RISKS OF RARITY: GENETIC ISSUES PART 1: BASIC GENETICS

Corresponding Readings in Primack, Richard B. Essentials of Conservation Biology.
Chapter 11: pages 283-301

Introduction:

Single-species conservation programs aim to reduce the risk of population extinction. Conservation genetics is important to this challenge for several reasons:

• Management of rare populations should extend over a long time -- decades to hundreds of years. This is a timeframe of possible genetic change.
• Small populations are at risk of extinction even if not declining, due to drift and in-breeding.
• Environments change, and without ample genetic variation, populations are unlikely to adapt to new circumstances, such as a different climate or new competitors.
• Genetics is a useful tool in evaluating the identity of a species. For example, if the Northern Spotted Owl turns out to be genetically indistinguishable from other sub-species, an argument for protecting its forests is lost. The red wolf, a captive breeding success story, may be a gray wolf/coyote hybrid.

Some basic ideas of population genetics:

We will review the basic ideas of genes and alleles, and introduce the idea of genetic variation. Then we need to ask what forces act on genetic variation. This will quickly lead us to see that, for small populations, a different set of factors are of critical importance compared to large populations. Then we can see how these principles are critical to endangered species management and captive breeding programs.

Some basic terminology and definitions: What is a gene, and what is an allele? One common idea is that a gene controls an observable characteristic, often called a "trait". For example, a gene controls tongue-rolling -- the ability to roll your tongue into a "U". Another definition, based on our knowledge of the genetic code, is that a gene is three letters of the genetic code. There are four bases -- Cytosine, Guanine, Adenine and Thymine, or C, G, A and T -- that make up the genetic code. A string of three of these is interpreted by the cell machinery as a particular amino acid. And, in case you've forgotten, a string of amino acids makes a protein.

Lots of traits -- most of the interesting ones -- aren't determined by a single gene but by the interaction of many. Height and eye color are good examples.

There may be two or more states of a trait -- tongue-rolling and not; red, white and pink pea flowers; and so on. These alternate states are called alleles. Because all individuals have two chromosomes, they have two copies of every gene (except XY), and these two copies may be the same or different. So we have the familiar terminology of individuals being:

AA Aa aa

homozygote heterozygote homozygote

If the Aa individual resembles the AA individual, then A is dominant to a.

Genetic variation exists when both alleles (A,a) are present in the population, and so multiple genotypes exist (e.g., AA, Aa, aa). This variation is quantified by determining the frequencies of alleles, genotypes, and phenotypes. Consult the population genetics exercise in the discussion course pack for further details.

Note that there is a qualitative difference between a population with p = .99, q = .01; and p = 1.0, q = 0. In the latter case the "a" allele has been lost, perhaps permanently. Usually, when we worry about the loss of genetic variability in a population it is allelic (gene) frequency that we emphasize.

How much genetic variation exists in a natural population? We can illustrate with tongue-rolling. For traits that don’t have such a visible marker, biochemical analyses of proteins or DNA document that most populations contain a surprising amount of genetic variability. 

What determines gene frequencies:

 It can be shown (see course pack) that, given certain assumptions, gene frequencies remain constant over time. This principle is referred to as the Hardy-Weinberg equilibrium. So for gene frequencies to change, one or more of the following five assumptions have to be violated:

1. the population size is large

2. there is random mating

3. there is no "assortative mating" (selection of mate based on genotype)

4. there is no migration in or out of the population

5. natural selection does not occur

In a large population, assumptions 1 through 4 generally are met, and the H-W Eqm is the basis for detecting natural selection at work. In a small population, assumptions 1 through 4 may be violated, with serious consequences. Thus this equation also is a useful starting point in assessing how gene frequencies in small populations may behave differently than gene frequencies in large populations.

When population size is small, by chance the genetic make-up may be different in the next generation. This is "sampling error", or "drift",. Meaning a random, undirectional change in gene frequencies. A small population with an initial frequency of A = a = 0.5, is certain to drift to all Aor all a with equal probability. The smaller the population, the faster this occurs.

Random mating is critical for the gene frequency to stay constant, and for the HW equilibrium to be valid. Any mate choice is likely to violate the HW eqm. Assortative mating, where individuals preferentially mate with individuals of similar phenotype (say, small males with small females, large with large), also creates complications.

Migration can change gene frequencies if a substantial number of individuals of different geneotype enter an area. This "swamping" effect is unlikely if the resident population is large, but possible if the resident population is small relative to the number of immigrants.

Transparencies: 1. Phenotypes, genotypes, and alleles 2. Genotypes at time 1 and time 2 3. Hardy-Weinberg equilibrium 4. Drift 5. Elephant seal and assortative mating

Links:

• Population Genetics: further information on the Hardy-Weinberg Equilibrium.
• Center for Conservation Genetics: Center that has come together to measure biodiversity in Australia.