Evolutionary Biology Overview

1.0 Introduction

• Evolution: Process populations adapt to their environment over time through natural selection.
• Taxonomy: Study of the morphological relationships between organisms.
• Systematics: Taxonomy related to evolutionary processes.
• Molecular Systematics: Use of molecular data to understand evolutionary processes.
• Classification: Naming species to reflect evolutionary relationships.
• Adaptation: The core of evolution.
• Alleles: Different forms of a gene.

1.1 Brief History of Evolutionary Biology

• Aristotle (350 BC): Proposed essentialism; species remain unchanged.
• Carl Linnaeus (1753): Developed binomial classification.
• Jean-Baptiste Lamarck (1809): Proposed transformism; species can change over time.
• George Cuvier (1813): Proposed catastrophism; species go extinct due to events.
• Charles Lyell (1830): Proposed uniformitarianism.
• Charles Darwin (1859): Proposed natural selection.
• Gregor Mendel (1920): Studied heredity.

1.2 Evidence for Evolution

• Artificial Selection: Humans select traits in species over time.
• Analogous Structures: Structures with similar functions but different evolutionary origins.
• Vestigial Structures: Structures that have lost their function over evolutionary time.

1.3 Fossils and Geological Time

• Fossils: Preserved remains of plants or animals.
• Petrification: Process of turning material into stone.
• Moulds and casts: Formed by minerals filling the space left by a decomposed organism.
• Biostratigraphy: Using fossils to determine the relative ages of rock strata.
• Paleomagnetism: Studying Earth's magnetic field in rocks to determine ages.
• Radiometric dating: Measuring radioactive isotopes to determine absolute ages.

1.4 Paleoclimates

• Biological proxies: Using biological remains to reconstruct past climates.
• Chemical proxies: Using chemical data in things like ice cores to reconstruct past climates.
• Archives: Historical records.

1.5 Natural Selection

• Excess fecundity: Producing more offspring than needed.
• Variation: Differences in traits within a population.
• Reproduction: Ability to create a new generation.
• Inheritance: Passing traits to offspring.
• Variation in fitness: Different traits result in different numbers of offspring.

2.1 Population Genetics

• Hardy-Weinberg principle: Under specific conditions, allele frequencies in a population remain constant.
• Assumptions of Hardy-Weinberg: No mutations, random mating, no gene flow, no natural selection, very large population size.
• Genotype and allele frequencies.

2.2 Breaking Hardy-Weinberg Equilibrium

• Non-random mating: When individuals choose mates based on similarity or dissimilarity.
• Gene flow: Movement of individuals or gametes between populations.
• Mutations: Permanent changes in DNA sequence.
• Natural selection: Differential reproductive success of individuals due to their traits.

2.3 Variations in Populations

• Mutations: Random changes in DNA sequence.
• Example: Considering a gene with two alleles, D and d, calculate the expected equilibrium frequencies of p and q given the mutation rates from D to d, and from d to D.

2.4 Genetic Drift

• Genetic drift: Random change in allele frequencies between populations.
• Founder effect: A small group of individuals establish a new population and reduces genetic diversity.
• Bottleneck effect: Population becomes smaller temporarily and reduces genetic diversity.
• Migration: Increases genetic variation within a population.

3.1 What is a Species?

• Species: Group of organisms that can interbreed and produce fertile offspring.
• Deme: Localized group of organisms sharing a gene pool.
• Cline: Gradual change in species characteristics along a geographical area.

3.2 Speciation Mechanisms

• Allopatric speciation: Speciation resulting from geographical isolation.
• Peripatric speciation: Speciation resulting from a small population that diverges from a larger population.
• Sympatric speciation: Speciation occurring within a single population.
• Polyploidization: Process where an organism gains additional sets of chromosomes, which can cause sympatric speciation.
• Parapatric speciation: Speciation occurring within a population with continuous geographic range where there is some contact and gene flow.

3.3 Molecular Clocks

• Molecular clocks: Evolutionary time scale based on the observation that genetic differences between species accumulate at a relatively constant rate over time.
• Mutations: Changes in DNA or protein sequences.

3.4 Artificial Selection

• Artificial selection: Humans selecting traits over multiple generations in animals and plants.
• Genetic engineering: Using technology to produce genetically modified organisms.

4.1 Human Evolution

• Hominidae: Superfamily of apes and humans..
• Hominins: Human ancestry.
• Sagittal crest: Bony ridge on top of the skull.
• Ardipithecus: Early hominin.
• Homo habilis: Early member of the genus Homo
• Homo erectus: More modern body proportions and tool use in humans.

4.2 Drivers for Human Evolution

• Bipedalism: Walking on two legs.
• Brain enlargement: Increased brain size leading to higher cognitive abilities.
• Changes to teeth and jaw: Changes associated with a diet that is less reliant on chewing.
• Culture evolution: Tools, rituals, symbolic expression, etc
• Changes in anatomical features

4.3 Neanderthals

• Derived from modern humans
• Adapted to colder climates
• Large body and brain size
• Used tools, had burials and symbolic behavior
• Interbreeding with modern humans
• Fossils show injuries and diseases

4.4 Ongoing Evolution in Humans

• Use genetic markers to trace migration patterns.
• Out-of-Africa hypothesis: Modern humans evolved in Africa and migrated to other regions.

5.1 Sex Chromosome Evolution

• Heterogametic: Sex determined by presence or absence of certain chromosomes.
• Homomorphic: When sex chromsome appear to be same in both sexes;
• Heteromorphic: When sex chromsome appear to be different.

5.2 Tree Building

• Molecular phylogenetics: Study of evolutionary relationships through molecular data.
• DNA Sequences: Order of nucleotides in organisms DNA.
• Protein Sequences: Amino acid Sequences.
• Methods: Distance, parsimony, maximum likelihood, Bayesian inference.
• Tree building process: Collect data, align sequences, choose evolutionary model, generate trees, select best tree,.

5.3 Hypothesis Testing

• Consensus tree: Summarizes whole set of trees generated in tree-building processes.
• Bootstrapping: Statistical method to assess confidence in a tree.
• Monophyly: Group containing all descendants of a common ancestor.
• Paraphyly: Group not containing all descendants of a common ancestor.

5.4 Phylogeography

• Phylogeography: Study of geographical distribution of species or individuals within a species. 5.5 Evolutionary Significant Units (ESUs)
• Methods to identify distinct populations
• Isolation Criteria
• Exchangeability

Explore the foundational concepts of evolutionary biology including natural selection, taxonomy, and molecular systematics. Delve into the history of key figures who shaped our understanding of evolution from Aristotle to Darwin. Test your knowledge of adaptation and genetic variation.