Processes that affect genetic diversity

Think back to the Hardy-Weinberg equilibrium. What processes made a population’s genetic structure non-equilibrium?

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. purpurea n = 26

C. williamsonii n = 9 C. virgata n = 5

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 partStamen: 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 self- incompatibility. 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 self-pollination 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?

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.

xsxsx wwwww /1/)(

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 = 0.171(for seed number) (for seedling survival)

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 insect-delivered 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 functionversus female function extends well beyond pollen and ovules,as indicated here among populations of Gilia achillefolia.

This indicates that there is a broadstrategy that accompanies adoptingselfing as a reproductive mode,extending into energetics and reproductive allocation.

We will see broad strategic patternsagain.