Introduction

• Evolution depends on variation.

• Understanding how traits and genes vary and how this variation is inherited is fundamental to understanding evolution.

Machinery of Inheritance

• The genetic material of almost all organisms on Earth is DNA (deoxyribonucleic acid).

  • Some viruses use RNA (ribonucleic acid) rather than DNA.

    • To replicate themselves, viruses use their host’s mechanisms to do the reverse transcription and convert their RNA to DNA. Then they insert the virus DNA into the host DNA to make mRNA and proteins, and finally release itself to infect other cells

• Base pairs – Adenine (A) and Thymine (T), Guanine (G) and Cytosine (C)

  • The average chromosome in humans has more than 100 million base pairs (bp).

• An organism’s genetic material is carried by one or more chromosomes.

  • Chromosomes, in eukaryotes, are long strings of DNA bases bound together with proteins.

  • In diploid species, chromosomes come in pairs (one from each parent) while in haploid cells, there is only one.

  • Genes are segments of chromosomes that perform a function.

• To make proteins, the cellular machinery reads a gene’s DNA in sets of three bases called codons.

  • Codons represent the amino acids that make up the protein

  • The genetic code is a set of rules that relates the codons to the amino acids they represent

  • There are 64 different codons, but only 20 amino acids because most amino acids are represented by more than one codon.

    • Changes to a codon that do not alter amino acids are called synonymous.

    • Changes that do alter amino acids are called nonsynonymous.

  • Proteins are synthesized in three steps:

    • (1) Transcription is the process where the DNA is changed from a gene into pre-mRNA.

    • (2) The pre-mRNA is spliced so that parts are removed to form mature mRNA.

      • Exons are segments of the gene that code for amino acids.

      • Introns are non-coding segments between the exons.

    • (3) The mRNA is translated into a string of amino acids that make up the protein.

• 98% of DNA in humans does not code for any gene product. Only a small fraction of this noncoding DNA affects how coding genes are expressed; the rest has no obvious function.

The Inheritance of Variation

• Phenotypes are observable characteristics.

• Genotypes are gene characteristics.

• Locus (loci) is a basic unit of genetic inheritance. It is a more formal term for “gene”.

  • A locus is polymorphic if the DNA sequence at the given locus varies among the chromosomes carried by different individuals.

  • Alleles are one of several forms of the same gene, presumably differing by mutation of the DNA sequence.

    • They are usually recognized by their phenotypic effects.

    • DNA sequence variants, which may differ at several or many sites, are usually called haplotypes.

    • Allele frequency refers to how often a variant occurs at a locus or a DNA base in a population.

  • Single nucleotide polymorphism (SNP) is a specific DNA base in the genome that varies among individuals.

Gene mixing by segregation

• Segregation is the selection of one of the two copies of a locus when a gamete is made during meiosis.

  • The fusion of an egg and sperm brings together the copy from the mother and from the father together. The resulting offspring can have a genotype unlike either of its parents.

• Hardy-Weinberg equilibrium tells us the relative proportions of genotypes in a population when segregation is the only factor that changes genotypes frequencies

  • Key conditions for the equilibrium:

    • An infinite population size

    • No natural selection

    • No mutation

    • No movement between populations

    • Random mating

Gene mixing by recombination

• Recombination is the process that combines in a gamete a gene copy at one locus that was inherited from the mother with a gene copy at the second locus that was inherited from the father.

  • In eukaryotes, recombination occurs during meiosis. It happens during crossing-over.

  • Recombination rate (r) is the probability that recombination occurs between a given pair of loci (genes).

• Linkage disequilibrium is the association of two alleles at two or more loci frequently (or less frequently) than predicted by their individual frequencies.

  • The key effect of recombination is to erode linkage disequilibrium.

  • Recombination moves the population toward a state where there is no statistical association between the alleles at the two loci, a situation called linkage equilibrium.

  • Linkage disequilibrium can be produced by natural selection.

  • A second important cause of linkage disequilibrium is the mixing of populations that have different allele frequencies.

• Epistasis is the situation in which the effect of an allele at one locus depends on the allele at a second locus.

  • If some combination of alleles has a high fitness, selection will generate linkage disequilibrium between them.

Gene mixing with asexual inheritance

• Horizontal gene transfer (HGT) is the movement of DNA between individuals without help from sexual reproduction.

Mutation: The Ultimate Source of Variation

• Mutations are errors in DNA sequences, made during replication, that account for genetic variation in all organisms.

Point Mutations

• Point mutations occur when a single DNA base is changed from one to another of its four possible states (A, G, C, T).

Structural Mutations

• Structural mutations affect more than one base pair; most happen as errors when chromosomes are replicated.

  • Deletions are when a segment of a chromosome is left out during replication.

  • Insertions are when a segment of DNA is added to a chromosome, either from nearby on the same chromosome or elsewhere in the genome

  • Duplications are a mutation in which a second copy of a gene is inserted into the genome.

    • Gene families are two or more loci with similar nucleotide sequences that have been derived from a common ancestral sequence.

      • Gene families are created when duplication is repeated several times.

  • Inversions are structural mutations that occur when a chromosome breaks in two places and the middle segment is reinserted in the reverse orientation.

  • Reciprocal translocation is the exchange of chromosome segments between two nonhomologous chromosomes.

  • Fusions are structural changes in which two nonhomologous chromosomes are joined. The opposite of these are fissions.

    • Fissions are when one chromosome breaks into two.

  • Whole genome duplication is when meiosis produces a gamete that carries the entire diploid genome, rather than a haploid with just one pair of chromosomes

  • Tetraploidy is if two unreduced gametes meet and fertilize each other, an offspring is produced that has four copies of each chromosome.

Rates and Effects of Mutation

Mutation Rates

• A mutation rate is the probability that an offspring carries a new mutation. They vary greatly among species.

Effects of mutations

• Despite the huge range of effects that mutations have, they show two general features:

  • (1) Pleiotropy occurs when a single mutation affects multiple traits.

    • Extreme example: achondroplasia – dwarfism, which occurs from a mutation in a single gene that interferes with the conversion of cartilage to bone during development

  • (2) Effects on an organism’s fitness

    • Fitness is the number of offspring it leaves to the next generation.

    • While most mutations have no detectable effect on survival or reproduction, most of those that do are deleterious (harmful to survival or reproduction).

    • Less often, mutations can be beneficial (increase fitness).

• Because most mutations are deleterious, natural selection favors lower mutation rates, at least in organisms with sexual reproduction

Germ line mutations and somatic mutations

• Germ lines produce gametes when the individual is sexually mature. They are set aside by the body early in development

• The soma consists of all the other tissues in the organism, made from the rest of the cells in the early embryo that are not dedicated to the germ line.

Is Mutation Random?

• There is substantial variation between the mutation rates of different regions of the genome, and between DNA bases

  • Transition mutations happen between A and G, and C and T.

  • Transverse mutations happen between all other kinds (ex: between A and C).

  • There are twice as many possible transversion mutations, but transition mutations are more common.

• Mutations are random with respect to what will improve survival and reproduction

Nongenetic Inheritance

• The vast majority of inherited changes involve alterations of the DNA (or RNA) sequence of a genome. However, other mechanisms also contribute to inheritance and so can play a role in evolution.

• Epigenetic inheritance is caused by inherited changes to chromosomes that do not alter the DNA sequence; instead, these changes affect the organism by altering how genes are expressed.

  • Most epigenetic changes are not stable and dissipate after a few generations

• Maternal effects occur when the genotype or phenotype of the mother directly influences the phenotype of her offspring.

• Cultural inheritance is transmitted by behavior and learning.

  • An important difference between cultural inheritance and other forms of nongenetic inheritance is that traits can be transmitted between unrelated individuals (as well as between parents and offspring).

Extra “Boxes” of Information

Box 4A: Estimating Mutation Rates

• Mutations are fundamental to genetics and evolution.

• Several strategies have been invented to estimate the mutation rate:

  • (1) Phenotype screening: The researcher screens a large number of individuals in a population for new traits caused by mutations. The mutation rate is calculated by dividing the number of new mutations found by the number of individuals in the population.

    • This method cannot account for mutation rates at the individual DNA bases, and it can be easy to mess up the count.

  • (2) Phylogenetic method: If a segment of chromosomes has no effect on fitness, it can be assumed that it will accumulate an x rate of mutations per generation. If two species share a common ancestor y number of generations ago, then the number of mutations in that segment would be 2xy. This can be calculated using DNA sequencing.

    • The big weakness of this method is that only neutrally evolving mutations can be used, and the number of generations from a common ancestor must be known.

  • (3) Mutation accumulation: Several populations are established in a lab from a single founding population. Over the course of many generations, the mutations are counted and used to estimate the mutation rate.

    • Due to limitations with establishing many populations of a species in a lab setting, there will be fewer mutations to study in the populations.

  • (4) Direct method: DNA of parents and offspring are sequenced to look for mutations.

    • The chance of a mutation in any specific gene is extremely small, which is a limitation of this method.