MUTATION AND VARIATION

Mutation is the ultimate source of variation. Without variation there could be no evolution, so mutations are of great importance to evolution. Important to point out that existing variation can be reshuffled by a variety of mechanisms that we don't always consider as mutations leading to increases or decreases in variation and thus altering the potential for evolution.

Mutation = a heritable change. This is often followed by the qualifier "in the DNA" or "in the genetic material". This is redundant with the term "heritable" but points out an important genetic issue: The mutations which are of primary concern are those in the germ line as these are the one that will be passed on. August Weismann was the first to point out the distinction between germ and soma. Mutations in your arm or knee cap are not going to get passed on because the germline is sequestered relatively early in development:

Weismann's doctrine was a serious blow to Lamarkian inheritance of acquired characteristics. However, in plants and some animals (clonal ones in particular) the germline is not sequestered into a single part of the part of the organism so somatic mutations can be inherited (a mutation during the differentiation of a branch on which a flower will develop: all pollen and ovules made by that flower will have a genotype different from the rest of the plant. Think about corals, too).

Probably one of the most important things to understand about evolution is that mutation is random, i.e., is not directed towards the problems presented by the environment (although some recent evidence has been published on bacteria that challenges this assumption: Lenski, R. E. Are some mutations directed? Trends in Ecology and Evolution vol. 4, pp. 148-150.).

Mutation is an ongoing process. There are measurable mutation rates and that there can be a genetic variation for mutation rates; "mutator strains" of bacteria exist. Mutations in the replication or repair machinery of DNA can alter mutation rates.

Types of mutation: point mutation now generally refers to a change at a single nucleotide site. These can be transitions (purine to purine [A to G or G to A], or pyrimidine to pyrimidine [C to T or T to C]) or transversions (from a purine to a pyrimidine or vice versa). Synonymous and non-synonymous substitutions with respect to the effect on the amino acid coded for by the DNA. Deletions and insertion will cause frameshift mutations.

Transposable elements are mobile genetic elements that can move from one part of the genome to another. Generally they have repeated sequences at their ends and code for protein(s) in the middle. In moving from one location to another they can cause mutations. If the element landed in the middle of the coding sequence of a gene, it most likely would lead to a frameshift mutation or introduce a stop codon, and knock out the function of that gene.

Gene duplications can occur by unequal crossing over where gene families exist on the chromosome, homologous chromosomes may misalign and cross over (recombine). The daughter chromosomes include one with an extra copy and one with one fewer copies. Chromosome rearrangements can also be viewed as mutations. Classic cases: inversions were a section of the chromosome is inverted with respect to the "normal" chromosome. Drosophila polytene chromosomes show characteristic banding patterns and allow for easy recognition of inversions. A paradigm of natural selection (more later).

Several important consequences: Inversions can act as suppressors of crossing over in the heterokaryotype (= heterozygote for two different chromosomal types). An inversion does not prevent crossing over per se but the recombination products that result from a crossover within the inversion either have two centromeres and are pulled apart in division, or lack a centromere and are not transmitted. Only the unrecombined parental chromosomes are transmitted.

How will the frequency of an inverted chromosome in a population affect it role as a suppressor of recombination? The more frequent the inverted type gets, it will be present in a "homokaryotypic" state and recombination will not be suppressed. If the "inverted" chromosome were fixed in the population (=100%) then we would no longer consider it "inverted".

Translocations are instances where part of a chromosome is "translocated" = moved to another chromosome. When entire chromosome arms are translocated or fused this can lead to changes in chromosome number. Can also lead to genetic incompatibilities that may lead to reproductive isolation (more in lectures on speciation)

LINKAGE AND RECOMBINATION

Gene loci on the same chromosomes are generally considered to be in the same linkage group because the alleles on each chromosome can be inherited as a "linked set" (like beads on the same string). But a chromosome can be long enough that the probability of a crossover (=recombination) event some where along the chromosome is very high. Thus genes at different ends of same chromosomes can be effectively unlinked. Conversely genes close to each other on the chromosome are usually tightly linked because the probability of a recombination event between them is very low.

Consider a pair of chromosomes, and think about the gene loci at each ends. Each locus carries two alleles and we will consider the case where the two alleles are different (each locus is heterozygous):

When this "individual" makes gametes, we can say that recombination occurs with a frequency (or probability) "r". Thus recombination does not occur with a probability (1-r). When recombination does not occur the gametes produced will be A B and a b (note only one letter is used at each locus because gametes are haploid); when recombination does occur the gametes will be A b and a B. (see figure 2.7, pg. 34).

If the loci were on separate chromosomes (unlinked) and we were "given" a gamete with the "A" allele, 1/2 of the gametes would be AB and 1/2 would be Ab (the under score is omitted as a shorthand notation). If we were "given" a gamete with the "a" allele, 1/2 the gametes would be ab and 1/2 would be aB. These four gametes would be in the relative proportions 1:1:1:1.

Now consider linkage. If the A and B loci were on the same chromosome, to determine the proportions of the four gametes we would have to know the probability of recombination between the two loci. This probability is r, so "given" an A allele, (1-r) of the gametes would be AB, and r of the gametes would be Ab (i.e., recombinants). Similarly, given the a allele, (1-r) of the gametes would be ab, and r of the gametes would be aB (recombinants). Since there are two kinds of recombinant gametes resulting from crossover (e.g., reciprocals: Ab and aB), these two types are split evenly within the proportion r of recombinants (r/2 of each reciprocal). For example, if r = 0.02 (i.e., 2%), then the gametes produced by a "double heterozygote" such as the one three paragraphs above will result in the following proportions

(1-r/2)AB : (r/2)Ab : (r/2)aB : (1-r/2)ab, e.g., 49%:1%:1%:49% respectively. For comparison, if there was no linkage between A and B, then the proportions of the four possible gametes would be 25%:25%:25%:25%. By definition then, ulinked loci have an r = 0.5. For loci at opposite ends of long chromosomes, r can be very close to 0.5 because a recombination event is likely to occur.

Recombination can shuffle existing variation and lead to new variants. Consider two diploid "individuals": ABcd/abCD and AbCd/aBcD and a cross between them:

can produce ABCD/ABCD and abcd/abcd individuals assuming recombination along the chromosome: new types previously not present in either population that may have different phenotypes from either parent. Note recombination will produce variation faster than mutation alone (assuming "normal" mutation and recombination rates). Above, assuming no recombination we might get: ABcd/aBcD and we would have to wait for:

one a --> A, two c --> C and one d --> D mutations to get the homozygous "capital" phenotype. We can thus think of extensive "latent" variation in chromosomes: there is the potential to generate extremes of variation given certain chance recombination and mating events.

Mimicry patterns controlled by tightly linked loci controlling several different factors, wing pattern, body color, "tails", etc. favorable combinations of alleles with all coordinate phenotypes will tend to become linked. This is an example of a supergene were many loci are tightly linked and certain alleles become associated such that they behave as single "locus".

Important to note that just as recombination can generate favorable combinations of alleles, recombination can just as easily break up these favorable combinations.

Recombination does not always take place between genes but can take place within a gene (=intragenic recombination). At a monomorphic locus (=no variation), intragenic recombination will have no effect. At a polymorphic locus, intragenic recombination will generate more types: variation breeds more variation.