animal biology

pp 553-566

based on topic of phylogenetics

• a hatch mark denotes the evolutionary character, including reversal of state traits
• systematics: classification of organisms and evolutionary relationships
• common name vs binomial nomenclature, from carolus linnaeus
  • genus (pl. genera) v. specific epithet
  • capital genus, full italics
  • “Newly created scientific names are also “latinized”: You can name an insect you discover after a friend, but you must add a Latin ending.)
    • not after yourself though lol
• linnaean system: ranks
  • domains
  • kingdoms
  • phyla
  • classes
  • orders
  • families
  • genera
  • species
  • taxa broader than genera are capitalized, but not italicized
• orders in a system do not hold equal weight in distinguishing a species in a lineage
• systematics do not represent evolutionary history
  • classification is not entirely compatible with phylogeny; systematics may misclassify species with no relation (reversal of state traits), classification depicts no evolutionary relationships
  • proposal of systematics based on evolutionary relationships changes classification of groups → aves clade becomes a subgroup of reptilia
• rooted tree: a branch point furthest on the tree represents MRCA
• early divergent lineage/species: basal taxon
• phylogenies show patterns of descent, not phenotypic similarity
  • morphology may differ depending on evolution rates and environmental conditions
• taxa/branch point ages cannot be inferred by a phylogeny without specific information
  • phylogeny chronology is relative vs. absolute
• no assumption of evolution of a species from its sister taxon/taxa
• phylogenetics can be used for cross breeding/genetic engineering (allelic reservoirs in maize) or homology (illegal whale meat harvest :()
• analogy: biological similarity resulting from convergent evolution; phenotype vs internal anatomy, physiology, and development (australian “mole” vs. african golden mole)
  • more likely to be homology when complexity is increased (structural and genetic)
• insertions and deletions in dna molecules accumulate over long periods of time
• cladistics: systematic approach with an emphasis on common ancestry (clades)
  • clades are distinct from linnaeus system
• outgroup is closely related to but not part of the lineage vs. ingroup (the lineage)
  • “A suitable outgroup can be determined based on evidence from morphology, paleontology, embryonic development, and gene sequences.”
• principle of maximum parsimony → maximum likelihood
  • maximum likelihood: phylogenetic approach which identifies a likely tree that produces expected tabular dna data based on probability rules for dna sequences and dna evolution
• “This is a good place to reiterate that any phylogenetic tree represents a hypothesis about how the organisms in the tree are related to one another. The best hypothesis is the one that best fits all the available data. A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees. Indeed, while many older phylogenetic hypotheses have been supported by new morphological and molecular data, others have been changed or rejected. Thinking of phylogenies as hypotheses also allows us to use them in a powerful way: We can make and test predictions based on the assumption that a particular phylogeny—our hypothesis—is correct.”
• phylogenetic bracketing: parsimonious prediction that features present in sister taxa were present in a common ancestor and its descendants unless proven otherwise
  • dinosaur assumptions: four-chambered hearts, singing, nests, egg care
• genomic history
  • rNA sequences for ancient diverged taxa (fungi v. animals v. plants)
  • mtDNA sequences for recent evolution (Native American ancestry)
• gene families: groups of related genes within a genome
• homologous genes
  • orthologous genes: (orthos → exact) homology resultant of speciation; different species (cytochrome c variation)
    • only occurs when genes are in separate species gene pools
  • paralogous genes: (para → in parallel) homology resultant of gene duplication; different copies of the gene have undergone divergence (olfactory receptor genes)
    • occur in multiple copies in one genome
  • basal taxa share orthologous genes and can be studied for similar systems equally
  • a number of genes per species does not increase via duplication at the same rate of assumed phenotypic complexity

ch22/pp 11-12, 497-501, 459-463

based on topic of microevolutionary processes via natural selection

11-12

introduction to evolution

• evolution → core theme of biology
  • Theodosius Dobzhansky, “Nothing in biology makes sense except in the light of evolution.”
• evolution: a process of biological change in which species accumulate differences from their ancestors as they adapt to different environments over time
  • diversity vs. unity
• diversity is a hallmark of life
  • 1.8mil species
    • 100,000 fungi
    • 290,000 plantae
    • 57,000 vertebrata
    • 1mil. insect
    • noninclusive counts of unicellular organisms
  • total estimated number of species: 10-100+ mil

459-463

genome usage in evolutionary studies

• large portion of eukaryotic genomes are transposable elements, causing evolutionary changes
  • promotes recombination
  • disrupts cellular genes or control elements
  • carry genes and exons to new locations
  • provides homologous regions for crossover
• incremental small heritable changes caused by transposable elements result in genetic diversity that is affected by natural selection
• highly conserved genes: genes that remain similar despite divergent evolution
• closely related species have very small gene differences (ex. human/chimpanzee)
  • 1.2% difference by single nucleotide substitutions in genome; 2.7% due to insertions or deletions in larger regions
    • most duplications or repetition; ⅓rd human duplications associated with human disease vs. chimpanzee retroviral provirus copies
• single nucleotide polymorphism: single bp sites where 1% or more of the population possesses variation
  • once in ~100-300 bp
  • millions exist
  • majority of human diversity
• copy-number variants
  • loci with a nonstandard number of homologs (1 or 3+) caused by inconsistent gene duplication/deletion
  • cause of phenotypic issues and complex diseases/disorders
• short tandem repeats: repetitive dna variations

ch. 22

• three key points
  • organisms are adapted for environments
  • unity of life
  • diversity of life
• evolution can be viewed as:
  • a pattern: scientific data (biology, geology, physics, chemistry)
  • a process: the mechanism which causes an observed pattern of change/evolution via natural phenomena
• aristotle affinity was scala naturae (scale of nature)
  • old testament account of creation; individual design from god, perfect
  • → 1700s: evidence of adaptation to an environment was used as evidence of perfection
    • nested classification was a byproduct: Linnaeus system in 1750s
• fossil evidence used for sign of change
  • fossils are found in sediment of sea, lake, swamp which is compressed into strata: superimposed layers of rock
    • may be eroded; deeper strata reveals through upper strata
  • paleontological evidence (George Cuvier, 1769–1832)
    • older stratum had fossils with dissimilar traits to newer fossils
    • species appeared and disappeared between strata
      • inference of extinction, but not evolution: natural disasters destroyed a population, but the ecosystem was repopulated via immigration
• 1795: James Hutton (1726–1797)
• Charles Lyell (1797–1875): processes happen at the same rate
  • Principles of Geology
• 1809, 18th century, Jean-Baptiste de Lamarck: 1744–1829; only proposed mechanism
• Charles Darwin, 1809–1882, Shrewsbury, west England
  • Robert FitzRoy, Beagle: Dec. 1831; chart S. American coast that was unknown to Europe
    • organismal features adapted to diverse environments: Brazilian jungles, Argentinian grasslands, Andes
    • temperate S. Am. biology resembled tropic S. Am. biology more than temperate European biology
    • fossils differed but still resembled extant S. Am. species
  • geological inspiration
    • earthquake in Chile → upheaval and rise of coastal rocks → ocean organisms were present in Andes after gradualist shifts
  • hypothesis of Galapagos species colonized by S. Am. organisms migrating and diversifying
  • early 1840s hypothesis → 1844 paper → mid-1850s continued working + discussion
• ARW 1823-1913, June 1858 manuscript; South Pacific islands, Malay Archipelago
  • Jul. 1 1858 presentation + 1844 essay excerpts to Linnean Society of London
• On the Origin of Species by Means of Natural Selection (The Origin of Species) → 1845
  • convinced within a decade
    ideas of the origin of species:
• branching points + extinction events explain broad morphological differences
  • over 99% of all species extinct
    • fossils “fill-in” gaps
      specific arguments of the origin of species:
• Observation #1: Members of a population often vary in their inherited traits.
• Observation #2: All species can produce more offspring than their environment can support, and many of these offspring fail to survive and reproduce.
• Inference #1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than do other individuals.
• Inference #2: This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations.
  data which supports pattern of evolution:
• direct observations:
  • directional selection of soapberry bugs due to consumption of golden rain tree seeds; rapid evolution via natural selection
  • bacterial drug resistance / antibiotic resistance (Staphylococcus aureus and MRSA → flesh eating disease, 1945+ history)
  • illustration of key points
    • natural selection is editing, not creating; extant variations only
    • evolution can occur rapidly
    • natural selection is dependent on time and place
• homology:
  • pseudogenes: molecular homologies similar to vestigial structures
  • convergent evolution: independent evolution of similar features in different lineages
    • marsupials and eutherians; sugar-gliders and flying squirrels
• fossil record
• biogeography: study of species by their geographic distribution
  • continental drift: gradualist movement of continents (merging and separation of Pangaea)
  • evolution + continental drift used to predict biogeographic trends and vice versa
    • fossil dating of Equus is at an origin point when NA/SA were separate continents, so assumption is Equus ancestral fossils should only be in NA
    • Galaxiidae freshwater fish are separated by regions of saltwater; common ancestor likely restricted to freshwater habitats at a time when Pangaea was breaking apart, leading to evolutionary divergence
• theory: a statement encompassing many observations and phenomena and maintained through thorough, consistent testing by experimentation and observation
  • not dogmatic; scientific skepticism
• “There is grandeur in this view of life . . . [in which] endless forms most beautiful and most wonderful have been, and are being, evolved.”

497-501

Natural selection is the only mechanism that consistently causes adaptive evolution

• not fully random process; blend of chance and “sorting”
  • directional selection: conditions favor one extreme of a variation range, skewing the frequency curve
    • caused by migration or extreme environmental change
  • disruptive selection: conditions favor both extremes, but disfavor the intermediates
    • different beak sizes of cameroon seedcracker finches with soft/hard seeds vs intermediates
  • stabilizing selection: conditions favor intermediates, but disfavor extremes
    • reduction of variation; maintenance of status quo for a phenotypic character
• genetic drift and gene flow increase allelic frequency, but not consistently vs. adaptive evolution
• darwin — sexual selection: individuals of one sex with certain characteristics are more likely to mate
• sexual dimorphism: different sexual characteristics between sexes of a species → size, color, ornamentation, behavior
  • intrasexual selection: same-sex selection; direct competition
    • male behavior of psychological patrols
  • intersexual selection: “mate choice” often dependent on showy appearance or behavior
    • plumage
    • hypothesis of preference for “good genes”
• balancing selection: the persistence of unfavorable alleles due to their appearance as recessive genes in heterozygous individuals or the preservation of variation at a given loci
  • frequency-dependent selection: a phenotype’s fitness depends on its presence/commonality within the population
    • left/right mouthed scale-eating fish (Perisssodus microlepis) stays close to 50% frequency each
  • heterozygote advantage: a genotypical advantage when two or more alleles are maintained at a locus
    • sickle-cell erythrocytes
      why can’t natural selection fashion perfect organisms?

1. selection only acts on extant variations; fashions most fit variations, not most ideal
2. evolution is limited by historical constraints; evolution co-opts ancestral structures and adapts to new environments
3. adaptations are often compromises; structural reinforcement is compromised for agility; trade-offs for organismal functions restrict adaptive evolution