Pop Ecol Lect 34

Lecture notes for ZOO 4400/5400 Population Ecology

Lecture 34 (25-Apr-08)

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Today we'll start on a new topic -- the genetics of populations. Traditionally, population genetics has been included in courses entitled "Population Biology" but not in courses labeled "Population Ecology". I am including population genetics in this course for two reasons. First, we do not have a Population Genetics course at this university, Second, the lines between the disciplines cross in so many ways that population genetic studies now often shed light on some of the core questions of population ecology, such as what factors limit the distribution and abundance of populations.

Population Genetics

Go to Glossary of genetic terms Go to worked example for take-home exam

(terms included in the Glossary will be highlighted in red below, up to the start of the explanation of the Hardy-Weinberg principle)

Introduction to population genetics

Population geneticists ask two primary questions: First what are the patterns of genetic variation (what is the genetic "structure" of populations), and second what are the major evolutionary forces responsible for the origin and maintenance of the extensive variation seen in natural populations? One of the foundations of population genetics is the Hardy-Weinberg principle. It predicts genotypic frequencies from allele (gene) frequencies.

Fig. 34.1. Punnett square diagram, illustrating the essence of the Hardy-Weinberg equilibrium concept. If we know the frequencies of alleles, we can predict the frequencies of genotypes. If we have one allele, A (whose frequency is p) and another allele a (whose frequency is q), we expect p² homozygotes with the AA genotype, 2pq heterozygotes with the Aa genotype, and q² homozygotes with the aa genotype. Notice that we can generate the Aa heterozygotes in two ways -- A from Dad and a from Mom, or vice versa.

What's useful about population genetics?

Management issues. We can answer questions about patterns and trends in genetic variability, gene flow (are populations genetically connected?), patterns of dispersal (do males or females tend to disperse further?), N_e (effective population size, which we will address below), fluctuations in population size (called "bottlenecks" and also addressed below), forensics applications (legal cases -- does the carcass in the suspect's freezer match the poached animal found by a warden), and population size estimation (using genetic mark-recapture techniques). Mangers now also need to be concerned about the genetic and population consequences of stocking and introductions -- is there genetic mixing between subspecies or species of trout? Are game farm red deer escaping and interbreeding with native elk?

Conservation of threatened and endangered species. Assessment of genetic variability to prevent inbreeding depression (reduced fitness manifested as lower fertility or survival), recognition of threatened and endangered species (is this candidate "species" actually distinct from a more widespread common form found elsewhere?), and molecular forensics for law enforcement (is this animal part from an endangered black-footed ferret or from a legally trapped mink?).

For empirical population genetic studies, we use special tools called genetic markers. A genetic marker is any trait used as a tag of genetic variation within and among individuals and taxa.

Types of genetic markers:

Quantitative/phenotypic: eye color, protein markers (allozymes can also be considered genotypic)

Genetic/genotypic: allozymes (enzyme variants that we resolve or "visualize" on electrophoretic gels), DNA polymorphisms (restriction fragment length polymorphisms [abbreviated RFLPs], microsatellites [simple sequence tandem repeats], RAPDs [randomly amplified polymorphic DNA], or DNA sequences) Different genetic markers have different scopes and different advantages and disadvantages. The choice of which genetic marker to use depends on the question being considered and the advantages and disadvantages in the particular context. How large is the budget? Do we need very fine-grained resolution of individual differences, or are we interested in patterns at higher taxonomic scales (comparing the relatedness of orders of mammals)?

Here are just a few examples of the many potential uses of genetic markers:

Help distinguish homology from analogy. Is biological similarity due to descent from common ancestors (homology) or due to convergence from different ancestors (analogy)? Recent interesting examples include the systematic placement of the whales and a major suggestion for rearrangement that would place the whales as relatives of hippos rather than with marine mammals such as seals. That is, the molecular data suggest that whales and hippos share homologous features and are each other's closest relatives, while the various similar features shared by whales and marine mammals such as seals may be due to convergence.

Provide common yardstick for measuring divergence of populations. Molecular data allows direct comparisons of relative levels of genetic differentiation among groups of organisms. How different are populations of elk, Cervus elaphus, in North America from conspecific red deer in Europe?

Facilitate mechanistic appraisals of evolution. Molecular markers (DNA sequencing) provide information about the fundamental molecular basis of evolutionary change. How does molecular variation arise, and what consequences does that have for adaptive change?
Application of genetic data to answer questions in natural history, organismal evolution, and forensics. Answer questions of individual identification, paternity, relatedness, gene flow, and mating system.

The basic structure of DNA: Here I provide a summary of what I see as absolutely essential basic knowledge. Most of the people in the room are probably most interested in organism that are diploid (two sets of chromosomes, one paternal, the other maternal -- most vertebrates are diploid) or polyploid (multiple sets of chromosomes, found in plants and fish -- plus one South American rodent!). Nevertheless, some of the tools for analyzing populations are haploid (mitochondrial DNA, pollen grains, sperm, unfertilized eggs, haploid male Hymenoptera). DNA has four kinds of building blocks, the nucleotides: A, G, C, and T. The nucleotides differ in their nitrogenous bases, which can be either purines or pyrimidines. A and G contain purines, while C and T (and U for RNA) contain pyrimidines. [Purine or pyrimidine nitrogenous base + ribose or deoxyribose sugar + phosphate group = nucleotide]. A chromosome consists of two complementary strands of DNA — the sense and antisense strands. The strands are arranged in an intertwined double helix configuration. Each base pair (the A, G, C or T are base pairs) has an orientation along the strand — a 5’ ("five prime ") group at one end and a 3’ ("three prime") group at the other. When the genetic code is translated into proteins, the reading goes from 3’ to 5’. During meiosis and mitosis replication turns single strands of DNA into double strands by the process of complementarity. Each base pair matches up with its complement -- A with G, C with T -- to regenerate a double strand from a single strand. An example of a stretch (sequence) of double-helix DNA is shown below:

...ACCGTAATGCTT ... Sense strand
...GTTACGGCATCC... Anti-sense strand

Coding and non-coding stretches: The DNA "code" consists of triplets that code for one of the 20 possible amino acids. For example the triplet CTG codes for the amino acid Leucine. Because there are 64 possible triplets (4*4*4 = 64) but only 20 different amino acids, the code is "redundant" -- meaning that two or more different triplets may code for the same amino acid. Usually, the difference between the triplets occurs in the third position. For example, the triplet CTC also codes for Leucine (we can have either G or C in the third place). Mutations that change the third position codon but do not change the amino acid that is produced are called silent or synonymous substitutions. The amino acids, in turn, are the building blocks of proteins (including enzymes). A chromosome's genes consist of portions that will be turned into protein product (exons) but also includes parts that are transcribed but not translated into proteins (introns), as well as long stretches not transcribed and not associated with any kind of gene (e.g., the satellite "junk" DNA usually found near the centromeres of chromosomes). At first glance one might think that the only interesting parts are the expressed genes -- they seem like the only parts that do anything and that should therefore matter in an evolutionary sense. In fact, though, much of what we will address in this section deals with non-coding DNA. The microsatellites that are my molecular tool are non-coding stretches of very simple motifs (AC repeated 20 to 30 times in different individuals’ chromosomes, or AGT repeated 12 to 25 times ).

Mendelian inheritance: Diploid organisms have two copies of each type of chromosome (the chromosome complement or karyotype number varies across diploid organisms from as few as 4 in Drosophila fruit flies to as many as 80 in a Nymphaea fly --humans have 23 different kinds. Each parent (mother and father) contributes one of its pairs of chromosomes to make up the complement in its offspring. Because of the process of independent assortment, offspring will receive differing combinations of the paired chromosomes (except for identical twins and clones). Given 23 chromosomes and independent assortment, each human can produce 2²³ combinations of chromosomes in her or his gametes -- more than 8 million possible types. Different chromosomes can have different stretches of DNA sequence at the same place (locus) on a particular chromosome. These variants are known as alleles.
You may tend to think of alleles as referring exclusively to expressed (coding) portions — they can however, refer to any stretch of DNA at which we can find variation. Indeed non-coding microsatellite alleles will be the stuff of the particular examples I provide. The existence of two different alternative alleles on the two homologous chromosomes produces the familiar possibilities of AA (both mom and dad contributed a "big A"), Aa (mom or dad contributed a "big A", the other parent a "little a") or aa (both mom and dad contributed a "little a"). (Fully) recessive alleles are expressed only when present as homozygotes (aa = white, AA and Aa = red ). Codominant alleles show an intermediate phenotype in heterozygotes (e.g., aa = white, Aa = pink, AA = red). Codominance will be very important even for our non-coding microsatellites, because the variants differ in size. A homozygote will show just one band (we can sometimes tell it is doubled by the density of the visualizing agent), whereas heterozygotes will show two different bands. The size difference in fragment lengths on the electrophoretic gel means that we have three distinguishable phenotypes for the three genotypes. Homozygotes will show just one (extra-thick) band on the gel (either long or short), while heterozygotes will show both bands.

As a contrast to the pattern of Mendelian inheritance, mitochondria are maternally inherited clones (we talk of haplotypes rather than alleles). The distinction has important ramifications for making inferences. For example, the effective population size is smaller.

Mutations: The most familiar type of mutation is a point mutation -- during replication a different nucleotide is placed in the chain (say an A, G, or T instead of the original C). Point mutations occur at a low rate (approximately 10^-6or once in a million replication events). A key point is the transition/transversion distinction mentioned above. Microsatellites (my almost exclusive tool) generally do not mutate by point mutations. Instead a process of slippage replication adds or subtracts the beads on the necklace so that we go from AC20 to AC19 or AC21 or from GCC18 to GCC17 or GCC19. It appears that the most common "mutation" is the addition or subtraction of a single repeat unit. This means that mutation is a "stepwise" process and, in theory, provides phylogenetic information. That is, all things being equal (in practice they rarely are) alleles that are more similar in size are more closely related to one another than alleles with a wider size disparity.

Make absolutely sure you understand the terms locus (plural = loci), allele, homozygote and heterozygote.

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