Life cycles and sexual reproduction

Because of mutation, a gene can exist in different forms.  Alternative forms of a gene are known as alleles.

The complete set of alleles contained within an organism is known as its genotype.

Asexual organisms exists as clones.   When they reproduce, their genomes are passed intact, except for those variations introduced by mutation, to their offspring.

In asexual organisms, all of the alleles within the organism share a common fate.  They are inherited together and so evolve together.

A lethal mutation in one gene leads to the extinction of all.

When a new allele arises, through mutation, it creates new challenges, opportunities and selective pressures.

If the effects of an deleterious mutation are not immediately lethal, these effects may be ameliorated by mutations in other genes - the genome adapts as a whole and complete with other genomes.

There are, however, ways for alleles to escape their home genome. 

A piece of DNA may then evolve to facilitate its own spread from organism to organism via horizontal gene transfer. 

It is commonly thought that viruses have their origins in such selfish genetic elements.

There can be a serious conflict between the "interests" of a selfish genetic element and its host.  The appearance of selfish genetic elements will in turn lead to a selective pressure to suppress their replication. 

The genomes of organisms are littered with inactivated remains of selfish genetic elements, ~50% of the human genome is composed of this parasitic DNA.

• How would you define the "normal" version of a gene?
• Can there be multiple "wild type" versions of a gene?
• How can different alleles for the same gene differ?
• What are the properties of a parasitic DNA sequence?
• Describe the changes in selection pressure that occurs within an asexual organism once a mutation arises? 

There is a second process by which combinations of alleles are shuffled and new alleles created to form new genomes, it is known as sex.

The process of sexual reproduction involves two organisms which cooperate to produce a new organism.

Sex in eukaryotes involves two processes, meiosis and syngamy.

Sexual organisms exist in haploid and diploid states. In the haploid state, they have a single (1N) set of chromosomes and so a single allele of each gene.

In the diploid state, they have two sets (2N) of chromosomes, one derived from each parent; they therefore have two alleles of each gene.

The maternal and paternal sets of chromosomes are homologous; they each contain the same set of genes in the same sequence along their length.

They may differ, however, in which allele is present at each gene position. 

The position of a gene within a chromosome or genome is located is know as its genetic locus.

human chromosome viewer

If mitosis and cytokinesis occurs accurately, each daughter cell ends up with the same number of chromosomes as the parent cell. 

If the parental cell is normal, that is contains the number of chromosome typical for the species, it is said to be euploid, which mean true number.

If there is a defect in mitosis, daughter cells can inherit more or less than the euploid number of chromosomes; such a cell is said to be aneuploid.   

Aneuploid cells are typically quite abnormal – such cells are often found in cancers.

• Why would you expect an aneuploid cell to be abnormal in terms of gene expression?
• How is a mutation in a haploid cell different from a mutation in a diploid cells, in terms of its possible effects on the phenotype of the organism?  

Sexual reproduction is associated with the process of meiosis - a modified form of mitosis. Meiosis occurs only in diploid cells, and produces haploid progeny.

The haploid (1N) products of meiosis are known as gametes.

During meiosis, homologous chromosomes align with one another in a process known as synapsis.

Each maternal chromosome aligns with its homologous paternal chromosome; this alignment is generally exact to the base pair.

A number of plants, such as the mosses, spend a significant amount of their organismic life cycle in the haploid state.

During this haploid phase, the organisms are known as gametophytes.

In most plants (like most animals),the gametophytic stage is quite short and contained with the diploid form, known as a sporophyte.

Gametes that do not undergo syngamy shortly after they are formed or activated, die. 

When gametes are of different sizes, the larger are called eggs and the smaller sperm.

Organisms that produce sperm are male, those that produce eggs are female.

In some species, an organism can produce both sperm and eggs simultaneously, such an organism is known as a hermaphrodite, after the Greek gods Hermes and Aphrodite.

There are also organisms that can change sex, these are known as sequential hermaphrodites.

Sexual identify is not necessary fixed; in a number of fishes, for example, it can be influenced by social interactions. 

• How long is the gametic phase in the human males? in females?
• What does male and female mean, biologically?  

During meiosis, alleles are shuffled and new alleles are created.  This is accomplished by two distinct processes.

The first is known as independent assortment.   During meiosis, homologous chromosomes within the original diploid cell align.

The process of independent chromosome assortment can produce 2²³ different gametes, a rather large number.

The second meiotic mechanism involved in shuffling alleles into new combination is known as crossing-over or meiotic recombination.

The order of genes is not changed, but pattern of alleles can be.

Crossing over holds the two homologs together until they are separated at meiosis I.

An obvious benefit of sexual reproduction is the appearance of large amounts of genomic variation with each new generation. 

Another is the elimination of deleterious mutations from the population. 

In asexual organisms, each lineage is distinct and must "stumble" upon evolution novelty on its own.

Alleles are changed one by one and tested in the same way.   In a similar manner, there is no ready way to get rid of deleterious mutation except to die.

This accumulation of mutations in asexual organisms is known as Muller's ratchet.

Meiotic recombination generates new chromosomes. Some have more deleterious mutations, some fewer.

• How might a new allele be generated during the course of recombination?
• Why does the set of alleles matter, isn't every trait determined by which the alleles of a specific gene?
• Does sexual reproduction lead to a reduction in the number of deleterious alleles in individuals or populations? 

During S phase of the cell cycle, each chromosome replicates. 

The replicated chromosomes, known as chromatids, remain attached to one another at a region known as the centromere. 

During mitosis, the attachment between chromatids is broken and one chromatid is segregated to each daughter nuclei. 

During meiosis, the centromeres of the chromatids do not separate until the second meiotic division. 

Occasional mutations will flip a stretch of DNA within a chromosome, producing an chromosomal inversion.

Sometimes, a chromosome may break and then be rejoined incorrectly to another chromosome  – this is known as a chromosomal translocations. 

Such chromosomal rearrangements complicate synapsis and can lead to a failure of meiosis, and hence sterility.

• Does a chromatid contain the same information as a chromosome? 
• Describe an inversion can occur without altering patterns of gene expression.
• How can an inversion lead to a mutation?
• How do chromosome rearrangement lead to reproductive isolation? 
• How might a chromosomal inversion lead to the loss of genetic information during meiosis?