Evolution (PCB4764) Lecture notes, Lecture notes of Evolutionary biology

Chapter 1 through Chapter 6 notes

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PCB4674 Exam 1 Notes
Module 1: History of Evolutionary Thought
The “Great Chain of Being”
- God Angels Demons Man Woman Animals Plants Minerals
Linneaus
- “Father of Taxonomy”
- Hierarchical classification of all life: Systema Naturae (1735)
Georges Buffon
- Argued that natural laws were required for explanation of natural phenomena
- Calculated an old earth (>70,000 years)
- Also wrote about heredity, formalized the notions of variation within species and
that offspring resemble their parents, even in other organisms
William Smith
- Surveyor of canal, railroads etc.
- Recognized same fossil assemblages in similar rocks
- Mapped stratigraphy in England (1815)
oRepresented the first systematic survey of the surface geology of England
Made possible by the widespread industrialization of the country
spurring new mines, railroads, and canals. These opened roadcuts
through hills, and allowed Smith to peer inside and describe the
stratigraphy
Erasmus Darwin
- Published a work on animal physiology in which he foreshadowed the evolutionary
ideas of Lamarck, that organisms were striving toward improvement, and those
improvements should be passed to the next generation
Lamarck
- Presented a potential mechanism of evolution in 1809:
oUse and disuse leads to developmental change and acquired characteristics
are inherited
- Published Flore francoise (1788) describing ~60 new species in the first work of its
kind
- Presented a potential mechanism of evolution in 1809: use and disuse leads to
developmental change and acquired characteristics are inherited
oImplied that new lineages were being constantly created to replace those
species that had improved to higher levels of development
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PCB4674 Exam 1 Notes

Module 1: History of Evolutionary Thought The “Great Chain of Being”

  • God  Angels  Demons  Man  Woman  Animals  Plants  Minerals Linneaus
  • “Father of Taxonomy”
  • Hierarchical classification of all life: Systema Naturae (1735) Georges Buffon
  • Argued that natural laws were required for explanation of natural phenomena
  • Calculated an old earth (>70,000 years)
  • Also wrote about heredity, formalized the notions of variation within species and that offspring resemble their parents, even in other organisms William Smith
  • Surveyor of canal, railroads etc.
  • Recognized same fossil assemblages in similar rocks
  • Mapped stratigraphy in England (1815) o Represented the first systematic survey of the surface geology of England  Made possible by the widespread industrialization of the country spurring new mines, railroads, and canals. These opened roadcuts through hills, and allowed Smith to peer inside and describe the stratigraphy Erasmus Darwin
  • Published a work on animal physiology in which he foreshadowed the evolutionary ideas of Lamarck, that organisms were striving toward improvement, and those improvements should be passed to the next generation Lamarck
  • Presented a potential mechanism of evolution in 1809: o Use and disuse leads to developmental change and acquired characteristics are inherited
  • Published Flore francoise (1788) describing ~60 new species in the first work of its kind
  • Presented a potential mechanism of evolution in 1809: use and disuse leads to developmental change and acquired characteristics are inherited o Implied that new lineages were being constantly created to replace those species that had improved to higher levels of development

 Led to many easily falsifiable predictions and was rapidly abandoned Charles Darwin

  • Born 1809
  • Trained in medicine, then tried clergy
  • Constantly distracted by natural history o Voyage of the Beagle  1831, Darwin began 5 yr voyage  Primary goal: survey the coastline of South America  Took Charles Lyell’s Principles of Geology
  • Wrote book “Voyage of the Beagle” about Galapagos Thomas Malthus
  • An Essay on the Principle of Population (1798) o Made first mathematical models for studying populations Module 2: Radiometric Dating, Paleontology and the History of Life Chapter 3 What the rocks say: how geology and paleontology reveal the history of life
  • Darwin’s early interests included geology o Applied rough estimates based on rate of sediment accumulation (after earthquake) and estimated some must be hundreds of millions years old Other attempted to calculate the Earth age
  • William Thomson, Lord Kelvin: estimated (1862) 20-400 million years, based on calculations of the rate Earth was assumed to cool from initial molten state o Error in assuming earth was only cooling ignored radioactivity, plate tectonics, etc. Radioactive isotopes allow precise dating
  • Radioactivity discovery led to a revolution in the study of earths history
  • Once a rock has cooled enough to crystallize, radioactive isotopes and their decay are fixed
  • Different half-lives of different radioisotopes give geologists a number of techniques to estimate the rocks age from any point of time in Earth’s history o Estimates from multiple tests with different radioisotopes are used to refine age
  • Radiometric dating allows for precise estimates of the age of geological formations

Biomarkers reveal traces of life

  • Biomarker: distinctive molecules only produced through biological activity o Presence of okenane reveals of purple sulfur bacteria 1.64 billion years ago Carbon isotopic signatures used to infer diet of early hominins
  • C4 plants have lower C13 than C3 plants o C13/C12 ratio used to infer types of plants eaten History of Life on Earth Revealed by Fossil Record Scientists search for evidence of life in old rock
  • Earliest life unlikely to be preserved in fossiles
  • Presence of carbon in early rocks suggests life
  • Isotopic signature more consistent with living than non-living carbon sources Earliest signs of life
  • Oldest evidence of life dates to 3.7 bya o Carbon contained in rocks o Claim in controversial
  • Oldest stromatolite (bacteria) fossils date to 3.45 bya How do early organisms fit in the tree of life?
  • Bacteria earliest fossils: potentially 3.45 byo; abundant by ~2.6 bya, corresponding to rise in oxygen
  • Eukaryota earliest fossils: ~ 1.8 bya
  • Archaea earliest fossils: ~3.5 bya Origin of multicellularity of a major transition of history of lie
  • Evolved independently in different lineages
  • Extant organisms provide clues about origin of multicellularity Eukaryotic multicellular life
  • Earliest fossils of algae date to 1.6 bya o Red algae: 1.2 bya o Green algae: 750 mya The dawn of animals
  • Early animal life resembled sponges o Oldest fossils 650 mya o Biomarkers also demonstrate existence of sponges during this time
  • Earliest animal tracks date to 585 million years ago Ediacaran fauna
  • Diverse and unique animals dominated the oceans from 575 – 535 mya o Many hard to place taxonomically
  • Currently existing lineages recognizable during the early Cambrian o Early cambrian: 542 – 511 mya o Chordates first appear ~515 million years ago Transition from ocean to land a major event in evolution
  • Prokaryotes colonized terrestrial environments first o Fossils date to 2.6 bya
  • Terrestrial animals, plants, and fungi, appeared much later First terrestrial plant and fungal life
  • Oldest terrestrial plant fossils are 475 mya
  • Large forest ecosystems within 100 million years
  • Fungi appear ~400 mya o Associated with plants First terrestrial animal life
  • Invertebrate trackways date to 480 mya o Probably relatives of scorpions and spiders o Not clear whether they lived on land permanently
  • Oldest fossil of fully terrestrial animal dates to 428 mya First terrestrial vertebrates
  • Oldest trackways date to 390 mya
  • Oldest fossils of tetrapods date to 370 mya Familiar forms of life did not emerge until recently
  • 350 million years ago many currently existing lineages had not yet evolved o Teleost fish o Mammals o Birds o Flowering plants Evolution of mammals
  • Mammals evolved from synapsids
  • Two forms: o Convergent evolution: independent evolution of similar trait o Evolutionary reversals: reversion back to an ancestral character state Principle of maximum parsimony
  • The alternative requiring the fewest evolutionary steps is usually best
  • Phylogenies are usually constructed from DNA sequence data
  • If more than one tree is equally parsimonious we can construct a consensus tree
  • Polytomy: relationships uncertain Ch. 4 Fossils and phylogeny
  • Fossils can be used along with phylogenies to make refined estimates of divergence times
  • Coelacanth fins are homologous to tetrapod forelimb
  • Phylogenies generate hypotheses
  • Tiktaalik: transitional fossil between fish and tetrapods
  • Tiktaalik forelimbs share more homologies with tetrapods
  • Phylogeny reveals how tetrapod traits evolved over time Homology can be obvious …or not
  • Homology between orangutan and human foot is obvious
  • But certain traits, like ear bones, have become heavily modified – can we discern this transition?
  • Mammalian ear bones are homologous to bones of the reptilian jaw
  • Fossils and phylogeny document transition of bones from jaw to ear
  • Homology evident in embryonic development “Ontology recapitulates phylogeny”
  • Ernst Haeckel’s theory that development of animals passes through stages corresponding to lower forms of animal life
  • Birds are dinosaurs: tracking the evolution of feathers and flight
  • Feather evolved before flight
  • Feathers originally involved in other functions

Exaptation

  • A feature whose original function was later co-opted in an evolutionary transition to a different function, i.e. feathers being used for warmth and later for flight Module 4: Alleles, Genotypes, and Phenotypes Ch. 5 Raw material: Genomes Theories of inheritance
  • Origin of species strongly critiqued – blending inheritance means variation always decreases
  • Natural selection couldn’t work
  • Mendel’s work suggested some traits had particulate inheritance, but ignored when first published
  • Mutation: any change to the genomic sequence
  • Eukaryotic DNA is organized into chromosomes o DNA is wound around histone proteins which allow the long molecule to be condensed into chromosomes for storage
  • In diploids, chromosomes come in homologous pairs
  • Ploidy can vary o Ploidy: number of copies unique chromosomes in a cell o Most familiar organisms are diploids (2 copies of each chromosome) o Some plants spend most of their lives as haploids o Other plants and some animals have more than 2 copies of each chromosome and are tetraploid or hexaploid o Odd multiples of chromosomes (triploids) impaire meiosis
  • Ribosomes translate mRNA into protein
  • Proteins are chains of amino acids
  • Gene expression can be regulated in a number of ways o Transcription factors are proteins that bind particular DNA sequences and affect the rate at which particular genes are transcribed
  • microRNA can block translation o coded by the genome, but don’t code for proteins o microRNAs are complimentary to certain sequences on other, protein coding messenger RNAs
  • microRNA can have phenotypic effects
  • RNA splicing can create multiple proteins from a single gene
  • Regulation of gene expression is flexible
  • Genomes vary in size and complexity

Environmental influences on gene expression

  • Phenotypic plasticity: changes in phenotype produced by a single genotype in different environments o Tailors organism to environment Ch.6 Hardy-Weinberg & Population Genetics Population genetics
  • Study of the distribution of alleles in populations and causes of allele frequency changes
  • Measurement: allele frequencies Some vocabulary
  • Genetic locus: location of a specific gene or sequence of DNA on a chromosome
  • Homozygous: individual carries two copies of the same allele
  • Heterozygous: individuals carries different alleles Hardy-Weinberg equilibrium
  • Population allele frequencies do not change if: o Population is infinitely large o Genotypes do not differ in fitness o There is no mutation o Mating is random o There is no migration Predictions from Hardy-Weinberg
  • Allele frequencies predict genotype frequencies o P^2 + 2pq + q^2 = 1
  • In Hardy-Weinberg equilibrium, allele frequencies do not change unless the forces of evolution are present
  • Thus: Hardy-Weinberg is a null hypothesis o Allow detection of evolutionary processes in real populations