Evolution & Gene Frequencies

Evolution & Gene Frequencies

Paleontology

• Fossil records provide insights into evolutionary transitions.
• Example: Transition from early reptiles to dinosaurs and early birds (e.g., Stagonolepis, Deinonychus, Archeopteryx).

Fossil Records

• Fossils in younger strata are more recent, while older strata contain older fossils.
• Fossils document transitions, such as the evolution of cetaceans from land to sea.

Biogeography

• Biogeography, the geographic distribution of species, offers evidence of evolution.
• Continents were once united as Pangaea and have since separated via continental drift.
• Understanding continent movement helps predict when and where different groups evolved.
• Examples of biogeographic regions: Sahara Desert, Ethiopian region, Palearctic region, Oriental region, Australian region, Nearctic region, Neotropical region.

Continental Drift

• Distributions of Triassic fossils (e.g., Cynognathus, Mesosaurus, Lystrosaurus, Glossopteris) illustrate biogeography via continental drift across South America, Africa, Antarctica, India, and Australia.

Endemic Species

• Endemic species are unique to specific geographic locations.
• Islands often have endemic species closely related to mainland species.
• Island species adapt to new environments, giving rise to new species.
• Example: Cuatrocienegas Valley, where not all "islands" are in the ocean.

Homologies and Evolutionary Trees

• Evolutionary trees are hypotheses about relationships among groups.
• Homologies form nested patterns in evolutionary trees.
• Trees can use anatomical and DNA sequence data.
• Phylogenetic tree example includes Fish, Amphibians, Reptiles, Dinosaurs, Birds, and Mammals.
• Key traits:
  • Vertebrae
  • Terrestrial locomotion
  • Amniotic egg
  • Synapsid skull
  • Diapsid skull
  • Adaptations for flight
• Groups:
  • Lepidosauria
  • Diapsida
  • Archosauria
  • Squamata
• Diapsids have a diapsid skull with two pairs of temporal openings.

Speciation

• Speciation, the origin of new species, is central to evolutionary theory.
• Evolutionary theory explains how new species originate and how populations evolve.
• Microevolution: Changes in allele frequency in a population over time.
• Macroevolution: Broad patterns of evolutionary change above the species level.

Biological Species Concept

• Emphasizes reproductive isolation.
• Species are grouped by comparing morphology, physiology, biochemistry, and DNA sequences.
• A species is a group of populations with the potential to interbreed and produce viable, fertile offspring; they do not breed successfully with other populations.
• Gene flow maintains the phenotype of a population.

Reproductive Isolation

• Reproductive isolation involves biological factors that prevent different species from producing viable, fertile offspring.
• Hybrids are offspring from crosses between different species.
• Isolation can occur before (prezygotic) or after (postzygotic) fertilization.

Prezygotic Barriers:

• Block fertilization by:
  • Impeding mating attempts.
  • Preventing successful mating.
  • Hindering fertilization if mating is successful.
• Types:
  • Habitat isolation: Species in different habitats rarely interact.
  • Temporal isolation: Species breed at different times.
  • Behavioral isolation: Unique courtship rituals.
  • Mechanical isolation: Morphological differences prevent mating.
  • Gametic isolation: Sperm and eggs are incompatible.

Postzygotic Barriers:

• Prevent hybrid zygotes from developing into viable, fertile adults.
• Types:
  • Reduced hybrid viability: Impaired hybrid development due to gene interaction.
  • Reduced hybrid fertility: Hybrids may be sterile.
  • Hybrid breakdown: Fertile first-generation hybrids produce feeble or sterile offspring in the next generation.

Limitations of Biological Species Concept

• Cannot be applied to fossils or asexual organisms.
• Emphasizes absence of gene flow, but gene flow can occur between distinct species (e.g., grizzly bears and polar bears producing "grolar bears").
• Species delineations can be difficult with distinct-seeming populations (e.g., Ring salamander, Ensatina eschscholzii).

Other Species Concepts

• Morphological species concept: Defines species by structural features (subjective criteria).
• Ecological species concept: Views species in terms of ecological niches (emphasizes disruptive selection).
• Phylogenetic species concept: Defines a species as the smallest group of individuals on a phylogenetic tree (can be difficult to determine required degree of difference).

Gene Pools and Allele Frequencies

• A population is a localized group of interbreeding individuals producing fertile offspring.
• A gene pool includes all alleles for all loci in a population.
• A locus is fixed if all individuals are homozygous for the same allele.

Hardy-Weinberg Equilibrium

• States that allele and genotype frequencies in a population remain constant from generation to generation.
• In random mating, allele frequencies will not change.
• Mendelian inheritance preserves genetic variation in a population.
• Describes a population that is not evolving.
• If a population does not meet Hardy-Weinberg criteria, it is evolving.

Allele Frequency Calculation

• Frequency of an allele can be calculated.
• With 2 alleles at a locus, p and q represent their frequencies.
• The sum of all allele frequencies in a population equals 1: p + q = 1.

Example

• Example:
  • If there are 16 red and 4 white beads p = frequency of C^W allele = 0.8
  • q = frequency of C^R allele = 0.2
  • p (0.8) + q (0.2) = 1

Hardy-Weinberg Equation

• If p and q represent frequencies of two possible alleles: p^2 + 2pq + q^2 = 1.
• p^2 and q^2 represent homozygous genotype frequencies.
• 2pq represents heterozygous genotype frequency.

Example 2

• Example: p=0.8 and q=0.2.
• 0.8^2 + (20.80.2) + 0.2^2 = 1
• 0.64 + 0.32 + 0.04 = 1
• Approximately 64% homozygous dominant (AA), 32% heterozygotes (Aa), and 4% homozygous recessive (aa).

Estimating Allele Frequencies

• Estimate p and q by measuring genotype frequencies.
• If frequency of aa = 20%, then q^2 = 0.2.
• You can find q by taking the square-root of 0.2 (\sqrt{0.2} = 0.44).
• p = 1 - q, so p = 1 - 0.44 = 0.56.
• Then the frequency of AA is 0.314 and Aa is 0.493.

Conditions for Hardy-Weinberg Equilibrium

• The Hardy-Weinberg theorem describes a hypothetical non-evolving population.
• In real populations, allele and genotype frequencies change over time.
• Natural populations can evolve at some loci while being in Hardy-Weinberg equilibrium at others.

Conditions Not Met In Nature

• Conditions for non-evolving populations are rarely met in nature:
  1. Extremely large population size (no effects of chance).
  2. No gene flow (movement).
  3. No mutations (or mutational equilibrium).
  4. Random reproduction (no differential success).

Genetic Drift

• The smaller a sample, the greater the chance of deviation from a predicted result.
• Genetic drift: Allele frequencies fluctuate unpredictably from one generation to the next.
• Genetic drift reduces genetic variation through losses of alleles.
• Examples:
  • The Founder Effect
  • The Bottleneck Effect

Founder Effect

• Occurs when a few individuals become isolated from a larger population.
• Allele frequencies in the small founder population differ from the larger parent population.

Bottleneck Effect

• Sudden reduction in population size due to environmental change.
• The resulting gene pool may no longer reflect the original population’s gene pool.
• If the population remains small, it may be further affected by genetic drift.

Effects of Genetic Drift

• Most significant in small populations.
• Causes allele frequencies to change at random (Neutral Evolution).
• Can lead to a loss of genetic variation within populations.
• Can cause harmful alleles to become fixed.

Gene Flow

• Gene flow: Movement of alleles among populations.
  • Emigration: Moving out of a population.
  • Immigration: Moving into a new population.
• Alleles are transferred through the movement of fertile individuals or gametes.
• Gene flow tends to reduce variation among populations over time.
• Example: Gene Flow in Polar Bear (Ursus maritimus) Populations.

Mutations

• Mutations occur but are less likely in equilibrium (mutated alleles that mutate back to the original form as often as they mutate in the first place…).

Natural Selection

• Differential success in reproduction results in certain alleles being passed to the next generation in greater proportions.
• Example: An allele that confers resistance to DDT increased in frequency after DDT was used widely in agriculture.

Sexual Selection

• Natural selection for mating success.
• Results in sexual dimorphism: Marked differences between the sexes in secondary sexual characteristics.
• Can appear to have a negative impact on survival, but reproductive success compensates.
• "Handicap Principle"- survival despite an obvious handicap indicates "good genes".

Types of Sexual Selection

• Intrasexual selection: Competition among individuals of one sex (often males) for mates of the opposite sex.
• Intersexual selection (mate choice): Individuals of one sex (usually females) are choosy in selecting their mates.
• Non-random mating.

Modes of Selection

• Three modes of selection:
  • Directional selection: Favors individuals at one end of the phenotypic range.
  • Disruptive selection: Favors individuals at both extremes of the phenotypic range.
  • Stabilizing selection: Favors intermediate variants and acts against extreme phenotypes.

Heterozygote Advantage

• Heterozygotes have higher fitness than either homozygote condition.
• Natural selection maintains two or more alleles at that locus.
• Example: The sickle-cell allele causes mutations in hemoglobin but also confers malaria resistance, giving heterozygotes an advantage over either homozygote condition.

Speciation and Geographic Separation

• Speciation can occur with or without geographic separation.
• Two ways speciation can occur:
  • Allopatric speciation- separate places
  • Sympatric speciation- same place

Allopatric Speciation

• In allopatric speciation, gene flow is interrupted or reduced when a population is divided into geographically isolated subpopulations.
• Example: The flightless cormorant of the Galápagos likely originated from a flying species on the mainland.

Process of Allopatric Speciation

• The definition of barrier depends on the ability of a population to disperse.
• Example: A canyon may create a barrier for small rodents, but not birds, coyotes, or pollen.
• Sibling species of snapping shrimp (Alpheus) are separated by the Isthmus of Panama.
• These species originated 9 to 13 million years ago, when the Isthmus of Panama formed and separated the Atlantic and Pacific waters.
• Regions with many geographic barriers typically have more species than do regions with fewer barriers.
• Reproductive isolation between populations generally increases as the distance between them increases.
• Example: Reproductive isolation increases between dusky salamanders that live further apart.

Sympatric Speciation

• In sympatric speciation, speciation takes place in geographically overlapping populations.
• Mechanisms:
  • Polyploidy
  • Habitat Differentiation
  • Sexual Selection

Polyploidy

• Polyploidy: The presence of extra sets of chromosomes due to accidents during cell division.
• More common in plants than in animals.
• An autopolyploid: An individual with more than two chromosome sets, derived from one species.
• An allopolyploid: A species with multiple sets of chromosomes derived from different species.

Habitat Differentiation

• Sympatric speciation can also result from the appearance of new ecological niches.
• Example: The North American maggot fly can live on native hawthorn trees as well as more recently introduced apple trees.

Sexual Selection

• Sexual selection can drive sympatric speciation.
• Sexual selection for mates of different colors has likely contributed to speciation in cichlid fish in Lake Victoria.

Review of Allopatric and Sympatric Speciation

• In allopatric speciation, geographic isolation restricts gene flow between populations.
  • Reproductive isolation may then arise by natural selection, genetic drift, or sexual selection in the isolated populations.
  • Even if contact is restored between populations, interbreeding is prevented.
• In sympatric speciation, a reproductive barrier isolates a subset of a population without geographic separation from the parent species.
  • Sympatric speciation can result from polyploidy, natural selection, or sexual selection.

Rates of Evolution

• Speciation can occur rapidly or slowly and can result from changes in few or many genes.
• Many questions remain concerning how long it takes for new species to form, or how many genes need to differ between species.
• Two major patterns observed:
  • Gradualism
  • Punctuated Equilibrium

Patterns in the Fossil Record

• The fossil record includes examples of species that appear suddenly, persist essentially unchanged for some time, and then apparently disappear.
• Niles Eldredge and Stephen Jay Gould coined the term punctuated equilibria to describe periods of apparent stasis punctuated by sudden change.
• The punctuated equilibrium model contrasts with a model of gradual change in a species’ existence.

Geological Time

• Ways to look at geological time and how the diversity of life fits into it.
• Note the overall scale vs. the time frames of organismal groups.
• Note the advent of major groups of organisms.
• Reminder of continental drift (at least from the latest supercontinent to the present).