Principles of Life, Ch. 15

15.1 Genomes Reveal Both Neutral and Selective Processes of Evolution

Evolution results from changes to gene sequences, location, and expression

• In organisms that reproduce sexually, both males and females contribute nuclear genes, but mitochondrial and chloroplast genes are usually transmitted only via the cytoplasm of one of the two gametes (often from the female parent).
• Mistakes in replication—mutations—provide much of the raw material for evolutionary change.
• A particular allele of a gene will not be passed on to successive generations unless an individual carrying that allele survives and reproduces
• The sequences of genes, as well as their location and expression, are subject to evolutionary change, as are the extent and location of noncoding DNA

Much of molecular evolution is neutral

• Synonymous Substitution: A change of one nucleotide in a sequence to another when that change does not affect the amino acid specified; aka silent
• NonSynonymous Substitution: A change in a gene from one nucleotide to another that changes the amino acid specified by the corresponding codon; missense & nonsense are included
  • Nonsynonymous are likely to be deletrious
• ==Substitution rates are higher at nucleotide positions that do not change the amino acid being expressed==
• Pseudogenes: A DNA segment that is homologous to a functional gene but is not expressed because of changes to its sequence or changes to its location in the genome.
  • The highest rate of substitution is found in pseudogenes
• Neutral Theory: A view of molecular evolution that postulates that most mutations do not affect the amino acid being coded for, and that such mutations accumulate in a population at rates driven by genetic drift and mutation rates.
• The rate of fixation of neutral mutations is thus equal to the mutation rate in populations of any size.
• As long as the underlying mutation rate is constant, genes and proteins evolving in different populations should diverge from one another in neutral changes at a constant rate.

Positive and purifying selection can be detected in the genome

• If a given amino acid position is under positive selection for change, the observed rate of nonsynonymous substitutions is expected to exceed the rate of synonymous substitutions in the corresponding sequences.
  • Positive selection: Natural selection that acts to establish a trait that enhances survival in a population.
• If a given amino acid position is under purifying selection, then the observed rate of synonymous substitutions is expected to be much higher than the rate of nonsynonymous substitutions in the corresponding sequences.
  • Purifying selection: The elimination by natural selection of detrimental characters from a population.
• Convergent evolution: Independent changes to the same state or trait in two or more groups of organisms.

Genome size and organization also evolve

• Therefore much of the variation in genome size lies not in the number of functional genes, but in the amount of noncoding DNA
• Why so much noncoding DNA?
  • No cost to carrying a lot of pseudogenes
  • Can become the raw material for the evolution of new genes with novel functions.
  • Help with maintaining chromosomal structure.
• In species with small populations, the effects of genetic drift can overwhelm selection against noncoding sequences that have small deleterious consequences.

15.2 Rearrangements of Genomes Can Result in New Features

Sexual recombination amplifies the number of possible genotypes

• Disadvantages to sex include recombination (breaks up adaptive combinations, reduces females passing on their genetic info, and dividing offspring into genders reduces the overall reproductive rate
• the effective reproductive rate of the asexual lineage is twice that of the sexual lineage because the sexual lineage will produce males, which cannot carry offspring
• Muller’s Ratchet: The accumulation—“ratcheting up”—of deleterious mutations in the nonrecombining genomes of asexual species.

Lateral gene transfer can result in the gain of new functions

• Lateral gene transfer: The transfer of individual genes, organelles, or fragments of genomes from one species to another, common among bacteria and archaea
  • Some species may pick up fragments of DNA directly from the environment.
  • A virus may pick up some genes from one host and transfer them to a new host
• Lateral gene transfer appears to be relatively uncommon among most eukaryotic lineages
• Hybridization leads to the exchange of many genes among recently separated lineages of plants. The greatest degree of lateral transfer occurs among bacteria.

Many new functions arise following gene duplication

• Gene duplication: A way that genomes can acquire new functions.

• The identical copies of a duplicated gene can have any one of four different fates:

  1. Both copies of the gene may retain their original function (which can result in a change in the amount of gene product that is produced by the organism).
  2. Both copies of the gene may keep the ability to produce the original gene product, but the expression of the genes may diverge in different tissues or at different times in development.
  3. One copy of the gene may be incapacitated by the accumulation of deleterious mutations and become a functionless pseudogene.
  4. One copy of the gene may retain its original function while the second copy changes and evolves a new function.

• Several successive rounds of duplication and sequence evolution may result in a gene family, a group of homologous genes with related functions, often arrayed in tandem along a chromosome.

15.3 Changes in Gene Expression Often Shape Evolution

A cascade of transcription factors establishes body segmentation in animals

• Morphogens: A diffusible substance whose concentration gradient determines a developmental pattern in animals and plants.
• Three classes of genes are involved in determining segments:
  • Maternal effect genes set up the major axes (anterior–posterior and dorsal–ventral) of the embryo.
  • These genes are transcribed in the cells of the mother’s ovary, and the mRNAs are passed to the egg.
  • Segmentation genes determine the boundaries and polarity of each of the segments.
• Three classes of segmentation genes act one after the other to regulate finer and finer details of the segmentation pattern:
  • Gap genes organize broad areas along the anterior–posterior axis.
  • Mutations in gap genes result in gaps in the body plan—the omission of several consecutive larval segments.
  • Pair rule genes divide the embryo into units of two segments each.
  • Mutations in pair rule genes result in embryos missing every other segment.
  • Segment polarity genes determine the boundaries and anterior–posterior organization of the individual segments.
  • Mutations in segment polarity genes can result in segments in which posterior structures are replaced by reversed (mirror-image) anterior structures.
  • Hox genes determine what organ will be made at a given location.
  • Hox genes encode a family of transcription factors that are expressed in different combinations along the length of the embryo, and help determine cell fates within each segment.
  • Hox genes are shared by all animals, and mutations in these genes have been linked to major changes in body structure among different animal groups.
• Homoeotic mutations: Mutation in a homeotic gene that results in the formation of a different organ than that normally made by a region of the embryo.
  • Example of a homoeotic mutation is when the gene Antennapedia causes legs to grow on the head of Drosophila in place of antenna
  • Homeobox: A 180-base-pair segment of DNA found in certain homeotic genes; regulates the expression of other genes and thus controls large-scale developmental processes.
  • Homeodomain: A 60-amino acid sequence within the homeobox that regulates the expression of other genes and through this regulation controls large-scale developmental processes.
  • The homeodomain recognizes and binds to a specific DNA sequence in the promoters of its target genes, “turning on” the formation of specific structures.

A common “toolkit” of genetic mechanisms controls gene expression in development

• Homologous: In evolutionary biology, one of two or more features in different species that are similar by reason of descent from a common ancestor.
• Genetic toolkit: A set of developmental genes and proteins that is common to most animals and is hypothesized to be responsible for the evolution of their differing developmental pathways.
• Genetic switches: Mechanisms that control how the genetic toolkit is used, such as promoters and the transcription factors that bind them; The signal cascades that converge on and operate these switches determine when and where genes will be turned on and off.

The amount, timing, and location of gene expression control many morphological features

• Heterometry: Alteration in the level of gene expression, and thus in the amount of protein produced, during development, contributing to the evolution of different phenotypes in the adult.
• Heterochrony: Alteration in the timing of developmental events, leading to different results in the adult organism.
  • An example of heterochrony is the length of a giraffe neck; signaling of apoptosis of chondrocytes (cartilage producing cells) is delayed so the vertebrae grow longer
• Heterotopy: Spatial differences in gene expression during development, controlled by developmental regulatory genes and contributing to the evolution of distinctive adult phenotypes.
  • An example of heterotopy is the difference between webbed feet and non-webbed feet between birds (ducks vs chickens)

Mutations in developmental genes can cause major morphological changes

• Sometimes a major developmental change is caused by an alteration in the regulatory molecule itself rather than a change in where, when, or how much it is expressed.

15.4 Molecular Evolution Has Many Practical Applications

Knowledge of gene evolution is used to study protein function

• An example of using evolution to study protein function is how pufferfish built an immunity to TTX as a toxin but humans did not; both have sodium channels but the pufferfish ones are resistent.
• Comparing the rates of synonymous and nonsynonymous substitutions across the genes in various lineages that have evolved resistance show how the TTX resistence evolved

In vitro evolution is used to produce new molecules

• In Vitro Evolution: A method based on natural molecular evolution that uses artificial selection in the laboratory to rapidly produce molecules with novel enzymatic and binding functions.

Molecular evolution is used to study and combat diseases

• Cross-species transmission of viruses has led to the global emergence of many “new” diseases.
• Speciation is what leads to the branching events on the tree of life, and is the process that results in the millions of species that constitute biodiversity.

\