Transcript Mutation and selection and breeding systems

Processes that affect genetic diversity
Think back to the Hardy-Weinberg equilibrium. What
processes made a population’s genetic structure nonequilibrium?
Natural selection
Genetic drift
Gene flow/migration
Mutation
Mutation (rare, uncorrected mistakes in the DNA sequence) is
the ultimate source of all polymorphisms and all genetic
variation.
What types of mutations occur?
a. base pair substitution
b. insertion or deletion (one to a few base pairs or
the number of repeats in a microsatellite)
c. a combination of deletion and insertion of a
transposon
How do mutations occur?
a. error in DNA replication (the most common
cause)
b. radiation induced damage
c. chemically induced damage or interference in
DNA replication
d. movement of transposons.
Transposons are what Barbara McClintock called “jumping
genes”. McClintock found them in corn; they are now known
in many species. Call these mutations translocations.
How frequently do mutations occur?
There are many approaches. One of the best is to breed to
create a uniform genetic line of heterozygotes. You mate
dominant homozygotes with homozygous recessives. The
result ‘should’ be all heterozygotes with the dominant
phenotype. Look for recessive phenotypes, which indicate
there has been the conversion of dominant to recessive genes
in this breeding.
Doing this in corn using a recessive gene that produces
shrunken kernels, the frequency of mutation at this locus is
about 1 per 106 progeny.
Most mutations are thought to result from copying errors
during DNA replication. Remember how many of these may
be silent mutations with no phenotypic or selective effect.
However, other possible sources, i.e. transposons, are much
more common than you may imagine. It is estimated that as
much as 25% of the genome of Vicia faba, the pea, is potential
transposon.
If the mutation rate at one locus in corn is typical – 1 per
million progeny, what is the overall rate of deleterious
mutations in offspring considering the whole genome?
The total number of genes in a genome is not very precisely
known. Estimates range from ~104 – 105 genes. The estimate
for both Drosophila and some plants is about 1 deleterious
mutation per diploid genome per generation.
Somatic mutations
Since plants reproduce vegetatively (e.g. by rhizome growth
and appearance of new shoots), there is the potential for
ramets to differ as a result mutation in meristems.
Some genets persist to extreme age, though individual ramets
are not that old. Examples: quaking aspen (Populus
trmuloides) - ~10,000 years; arctic dwarf bitch (Betula
glanulosa) - ~7,000 years
Mutation in meristematic cells affects all cells of the new
ramet. It is, thus, heritable variation.
Gene flow/migration also tends to increase genetic diversity
in populations. Migrants arrive from other populations. Other
populations are likely to ‘contain’ genes not present in the
population under observation. Migrants have a reasonable
probability of carrying those genes into the population.
Remember that gene flow can occur not just by movement of
seeds, but also through pollen flow. More about seed and
pollen flow comes later. Distances moved can be surprisingly
long.
Other processes – drift and selection – generally decrease
genetic variability in populations.
Genetic drift results from random sampling in various stages
of reproduction: in meiosis to produce gametes, in pollination
as an effect of randomness in wind-driven pollen movement
or movement of pollinators among plants and in the particular
pollen grains that achieve fertilization, and in which seeds
germinate, successfully become established and mature.
The effect of drift is generally inversely related to population
size, as demonstrated (next slide) by the amplitude of
differences when a starting population was 9 individuals (2N
= 18) versus a starting population of 50 (2N = 100).
Thus far the concern has been variation within populations.
What is the effect of these processes on variation among
populations?
Mutation and drift increase variation among populations.
Gene flow/migration decreases variation among populations.
Natural selection can have either effect. It can ‘select’
adaptations that differ among populations if environmental or
biological conditions differ. If a trait is advantageous in most
or all populations, then selection will tend to make the
populations more similar.
Think back to the ecotypic variation among populations of
yarrow at different sites along the Sierra Nevada. Natural
selection produced characteristic genetic variation among the
populations.
Persistent differentiation among populations is a step along
the path to speciation. However, plants have some unique
means to achieve speciation.
Plants undergo polyploidization – the duplication of the
genetic complement to (usually) double the number of
chromosomes.
How does polyploidy occur?
Frequently by the accidental formation of gametes without the
reduction division in meiosis. Gametes then have 2N
chromosomes.
Once formed, consider what happens in normal meiosis of the
new polyploid individual. A gamete is produced that has 2N
chromosomes.
Even if successful fertilization occurs with other members of
the (original) population, can this new individual, produced by
a cross between individuals with chromosome complements of
4N and 2N, undergo successful meiosis?
Offspring produced by a cross between a polyploid and a
normal individual are usually sterile (if they survive).
For polyploidy not to be a dead end, how can newly formed
polyploids reproduce successfully?
Clearly through self-pollination.
Also by exchanging gametes with 2N individuals that produce
unreduced gametes, called autoployploidy. Or other species
that have a 4N chromosome number. When this occurs
between individuals of different species it is called
allopolyploidy.
Ploidy can also double more than once. Ploidy level can even
vary within what we deem species taxonomically, e.g. in
Atriplex canescens (saltbush). Ploidy varies from 2N to 20N
among populations in and around Idaho. The result of ploidy
variation is size variation, for example in height that ranges
from 1 foot to 10 feet.
Plant species with ‘weird’ chromosome numbers can also
occur as a result of hybridization. One of the most famous
mixtures of ploidy levels within a genus occurs within Clarkia
(haploid chromosome number given beside species names).
Pictures of a few Clarkia species from the diagram:
C. unguiculata n = 9
C. virgata n = 5
C. purpurea n = 26
C. williamsonii n = 9
Plant Breeding Systems
Genetic variety is generated at three points in a reproductive
cycle:
as a result of crossing-over between homologous
chromosomes during the first division of meiosis
through independent assortment at metaphase of the
first meiotic division
through random gametes being involved in syngamy
Of course, this assumes that we are considering ‘normal’
sexual reproduction. Plants have a variety of ways of
achieving reproduction, some of which do not involve all of
those steps.
Plants (some) can reproduce asexually. Asexual reproduction
can occur through vegetative processes (budding from
rhizomes, stolons, etc.) or through apparently sexual processes
(apomixis with or without pseudogamy).
Plants can reproduce sexually. The genetic consequences
depend on how the flowers are arranged, the timing of
maturity of male and female flowers, and whether self
pollination can occur.
To begin sorting this out, we first need to explore the
mechanics of fertilization in plants.
General anatomy of a flower
Pistil: Female part
Stamen: Male part
Fertilization
Plants are described has having “double fertilization”. There is
separate fertilization of the ovule by one sperm nucleus
forming the embryo and fertilization of two polar nuclei by a
second sperm nucleus to form the endosperm.
Now back to apomixis. Apomixis occurs in two forms:
In agamogenesis the embryo is formed from the unfertilized
egg by a modified meosis. In essence the products of one of
the meiotic divisions fuse, instead of separating.
In agamospermy there is endosperm fertilization, forming a
nucellar envelope, though the egg is not fertilized. This is
called pseudogamy.
The most common example is Taraxacum officianale, the
common dandelion.
Now for sexual reproduction.
If all individuals are identical (usual terminology: sexually
monomorphic) most commonly all individuals are
hermaphroditic. That means flowers have both male and
female parts functional.
Individuals may also be monoecious. This means that male
and females flowers are separate, but flowers of both sexes are
present on all individuals.
There are, finally, plants that have both hermaphroditic
flowers and also flowers with only female parts functional
(gynomonoecy) and, symmetrically, plants with both
hermaphroditic and male flowers (andromonoecy).
The domesticated (cultivated) rose is a good example of a
hermaphroditic flower
Birches, e.g. dwarf arctic birch, Betula glandulosa, is
monoecious. Each plant has separate male and female flowers.
female catkins
male catkins
Plants that are gynomonoecious have female (male-sterile)
flowers and hermaphroditic flowers with both sexes
functional. This system is most common in the Asteraceae.
Aster bellis
Solidago rigida
Andromonoecious plants have male (female-sterile) and
hermaphroditic flowers. This is common in the Apiaceae, liike
the Queen Anne’s lace plant shown.
Daucus carota
Dioecious species have male and female flowers on separate
individuals. A number of maple (Acer) species are dioecious;
numerous male flowers occur on some trees, but not the
winged seeds. Other (female) trees produce the winged seeds.
Acer negundo
Box elder
Gynodioecious species contain individuals that are either
female or hermaphrodites. They are not uncommon. One good
example is thyme.
Thymus serpyllum
Androdioecious species have either male or hermaphroditic
flowers on separate plants. This strategy is very rare.
Mercurialis annua
It can be very difficult to tell whether a plant species is
reproducing apomictically, by self-fertilization, or by
outcrossing.
There are a number of signs and experiments that can provide
an answer:
a. If a population is entirely (or virtually all) female, it must be
reproducing asexually.
b. If a population has both sexes, but isolated individuals
produce seeds, it could be either apomictic or selfing.
Remove the anthers on isolated plants. If they still produce
seeds they must be apomictic.
c. If those isolated plants do not produce seeds after anthers
are removed, they might be pseudogamous or are either
self-fertilizing or outcrossers.
d. To sort out those possibilities, use molecular markers
and pollinate with a separate male. Check the seeds.
If the markers in the seeds indicate they are progeny
of the other male, they are not produced by
pseudogamy apomictically, and they are not obligately
selfing.
Finally, dioecious (male and female flowers found on different
plants) species outcross. However, there are also plants that
have both female and hermaphroditic flowers (gynodioecy),
and plants that have both male and hermaphroditic flowers
(androdioecy). These latter types may be capable of both
outcrossing and selfing.
Given the importance of genetic diversity, are apomixis and
selfing old or recently evolved mechanisms for reproduction?
Apomixis and selfing are suggested to both be evolved
adaptations to low density or isolation. That indicates little
about whether these strategies are ancient or recent.
The observation that a large fraction of apomicts are
pseudogamous, requiring fertilization of the endosperm by
pollen nuclei, suggests that apomixis must be relatively recent,
not ancient.
The requirement for pollen in pseudogamy leads to
questioning the common wisdom that apomixis, at least, if not
selfing as well, is an adaptation to low density, absence of
pollinators, or any of the other obvious limitations to sexual
reproduction by pollination.
If genetic diversity (and heterozygosity) are important to
evolutionary success, why is self-fertilization a common
occurrence among plants?
Remember all those mechanisms to mix genes during meiosis.
Selfing does not necessarily dramatically increase
homozygosity in the short term, but usually will in the long
term.
Even so, there are important mechanisms to prevent selfing in
many species.
If selfing is, in the long run at least, a reproductive mode that
reduces genetic diversity, how is selfing prevented?
a. Structurally – flowers may locate anthers as far away as
possible from the receptive surface of the stigma. However,
it is notable that in some of these plants anthers bend in the
absence of pollen receipt to exchange self pollen. One
example: the 4 o’clock, Mirabilis hirsuta.
b. Timing – if male parts of hermaphroditic flowers are
mature at a different time than the female parts, then
pollen cannot be exchanged between them. Botanists
have a term for this – dichogamy.
Temporal separation can occur with the male flowers
or parts ripening first (protandry) or with the female
functions occurring first (protogyny). One good
example of protandry is the dwarf arctic birch, Betula
glandulosa.
c. self-incompatibility – a number of species have
genetic-biochemical mechanisms to reject self-pollen.
The rejection is controlled by the S-locus. There are
many different alleles possible at this locus. In a plant
that shows self-incompatibility, pollen is rejected if it
has the same S allele as the plant receiving that
pollen.
There are two ways this is achieved. In gametophytic
incompatibility, the haploid genotypes of the pollen
nuclei determine incompatibility.
Assume there are three possible S alleles, S1, S2, and
S3. If a particular pollen grain contains allele S1, it will
be rejected by plants with any genotype containing
S1, i.e. S1S1, S1S2, or S1S3.
The other form of S-allele incompatibility is called
sporophytic. In this form the alleles determining
incompatibility are those of the plant donating the pollen.
Interestingly, there seems to be dominance among S-alleles.
The dominant S-allele in the parent plant determines the
incompatibility type of all pollen produced by the plant. Thus,
the mechanism must be biochemical. This is the mode of
incompatibility found in most Asteraceae.
d. Polystyly (or heterostyly) – self-incompatibility based
on S-alleles is not visible in the phenotype. There is,
however, one readily evident form of selfincompatibility. Some flowers have differing morphs
with respect to the lengths of anthers and style. Some
species are distylous (2 lengths, distyly), and others
are tristylous (3 lengths, tristyly). Purple loosestrife is
a well-known trisylous species.
How can we figure out the frequency with which selfpollination occurs?
The basic method, in the few cases it is possible, is to use
enzyme electrophoresis to recognize and separate genotypes
Aa and aa (though they may not be visibly separable).
Allow reproduction of a recessive homozygote in an
environment otherwise made up of dominant homozygotes.
The fraction (or frequency) of heterozygous offspring
measures outcrossing, the fraction of recessive homozygous
offspring has to have been produced by selfing.
When we measure the frequency of selfing and apomixis, we
find some interesting patterns among plant types and within
species’ distributions:
Apomixis and autogamy (selfing) tend to occur in populations
at the extremes of a species’ range within species (or species
groups) that are otherwise self-incompatible.
Apomicts are also more frequently polyploid than might be
expected. At the occurrence of polyploidization, the new
polyploid is frequently sterile or isolated from its source
population reproductively. Apomixis would then permit
reproduction to occur.
Weedy species tend to be capable of selfing or apomixis.
Long-lived species tend to be outcrossers.
Apomixis preserves the parental genotype, including all
heterozygosity present. Its limitation is the lack of variety as a
mechanism to permit evolution by natural selection.
Self fertilization inevitably increases the amount of
homozygosity, and is a potential cause of inbreeding
depression.
The result is a general suggestion that the evolutionary
lifespans of selfing species are shorter than those that outcross
(and particularly if self-incompatibility mechanisms are
present).
Inbreeding depression can be measured when pollination is
controlled (e.g. by hand pollinating particular flowers on a
plant with self pollen and others with outcross pollen). How
much is fitness depressed?
  ( wx  ws ) / wx  1  ws / wx
Assume this equation deals with the depression of one fitness
trait, e.g. survival. If the number of seeds produced and the
germination of seeds were also affected, these are likely
independent effects, and the s would multiply to determine
the overall inbreeding depression. This pattern of multiple
effects is evident in Cucurbita.
Cucurbita foetidissima, buffalo gourd, is a member of the
cucumber family. It is gynodioecious. Hermaphrodite flowers
were either self-pollinated or pollinated with pollen from
different individuals. Seed number and seedling survival were
affected.
Remember the basic idea that the effects on different life
stages are independent, and therefore the depressive effects
multiply. What’s happening in the gourd?
There is so little effect on seed mass
that we’ll discount that.
Seed number is decreased to the
ratio of ~180/275 = 0.65
Seedling survival to summer 1986
is depressed to the ratio 0.15/0.225
= 0.667
Seedling survival to summer 1987
was depressed to 0.05/0.19 = 0.263
The two survivorships measure different periods; the best
overall estimate to consider the whole life cycle is the second
one. What is the overall depression evident here?
0.65
x
0.263
(for seed number) (for seedling survival)
=
0.171
Thus inbreeding depression in buffalo gourd reduces overall
fitness by 82.9%. That’s significant!
There are plants that “do things differently”. Mirabilis hirsuta,
as you saw earlier, self-pollinates in the absence of insectdelivered cross pollen. It is not clear that those seeds are
smaller or less viable than outcross seeds.
The genetic responses and consequences of inbreeding
depression can include:
overdominance – the fitness of the heterozygote
exceeds that of either homozygote. That will maintain
polymorphism at the locus.
heterosis (or hybrid vigor) – when inbred strains
are crossed, the recessive mutations depressing each are
unlikely to be the same. The mutant loci become
heterozygous, and fitness is typically significantly
increased.
Bob Cruden looked at pollen-ovule ratios (number of pollen
grains per ovule) in plants with varying reproductive
strategies. As you might expect, self-pollinating plants had far
lower ratios. The difference in allocation to male function
versus female function extends
well beyond pollen and ovules,
as indicated here among
populations of Gilia achillefolia.
This indicates that there is a broad
strategy that accompanies adopting
selfing as a reproductive mode,
extending into energetics and
reproductive allocation.
We will see broad strategic patterns
again.