bb
cc
DD
ee
aA
Bb
Cc
dD
Ee
F1
hybrid
F2 generation
following
recombination
Where F2s are
homozygous for
genes from Parent 2,
they may not be well
adapted to Parent
1’s environment
Hybrid Breakdown
Parent 1
Homozygous
diploid
parents
aa
BB
CC
dd
EE
X
aA
Bb
Cc
dD
Ee
F1
hybrid
F2 generation
following
recombination
Parent 2
AA
bb
cc
DD
ee
Mean Population Fitness
Possible Outcome of Hybridization between Resident
and Introduced Genotypes
F1 generation
exhibits hybrid vigor.
After the first
generation of
hybridization,
population mean
fitness declines as
homozygotes are
reconstituted
Residents
Hybrids
Residents
+ Hybrids
Mean Population Fitness
Possible Outcome of Hybridization between Resident
and Introduced Genotypes
F1 generation exhibits
genetic swampling or
dilution. After the first
generation of
hybridization,
population mean
fitness increases as
resident homozygotes
are reconstituted.
Residents
Hybrids
Residents
+ Hybrids
After 1st generation,
population mean fitness
declines as adaptive
combinations are shuffled
Mean Population Fitness
Mean Population Fitness
Possible Outcomes of Hybridization between Resident
and Introduced Genotypes
Magnitude of decline will
depend on strength of
natural selection
Residents
Hybrids
Residents + Hybrids
Up and running: common vocabulary
Population
genetic
processes
Genetic
phenomena
Ecological
considerations
Inheritance in a nutshell
Ecotype
Phenology
Local adaptation
Heterosis & “hybrid vigor”
Pollen limitation
Genetic differentiation
Inbreeding depression
Climate change
Genetic drift
Outbreeding depression
Founder effect
Hybrid breakdown
Genetic swamping
Up and running: common vocabulary
• Phenology
The study of the timing of biological events
Up and running: common vocabulary
• Phenology
The study of the timing of biological events
Includes critical events such as:
The timing of germination, which often influences
early seedling survivorship
The timing of flowering, which determines the
attraction of pollinators, the availability of mates,
and reproductive success.
The timing of seed ripening, which may determine
the likelihood of seed dispersal by animals.
Up and running: common vocabulary
• Phenology
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Yellow star thistle
Up and running: common vocabulary
• Phenology
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Silene nutans
Up and running: common vocabulary
• Pollen limitation
The phenomenon in which plants do not produce
as many seeds as they are capable of, simply
because they don’t receive enough pollen.
Causes:
Flowering too early or too late to attract pollinators
Flowering too early or too late relative to other
plants in the population
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Long-term consequences:
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
Long-term consequences:
reduction in mean
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Long-term consequences:
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Reduced genetic variation
Long-term consequences:
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Reduced genetic variation
Long-term consequences:
Hybrid breakdown
poor performance of F2 and
subsequent generations
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Reduced genetic variation
Long-term consequences:
Hybrid breakdown
poor performance of F2 and
subsequent generations
Potential for phenological mismatch
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Reduced genetic variation
Long-term consequences:
Hybrid breakdown
poor performance of F2 and
subsequent generations
Potential for phenological mismatch
Potential failure to be pollinated
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Reduced genetic variation
Long-term consequences:
Hybrid breakdown
poor performance of F2 and
subsequent generations
Potential for phenological mismatch
Potential failure to be pollinated
Pollen-stigma incompatibilities
Synthesis: Consequences of inappropriate source selection
Short-term (more or less immediate) consequences:
Genetic swamping or dilution
population performance
High mortality
reduction in mean
reduced population size
Reduced genetic variation
Long-term consequences:
Hybrid breakdown
poor performance of F2 and
subsequent generations
Potential for phenological mismatch
Potential failure to be pollinated
Pollen-stigma incompatibilities
Inability to adapt to climate change (due to limited genetic
variation).
Surviving stand of Nassella pulchra
(a native perennial bunchgrass)
Nassella pulchra
Bromus carinatus
Elymus glaucus
Genetics 101: Genetic differentiation in the age
of ecological restoration
Susan J. Mazer
Department of Ecology, Evolution & Marine Biology
University of California, Santa Barbara
[email protected]