BIOL 111 Final Study Notes PDF

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BIOL 111 Final Study Notes FUNGI Phylogeny - One of 3 major lineages of large, terrestrial eukaryotes - Few fossils, evolutionary history hard to study - First fungi (aquatic) 800-1000 mya - Colonized land 500 mya (before plants) - Key innovation: how to extract nutrients in a terrestrial env. Fungi...

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BIOL 111 Final Study Notes FUNGI Phylogeny - One of 3 major lineages of large, terrestrial eukaryotes - Few fossils, evolutionary history hard to study - First fungi (aquatic) 800-1000 mya - Colonized land 500 mya (before plants) - Key innovation: how to extract nutrients in a terrestrial env. Fungi today - 110,000 named species - Taxonomy mostly based on reproductive structures & DNA - From single cells (yeasts) to huge multicellular structures - Critical to ecosystem functioning - Wide range of human uses - Diseases: athlete’s foot, yeast infections, etc Largest organism in the world: armillaria ostoyae “honey mushroom” Defining features 1. Structure: single celled or made of filaments. No complex transport systems. Cell walls (like plants) but contain chitin (more like animals) 2. Nutrition: absorb food directly from surroundings 3. Reproduction: sexual, asexual, diverse 4. Dispersal: spores Structures - Yeasts = single cells - Mycelia  made of hyphae: long, thin filaments o whole fungi made up of hyphae  more compact in fruiting body (mushroom) - yeast vs bacteria: bacteria are prokaryotes (no membrane enclosed nucleus) and fungi are eukaryotes - Hyphae usually separated by cross-walls called septa  separate the long hyphae into compartments and allow the passage of whole organelles and even nuclei - Fungi (mycelia) are called multicellular organism but they are in a slight grey zone b/c they don’t have fully compartmentalized cells - Hyphae are incredibly thin  100x thinner than the thinnest plant root: have huge S.A. to volume ratio b/c it makes them great at absorbing nutrients but mean they loose material (esp. water ) v easily  only live in moist environments - Septa have large pores that allow passage of nutrients, even nuclei - Hyphae are 100x thinner than the thinnest plant root - Fungi occur mostly in moist habitat

Nutrition - Implications of structure for nutrition o Thin hyphae  master absorbers o Need for moisture  often symbiotic (can by symbiotic or parasitic) - Don’t photosynthesize, secrete digestive enzymes externally o Saprophytes (eat dead things) o Symbionts - Novel methods of absorbing nutrients (moving from food source to food source) drove fungi diversification - Key in carbon, nitrogen, phosphorus cycles  w/o fungi these cycles would function at a much reduced rate b/c fungi are the main decomposers of complex organic molecules - Main decomposers of cellulose & lignen (wood) (most abundant molecules on earth) o Lignen allows plants to support themselves and grow huge o Fungi allows for decomposition of lignen (wood) b/c they break it down to get at the cellulose inside for energy Nutrition implication: ecology - Famous symbiosis: - Lichens o Fungi + algae or cyanobacteria o 20,000 species o 6% of earth’s surface o Potential asymmetry where the algae could be free-living but the fungi cannot  not completely beneficial to both - Mycorrhizae o 80% of angiosperms partner with fungi to get nutrients from soil o Non-existence of mycorrhizae partners can limit plant species distributions o Introduction of mycorrhizal partners can enable invasion o Plants can survive without the fungi, but not as well/ don’t grow as quickly

Reproduction - Complicated. Many species reproduce in multiple ways, sometimes during both haploid and diploid phases - Asexual o Fragmentation o Mycelial breaks and both parts form new organisms o Vegetative spores (conidia)  act like sexual spores (small, spread by wind), produced on equivalent of fruiting body, no recombination (still asexual) o Produced on conidiophores - Sexual o Often only see sexual reproductive structures (mushrooms/fruiting bodies) o Very dif. From sex in plants or animals o E.g. ascomycetes & basidiomycetes (incl. almost all the cap mushrooms)  form monophyletic group o Compatible individuals fuse their mycelia, to initiate sexual cycle (anastomosis/plasmogamy) o Two mycelia fuse, and share nuclei  dikaryotic (two-nuclei) stage – this stage can last for decades = not transient but can be a major component of life cycle o Basidiomycetes: produce mushroom o Basidia: specialized end cells of mushroom gills (spore bearing) o Nuclei fuse  meiosis  spores o Mushrooms are more like fruit because spores are akin to seeds *look at reproductive diagrams Dispersal - Unlike hyphae, spores tolerate dry conditions - Important for dispersal - Small size facilitates airborne dispersal - Some have ejection mechanisms (e.g. puffballs) - Some use animal dispersers (e.g. stinkhorns that attract insects to disperse them)

ALGAE Phylogeny - Taxonomy of photosynthesizers is messy - 1735 Linnaeus classification three kingdoms: plants, animals, fungi - 1969: five kingdoms: plantae, fungi, animalia, Protista (slightly inaccurate – not a uniform group), monera - Current eukaryote phylogeny: plantae (incl. land plants), excavates, rhizaria, unikonts (incl. animals), Chromalveolata - “protist”: inlc. Huge diversity of organisms, vast majority of eukaryotes *ability to photosynthesize found widely in the tree of life: plantae, bacteria, etc - how did it evolve and spread if its found in many different branches?

Photosynthesize - First evolved 3 bya - First organism to photosynthesize was a bacteria  cyanobacteria - How did eukaryotes get photosynthesis? o All photosynthetic eukaryotes use chloroplasts (bacteria don’t)  development of chloroplasts closely linked to that of photosynthesis o Photosystem I and photosystem II evolved in bacteria  implies there is a common ancestor Endosymbiotic Origin of Chloroplasts Hypothesis: eukaryotic chloroplasts originated when a protist engulfed a cyanobacteria Support: - chloroplasts similar to cyanobacteria and behave somewhat independently of cell – don’t act totally as integrated part of cell o Replicate by fission, independently of cell division – doesn’t depend on the speed at which the cell divides – similar to how bacteria divide o Manufacture some of their own proteins o Have their own DNA, organized into circular molecule very similar to those in some cyanobacteria – both in structure and content o Peptidoglycan in cell wall of some chloroplasts – also found in some cyanobacteria o Have (at least) a double membrane – one from the protist and the other from the original cyanobacteria - Extant endosymbiotic cyanobacteria live in cells of protists and animals How did chloroplasts spread to 4/5 major eukaryote lineages? - All species in plantae have chloroplasts - Plantae chloroplasts have double membrane - Chloroplasts and other protist lineages have more than 2 membranes Hypothesis: - Endosymbiosis leading to chloroplasts first occurred in common ancestor of plantae - Ancestor of other groups acquired chloroplasts via secondary endosymbiosis Secondary endosymbiosis leads to chloroplast with 4 membranes 1. Photosynthetic protist is engulfed by predatory protist 2. Nucleus from photosynthetic protist is lost 3. Organelle has four membranes Brown algae (phaeophytes) - Chloroplasts with 4 membranes - 1500 – 2000 species - Multicellular marine organisms - Individual = thallus (no complex vascular system) - Brownish colour from carotenoid pigment fucoxanthin used in photosynthesis

Famous phaeophytes: Kelp - Greater than 120 species - Fastest growth rate of any seaweed - Max growth rate 3.5m/week - Final height up to 80m Kelp forests - Largest biogenic (habitat created by living organisms) marine habitat - Biodiverse: more than 100 000 mobile invertebrates per 2m of kelp tissue Kelp in ecology: - Keystone species (impact on ecosystem greater than expected) - Trophic cascades (by removing on organisms you have a cascade effect on the rest of the ecosystem) - Otters hunted for their pelts  influx of sea urchins  loss of kelp forests  loss of habitat Alternation of Generations - Occurs in many multicellular protists incl. algae, kelp - Alternate between multicellular haploid (n) form (gametophyte) and multicellular diploid (2n) form (sporophyte) - Gametophytes produce gametes (n) by mitosis - Sporophytes produce spores (n) by meiosis - Spore: single haploid cell. Can grow into multicellular organism without fertilization *Don’t need to memorize alternation of generations but do need to understand concept Red Algae - Most diverse marine seaweeds - More than 7000 species - Red colour from carotenoid pigment phycoerythrin used in photosynthesis - Can live at great depths - Red pigment good at absorbing blue wavelengths - No flagella  non-motile sperm - Alternation of generations (both diploid and haploid both multicellular) - Some unicellular species found in sulphuric hotsprings - Rare in freshwater - Very small genome for multicellular organism (fewer than single-celled green algae)maybe due to evolutionary bottleneck from gene loss - Shed everything they didn’t need to survive in harsh habitat  loss of genetic diversity Coralline red algae - Calcareous deposits in cell walls - Contribute to coral reefs w/ structure - Max growth rate of 0.8 cm/yr - Diversity plummets with the evolution of parrot fish

NON-VASCULAR PLANTS Viridiplantae - Green algae: dominant photosynthesis in freshwater - Land plants: dominant photo synthesizers in terrestrial systems - Monophyletic as a group : green algae are paraphyletic b/c land plants eveolved from green algae - All viridiplantae contain chlorophyll a & b Green algae - 8000 species - 90% freshwater - Main primary producers in freshwater - Unicellular & multicellular Algae response to elevated CO2 - Atmospheric CO2 expected to increase from 400 ppm to 700-1000 ppm over the next century - Phytoplankton are important in global cycles, carrying out half of the worlds photosynthetic carbon fixation o When primary production increases, more CO2 is removed from the atmosphere o Some of the carbon is stored in long-lived carbon sinks, as phytoplankton die and fall into deep ocean sediments - Dr bell & co used long-term experiment (1000 gens) to test how phytoplankton changes at high CO2 o used unicellular green algae chlamydomonas o hypothesis: phytoplankton have higher productivity in high CO2 env. o Prediction: higher production in high CO2, o Result: both lines had higher CO2 uptake at higher CO2 env. Algae that eveolved at high CO2 uptake had lower CO2 uptake than the the algae that evolved in low CO2: carbon concentrating mechanism degenerated over time when algae didn’t need it (accumulation of mutation in absence of selections) o Conclusion: primary production might not increase as much as expected from increase in CO2 uptake due to increase in CO2 in env. Transition to land - Green algae = origin to land plants - 1.5 my : angiosperm raditation - 8 my: green algae to land plants - 1 by: clonal cyanobacteris to green algae - 2 by: photosynthesis to land plants - 4 by: first oceans to today

Molecular phylogenies suggest major, difficult transitions - Land plants are monophyletic: implies only one successful transitions from water to land  transition to land from freshwater = really challenging - Nonvascular plants = earliest branching group of land plants: most ancient living group of land plants - Nonvascular plants are paraphyletic o Include some but not all descendants of one common ancestor - Vascular plants as a whole are monophyletic: vascular tissue eveolved only once - Seed plants (gymnosperms & angiosperms) Why is transition to land so difficult? - Molecular phylogenies suggest transition to land happened only once - Advantages: o No competition o Direct source of sunlight o Source of CO2 in the air - Challenges o Dehydration o Gravity: need supportive structures o Reproduction (dispersal of seeds) o UV radiation – water protects from damage of UV rays - Plants out of water exposed to harmful UV rays o UV light damages DNA o Water absorbs UV light, so less of a problem for alage - The algae that survived on labnd were those that made compounds that absorb UV light - Most plants today accumulate UV-absorbing compounds (flavonoids) – seen in autum leaves  degradation of chlorophyll in leaves & you can see flavonoids and carotenoids - Key innovation: cuticle % stomata o Cuticle: watertight sealant covering aboveground plant parts o Prevents water loss but keeps CO2 out o Nonvascular plants have rudimentary cuticle to deal w/ this problem to leave room for gas exchange o Vascular plants use stomata to open and allow gas exchange and close to prevent water loss (opening surrounded by specialized guard cells – open during day & closed during night - How do plants reproduce on dry lands? o Harsh conditions for gametes o 1. Spores encased in tought coat of sporopollenin o 2. Gametes produced in complex multicellular o 3. Embryos retained on and nourished by the parent plant - Dessication resistant spores o Spores resist drying because they are encased in a tough coat of sporopollenin

o Tough outer coating of spores helps them survive for fairly long periods of time o Can be dispersed hundreds of km by wind – resistant, lightweight

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Protective, complex reproductive organs o Fossilized early plants conatin specialized reproductive organs: gametangia o Produced gametes from drying & physical damage o Present in all modern plants except angiosperms (structures insides flowers preform same fn) o Individuals proce distinctive male and female gametangia (leanr which is which) Embryos nourished by parental tissues o Instead opf shedding their eggs into the water or soil, land plants retain them  Eggs form inside of archegonia

Nonvascular land plants - Mosses, liverworts, hornworts o Lack vascular tissue (no xylem/phoelem). Absorb nutrients through their leaves o Don’t have normal root structures: don’t absorb nutrients just used to hold them in place – absorb nutrients through their leaves : need rudimentary cuticle o Use spores and not seeds for reproduction and dispersal o Rudimentary cuticle and stomata o Small, low-growing usually in damp habitat, but don’t have/need roots so can grow on rocks/shallow soil o Advantage: can grow on bare rock o Distadvantage: need very moist conditions o Alternation of generation, gametophyte phase (1N) dominant (seperates these plants from most other land plants) o Need water for reproduction: thin layer of water on plant allows sperms to move to move between gametophytes o Spores don’t need water for dispersal but sperm does - Famous moss: peat moss (genus sphagnum) – combination of plants mostly sphagnum o Peat forms when plant material does not fully decay in acidic and anaerobic conditions o 13% of canadas area = peatlands o Peat bogs = most efficient C sink on planet o Harvested for gardens and fuel

VASCULAR PLANTS – seedless plants Nonvascular plants colonize land Advantages: - Huge uncolonized area (low competition)

- Abundant light &nutrients Challenges: - UV radiation (flavonoids) - Dehydration (cuticle) - Reproduction/dispersal (hardy spores, gametangia) New challenges after transition to land: overcome competition - Colonize dryer env. - Get taller – first access to light - Go deeper – get more nutrients The Silurian landscape  all low plants & huge fungi - Prototaxites: giant meter tall fungi Drier: key innovation = stomata - Cuticle: waxy covering prevents water loss BUT also keeps CO2 out of plant - Stomata: opening (pore) surrounded by specialized guard cells o Allows gas exchange when open and prevents water loss when closed - Enable evolution of full cuticle Taller: key innovation – vascular tissue - 2 fns: transport (water, sugars, nutrients) & support – o the taller you get the farther apart everything becomes  vascular tissue allows dispersal throughout cells of plant - nonvascular plants have conducting cells but no secondary thickening – some conductance but no support - earliest vascular plants: cooksonioids, rhyniophytes o thickened conducting cells o some branches but no leaves (used photosynthetic stems) or roots (used rhizoids) o increasingly effective vascular tissue, from spongy cork-like tissue to hollow lignified tubes Deeper: key innovation = roots - wasn’t a single origin of roots – evolved simultaneously in different groups - 2 main functions: nutrient acquisition, support - Also network trees together and help them communicate (boreal forest) - Multiple independent evolutions through Devonian - Mycorrhizal fungi symbionts present even in simplest rhizoid-based systems – land plants couldn’t have evolved w/o these partners Devonian: age of forests (or fishes) - Early: tallest plants 1m, dwarfed by prototaxites - Mid: shrub-like forests of lycophytes, ferns & horsetails o Competition for light  leaves o Competition for nutrients & need for support  roots - Late: world’s first forests

Reduction of gametophyte is one of the strongest trends in land plant evolution - Nonvascular plants: sporophyte is small, short lived, depends on gametophyte for nutrition o Gametophyte-dominant life cycle - Vascular seedless plants: sporophyte is much larger and longer lived than gametophyte o Sporophyte-dominant life cycle - Seed plants: gametophytes are microscopic - Advantages of sporophytes o Diploid cells can respond to varying environmental conditions more efficiently o Especially if the individual is heterozygous at many genes Extant vascular seedless plants - Clubmosses, whisk ferns, horsetails - Have vascular tissue (specialized tissue to conduct water and nutrients that is structurally reinforced) - Complex leaves & roots - Reproduction via spores (not seeds) - Sporophyte-dominated life cycle - Dominant vegetation in Devonian - Taxonomy still messy Clubmosses - fungi > ferns > gymnosperms  3x more diverse than next most diverse group & still undergoing speciation - Associated w/ three key adaptations o 1. More efficient xylem  fewer cuticle barriers o 2. Flowers o 3. Fruit - Allow angiosperms to transport water, pollen & seeds efficiently - Why else might these traits be associated with high speciation? o Selection on flowers can more quickly lead to reproductive isolation  new species occur from isolation & flowers are directly involved in reproduction 1. Flowers are reproductive organs for plants o Contain female parts (carpel) male parts (stamen) or both

o Ovules develop in ovary o Pollen develops in anther o Later plants enclosed carpels & stamens in sepals & petals which eveolve from leaves o These four structure (carpel, stamen, sepals, petals) diversified  fantastic array of sizes, shapes & colours

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Adaptive significance of floral traits: o Pollinations definitely involved in speciation of lineages w/ complex flowers o Experimental crosses & genetic analyses show large changes possible w/ single mutations  dependent on type of animal pollinating o Flowers evolve adaptions to attract specific type of insects o Simple changes in flowers (eg colour, nectar spur length, flowering time) can lead to pollinator shifts o b/c flowers are reproductive organs you can have small genetic variation that leads to dramatic new characteristics colour & floral features combine to o attract good pollinators o deter non-pollinating visitors o manipulate visitor behavior to maximize pollen transfer was angiosperm radiation driven by flowers? o Gymnosperms had pollinators o Early angiosperms evolutions associated w/ decline in diversity & extent of plantpollinator relationships in gymnosperms – 35 my gap between when they start evolving and when pollination took off o Early angiosperms may have had boring flowers

2. Angiosperm radiation: fruits o Unlike gymnosperms, angiosperm ovules develop in an ovary o First things to evolve generally on inside  1st reproductive structure = spores o Review of strictures: 1st to develop  (mega)spore (spores in algae)  (mega)sporangium (sporangia evolve in first land plants) – nucellus  Ovule (includes integument around megasporangium  seed coat) – gymnosperms  Ovary (additional maternal tissue around ovule) – first seen in angiosperms – ovary wall o After fertilization (usually) ovary tissue ripens  fruit o Functions: protect developing seed, seed dispersal o Must seed-dispersal structures develop from ovary wall (pericarp) and/or tissue

o Not all fruits meant to be ...