Organisms and Environment - Evolution

Archaean - "The beginning" (3800-2500 MYA) 

• Few islands - mostly ocean 
• First prokaryotes - mostly Archae, marine bacteria towards end
• Heat flow three times modern day - but cooling 
• High [carbon dioxide] - barely any oxygen, but evolution of photosynthetic cyanobacteria produces enough oxygen for oxidation reactions to evolve for ATP synthesis - oxygen toxic to most anaerobes acts as selective force for "protective" metabolism 

Proterozoic - "Early life" (2000-542 MYA)

• More oxygen builds up - chemical "sinks" filled e.g. iron oxidised
• Marine eukaryotes appear and diversify - 1500 MYA onwards, many photosynthetic and colonial e.g. plankton and biofilms
• Late "Ediacaran" (635-542 MYA) - evidence of complex multicellular marin animals

Cambrian - "Explosion" (542-488 MYA)

• [Oxygen] approaching current
• Continents converge - several land masses e.g. Gondwana
• Rapid diversification of animal groups - almost all marine e.g. sponges, arthropods, mollusks, first evidence of early vertebrates towards end, predatorial "evolutionary arms race" to develop hard protection
• Anomaclaris - "puzzle" discovered 1892, fossils showed parts of organisms initially not assigned to organism e.g. looked like shrimp abdomens but actually paired grasping appendages, 1996 = 0.6m mobile predator with large ventral mouth and eyes 

Ordovician (488-444 MYA)

• Continued marine evolution but limited freshwater/land
• Radiation of mollusks, brachopods and echinoderms
• Mass extinction - Gondwana glaciers, sea level -50m, water cool, 75% animal species gone
• *Orthocones - straight, nautiloid, cephalopods, <11m, mobile midwater, tentacles, beak
• *Eurpterids - "sea scorpions", largest arthropod <20cm but 2m+ later period, benthic

Silurian (444-416 MYA)

• Marine rebound
• Jawless fish vertebrates
• FIrst terrestrial vascular plants - in/around freshwater, provide food supply
• First terrestrial arthropods - e.g. scorpions, millipedes

Devonian (416-359 MYA)

• N Laurasia and S Gondwana converge
• Early - warm and humid
• Radiation - of corals, shelled cephalopods and jawed fish, all major current groups now present 
• Sea - "Age of the Fishes", diverse but jawed fish dominant predators, 
• Mass extinction - 75% marine suddenly wiped out at end, unknown cause
• Land and Freshwater - rapid plant evolution e.g. ferns, roots accelerate weathering to make soil, early wind-pollinated e.g. Runcaria, fish-like amphibians start occupying land, first fossils of centipedes, spiders and insects 

Carboniferous (359-297 MYA)

• Climate - started warm, but glaciers formed over high-lattitude Gondwana
• Tropical - swamp forests, petrification ("coal measures"), dominated by large ferns and horsetails
• Terrestrial animal diversity increases - snails, insects etc., amphibians better adapted to land (all carnivorous to invertebrates)

Permian (297-251 MYA)

• Pangea supercontinent
• Most modern insect groups appeared
• Line of amphibian evolves to reptile "amniotes" - well-protected eggs laid on land
• Lineage to mammals diverges
• Mass extinction - conditions deteriorate, massive volcanic activity, sunlight blocked, climate cools, largest glaciers recorded, oxygen {30%] to [12%], most dramatic, 96% species lost e.g. trilobites 

Triassic (251-200 MYA)

• Pangea separates
• Sea levels rise - continental-shelfs reflooded, inland seas
• [Oxygen] slowly rises
• Diversification but from different starting point - reptiles to dinosaurs, new seed plants e.g. conifers
• Mass extinction - possible meteorite impact in Quebec, 65% species disappear

Jurassic (200-145 MYA)

• Laurasia and S. Gondwana re-form 
• Flight - first birds (secondaril from feather insulation/display), pterosaurs (reptiles, weak, relied on vantage points), early mammals (bats)
• Ray-finned fish, salamanders, lizards
• Dinosaurs - quadrupedal herbivores, bipedal carnivores, physiological temp. control

Cretaceous (165-145 MYA)

• Laurasia and Gondwana further apart - continuous tropical seas
• High sea levels - warm and humid 
• First snakes, small mammals and flowering plants (incl. insect-pollinated)
• Mass extinction - land animals >25kg perished, all dinosaur groups, evidence for mass environmental change e.g. wild fires, falling sea levels, probably meteorites

Tertiary (65-1.8MYA)

• Continents as today - but Atlantic ocean narrower and Australia/Antartica attached
• Cooler and dryer 
• Flowering plants - diversify, dominate all but coldest regions
• Birds and mammals - huge diversification, 3 waves from Asia to North America across land bridge

Quarternary (1.8 MYA - NOW)

• Pleiostocene - 15,000 YA, 4 major ice ages, dramatic fluctuation
• Holocene - <10,000 YA
• Evolution of hominoids - now Homo sapiens, all others extinct
• Large birds and mammals - extinctions in Australia and Americas 

Proposed:

1. Random, heritable variation exists within species
2. Variation arises without reference to needs of organism
3. Large abrupt changes are rare, usually gradual
4. Small variations which improve fitness are increased in frequency through natural selection
5. Limited resources lead to struggle for existence and survival of the fittest

Previously:

• Immutable units of God BUT e.g. geology (effects of weathering), fossils (e.g. Mary Anning Jurassic Coast 1820s), anatomy (explanation of degenerate parts e.g. appendices) 

Weaknesses:

• Uncertainty about Earth's age - estimated 100MYA, not enough time for slow process
• Genetics unknown - Mendel's ideas not discovered in Darwin's lifetime yet came so close
• Rate of evolution unkown - gradualism vs. punctualism

• Artificial selection - variation range huge, can change phenotype frequencies dramatically over few generations
• Ecological genetics - e.g. peppered moths (normal unseen on lichen, melanic can't be seen on sooty tree Industrial Revolution), e.g. pesticide and antibiotic resistance
• Synthesis of new species - possible to generate reproductively capable hybrids i.e. polylpoidy
• Molecular phylogenetic evidence - DNA, RNA
• Biogeographical - e.g. ring species Herring gull vs. lesser black-backed gull gradation of intermediates can interbreed (1. Clines - variation along ecological gradient, 2. Plate tectonics/continental drift - species developing differently, 3. Fossil record - radioisotope dating, build phylogenies)

"endless forms most beautiful... have, and are being, evolved"

Mechanisms of evolutionary change 

• Mutations - origin of genetic variation
• Gene flow - movement of individuals between populations, subsequent reproduction introduces new genes, high rates of mixing prevent genetic differentiation
• Genetic drift  - random changes in allele frequencies are large between generations in a small population * Founder effect - small colonising populations have less variation than source so biodiversity is reduced * Bottlenecks - conservation issue, following sharp reduction e.g. flood/fire, recover numbers but altered diversity e.g. Florida panther
• Non-random mating - sexual selection favours evolution of a characteristic

Selection forces

• Stabilising - towards mean, away from extremes, e.g. human birth weight
• Directional - mean changes, one extreme selected for, e.g. tetrodotoxin resistance in predator snake
• Disruptive - extremes selected for in different ways, e.g. large billed vs. small billed birds have different diets 

Species concepts

1. Morphological - Carl Linnaeus, dichotomous keys, conventional features observes, no genetic knowledge, mistakes e.g. thought female and male mallard ducks were different species
2. Biological = "groups of actually or potentially interbreeding populations that are reproductively isolated from other groups" - Ernst Mayr 1940, emphasises reproduction isolation, conclusive and testable, inconvenient everyday (no use for fossils, not all organisms reproduce sexually, hybrids explained how?)
>> 3. Evolutionary - reflects phylogenetic relationships, evolutionary trees, cladistics, molecular methods can accurately reflect true relationships but not biological species compatability 

Isolating mechanisms

• Pre-mating - eclogical (spatial/geographical e.g. post-earthquake, or temporal e.g. migration), or reproductive (temporal e.g. diurnal, or ethological e.g. rituals, or mechanical)
• Post-mating - prezygotic (reproductive mode or cross incompatability) or postzygotic (abortion, inviability, sterility)

Breeding systems

• Asexual (vegetatative) - no wastage of energy in a stable environment, no recombination, common in plants e.g. 80% redwood trees are clones
• vs. Sexual - cross-fertilisation and meiosis, recombination, new geno/phenotypes, selection, potential for rapid evolution, high wastage of poorly adapted, ideal would be panmixis but probably never occurs
• Partial inbreeding - starting population small or isolated, genetic differentiation due to genetic drift
• vs. Outbreeding - tendency towards interbreeding e.g. some plants self-incompatible, still become differentiated into local races if dispersal is short

Speciation

Organism must be able to replicate and produce excess offspring whose survival is related to particular adaptations which must be heritable.

1. Allopatric - most common, a. physical isolation (barrier or long-range dispersal starts new colony, b. differentiation (as selection pressures change so do gene frequencies), c. merger of range (barriers to interbreeding = new species vs. if can still interbreed = i. 2 populations hybridise to become one, ii. one replaces the other in *competitive exclusion principle (Gause 1934), iii. character displacement results in adaptive radiation e.g. Darwin's finches, or iv. character displacement if ranges overlap as hybrids have reduced fitness) 
2. Parapatric - "catastrophic", rare, random fluctuations in size of small peripheral population, abrupt, often chromosomal rearrangements leading to reproductive isolation, due to extremes of habitat not geographical barrier, e.g. naked mole rats mode of life limits inter-colony contact
3. Sympatric - reproductive isolation precedes differentiation, no geographical barrier, e.g. host plants switching with hawthorn fly chemoperception (apple to cherry)

• 50% earth's protoplasm is bacterial (mass UK!), pathogenic minority, only 1% in/on animals
• Big - SA:vol issue (invaginated membranes, swimming exchange, intracellular deposits), e.g. "Eupolos" 1985 in surgeon fish initially thought protozoan "has babies"
• Small - most bacteria 0.2-2um, some similar size to viruses (4th domain?) "megaviridae" (e.g. mimivirus 1992 inside amoeba in water tower) ds DNA and infect eukaryotes
• Hot - thermophiles e.g. Yellowstone hot springs, hydrothermal vents Pyrolobus fumarii, thermostable DNA polymerase PCR (proteins have more interactions and rigidity, DNA probably stabilising protein)
  
• Cold - psychrophiles (more mobile and flexible proteins to combat low metabolism)
• Salt - halophiles e.g. in Dead Sea, intracellularaccumulations to prevent water exodus
• Acid/alkali - acido/alkaliphiles e.g. Cyanidium caldarium pH 0, Spirulina pH 10.5 +vely charged membrane to repel H+, or "snottites" mucilaginous products protect from H2SO4
• Radiation - e.g. Deinococcus radiodurans, 8 chromosome copies tightly packed do not diffuse when damaged, novel proteins at ends not degraded as lack certain exonucleases, manganese absorbs ROS, survive dessication causing similar breaks
• MARS - low pressure, methane arose naturally, liquid water or SPACE - panspermia? e.g. Bacillus subtilis spores survive 6 years in protected conditions

• Prokaryotes
• Formyl-methionine initiator tRNA
• One RNA polymerase (4 subunits)
• Ester links between polar heads and fatty acid tails
• Peptidoglycan/murein cell walls (Gram +ve = thick pdg layer, single membrane, dye retained, purple after decolourisation with alcohol or Gram -ve = thin pdg, outer and inner membrane, dye lost, pink)
• 23 phyla

1. Cyanobacteria - oxygenic phtosynthetic, chlorophyll a and phycobilins, Calvin cycle
2. Proteobacteria - 5 classes, Gram -ve, large and complex e.g. E. coli, Vibrio, Rhizobium
3. Firmicutes - 3 classes (Clostridia anaerobic e.g. C. tetani, Mollicutes e.g. Mycoplasma Gram +ve but no cell walls, Bacilli e.g. Streptococcus, Staphylococcus
4. Actinobacteria - 2 classes (Mycobacteria mycolic acids in cell walls cause e.g. TB or leprosy, Streptomyces produce antibiotics e.g. neomycin)
5. Spirochetes - helical, motile, Gram -ve e.g. syphilis, Lyme disease

Viruses

• Simple, acellular
• Obligate intracellular parasites
• Nucleocapsid - nucleic acid (R/DNA, linear/circular, ds/**) surroundedby protein capsid (helical, isosahedral or complex symmetry), self-a**embles from protomers
• e.g. Herpes, Ebola, HIV

Archae

• No peptidoglycan, ether bonds
• S layer composed of glycoproteins
• Grame +ve/-ve
• Diverse morphology and habitats
• Metabolic proce**es and structure like bacteria
• BUT DNA replication, transcrip/lation (several RNA polymerases 8-12 subunits) like eukaryotes
• 5 groups e.g. Xena/Korarchaeota only in hydrothermal environments

• NB: Protists - not plants, animal or funghi, convenience terms, not a phylogenetic group (paraphyletic only), motile (amoeboid or cilia/flagella) or immotile, uni/multicellular, photosynthetic/heterotrophic, microscopic or huge, membrane-bound organelles or not...

Evolution 

• Environment changed dramatically from anaerobic to aerobic
• Host acquired mitochondria (similar size to bacteria, own circular DNA) and chloroplasts (secondary/tertiary to green/red algae 1.2bn YA) through endosymbiosis (common e.g. bacteria living in plants as obligate mutualists supplementing poor diet passed vertically)
• Required flexible cell surface, cytoskeleton, nuclear envelope and digestive vacuoles 
• Mostly aquatic e.g. plankton but some in damp soils etc.
• 5 major clades

1. Unikonts - single flagella, complex amoeba e.g. a/cellular slime moulds, fungi, frogs 
2. Chromalveolates - ciliates e.g. paramecium, dinoflagellates (brown sea) and diatoms (silica)
3. Rhizaria - unicellular, aquatic e.g. foraminifera (CaCO3), radiolarians (pseudopods extend shell)
4. Plantae - single incidence of endosymbiosis, e.g. land, red(phycoerithrin)/green algae
5. Excavates - lack mitochondria (lost evolution) e.g. diplomonad Giordia lamblia diarrhoea