BIOL 111 Notes.pdf

Intro, Part 1 - species live in populations, interact with each other - ecology is the study of natural communities - biogeograph - patterns in the distributions of organisms and communities - eg. the Wallace line (due to tectonic plate shifts) - trait variation can often be explained by ecosyst...

Intro, Part 1 - species live in populations, interact with each other - ecology is the study of natural communities - biogeograph - patterns in the distributions of organisms and communities - eg. the Wallace line (due to tectonic plate shifts) - trait variation can often be explained by ecosystem and environmental factors - eg. filling ecological niches - transmutation of species…via evolution by natural selection - selective event - imposes selection on a species for specific traits - eg. change in environment - evolution occurs within the human lifetime often - evolution by natural selection (non-random survival) - Darwin, Wallace - leads to transmutation of species (one into another over long time periods) - “Great discoveries start with keen observations and seeing what others have missed” - Grants - acts in real-time in observable time periods - organisms evolve in response to their environment and other organisms - natural selection and variation of species shapes variation based on environmental factors and selective events (eg. drought) - by genetic selection/evolution - phylogeny - a (usually) branching tree depicting evolutionary (ancestor-descendant) relationships among a group of organisms with a common ancestor - insects - millions of species perhaps 1/2 of all species on earth - evolutionary/phylogenetic biodiversity varies through time and space - extinction events and other things cause fluctuations - evolution - changes in allele frequency across generations (genetic) - key mechanisms of evolution: - mutation - mutations change the genetic code, which generates new “alleles” which may change amino acid sequences or alter gene expression, which may have phenotypic effects - eg. roundworm mutation rate is 1/100 million nucleotides copied - so 2.1 mutations per genome per generation - most mutations decrease fitness (ie. survival and reproductive success) and are considered deleterious - average mutation decreases fitness by ~2% - the few beneficial mutations are likely to be of small effect (ie. “hopeful monsters” are extremely rare) - genetic drift - genetic drift causes random changes in allele frequency - each survivor clones itself, then dies - evolution happened but was completely random - random events can generate changes, but selection is very low - works best in small populations, because they can experience genetic change much faster - natural selection  - Darwin and Wallace’s insight - all organisms have the potential for exponential growth and yet most populations remain relatively stable in the number of individuals - implies high morality in nature - traits - vary among individuals, influence survival, and are heritable - prediction: traits that improve survival should increase in frequency (or size) through time - ex. domestic breeds show the power of selection - selection and evolution are highly variable - some of the genes underlying a heritable trait variation have been identified and shown to also change in allele frequency during selection in the population - sexual selection - intra-sexual → eg. male-male competition - inter-sexual → eg. female choice - can sometimes work in opposition to other mechanisms of evolution - gene flow - movements of genes between populations - often opposes the effects of divergent natural selection - eg. exchanging individuals between the two selection lines of Drosophila would reduce their divergence - two basic ways of studying evolutionary change - depending on the two types of genetic variation → Mendelian or Quantitative - Mendelian genetic variation example - consider one gene with two possible alleles (A and a or X1 and X2) - diploid individuals will have two copies of this gene, one from each parent - an individual can be one of three genotypes: - homozygous AA - homozygous aa - heterozygous Aa - genetic variation at this gene occurs when all individuals are not identical (ie. not all AA or aa) - populations can be considered as pools of genotypes and alleles (ie. the “gene pool” with genes dissociated from bodies) - allele frequencies - count up the total number of one type of allele and divide it by the total number of alleles (two times the number of individuals) - Quantitative - genetic changes in quantitative traits are controlled by changes in allele frequency at multiple genes and are often heavily influenced by the environment - An example of quantitative (polygenic) variation - the changing beak size of Darwin’s finches Intro, Part 2 - biodiversity produced by natural laws around us - can be studied and observed - all life evolved from a single ancestral (common) form - evolution is occurring all around us all the time - beetles - 40 000 species, 40% insects, 25% living things - weevils - 70 000-97 000 species - the first single-celled organism from which all life has descended arose 3.5 billion years ago - Mendelian - 2 alleles competing at a single locus and single gene - Quantitative - many different possible traits, descriptive study, bell-shaped distribution - must have multiple loci with many possible genetic combinations (combines both Mendelian and quantitative) - quantitative analysis can be underlaid by Mendelian genetics - mutations are the ultimate source of all genetic variation - after this, evolution is determined by the other 4 ways - can affect proteins, can affect traits of individual - each person carries (on average) 2 new mutations - relatively rare per nucleotide but relatively common per genome - artificial selection is extremely effective BUT natural selection can also occur in short time periods - secondary sexual traits evolve as a compromise between natural and sexual selection (less vs more conspicuous) - natural and sexual selection can oppose each other Intro, Part 3 - Phylogeny - way of showing the relation between taxa, more often than not a hypothesis - even when made using genetics - sister group - the most closely related group that isn’t in the group being shown - go back to last common node to find last common ancestor between two families or groups - can’t see extinctions on phylogeny - can’t know diversification rates from this alone - any two species that exist currently are equally evolved so neither is more primitive than the other - can say that a *group* is more primitive - extant species are equally evolved - factors that affect biodiversity - faster reproductive rates - give more generations in a shorter time span/higher mutation rates - higher genetic diversity in a group - ecological opportunity - lots of environmental diversity to occupy - geographic changes that separate groups - what does it take to get speciation? - reduced gene flow between two lineages (usually) such as… - geographic separation (eg. different islands) - local physical separation (eg. canopy vs ground floor) - temporal (time) separation (eg. flowering early vs late in season) - different evolution between lineages - via different selection (eg. for red flower in one population, yellow in another) - separate morphs within same species - - requires enough genetic variation that selection can lead to differentiation  - and/or via drift → differentiation by chance - requires small enough population or enough time that drift leads to differentiation - reproductive isolation - species physically or genetically unable to mate and produce viable offspring - species no longer recognize each other as mates - species no longer encounter each other - why are there so many species of…? - possible explanations include anything that could promote a speciation - increased likelihood of reduced gene flow among lineages - big geographic range enabling subsequent splitting into local populations - use habitat or live in an area with lots of geographic separation (eg. islands) - lots of locally isolated habitats (eg. populations spend generations on one plant) - increased likelihood of differing selection and/or response to selection - lifestyle leads to narrow niche (eg. parasites with only 1 host species) - high mutation rates (creates diversity) or short generation time (facilitates response) - temporally stable (not fluctuating) environment → consistent selection - increased likelihood of reproductive isolation - mating system that favours reproductive isolation (eg. via strong sexual selection) - prone to genome duplication (ploidy) - most weevil species have close association with a lineage of flowering plants - flowering plants underwent dramatic diversification - thought that weevils hitched an evolutionary ride - lifestyle leads to a narrow niche (weevils are often specialist herbivores) - lots of locally isolated habitats (weevil populations often live and breed on host plant) - short generation time (although it depends on who you’re comparing to) - lots of examples of how environment influences selection and speciation - industrialization is influencing all of these - species are responding in all kinds of ways all over - three responses to change - move, adapt, or die out - moving - eg. range shifts - adjusting - eg. phenotypic plasticity - when you get different phenotypes (ie. different morphology, physiology, or behaviour) from the same genotype - or evolution - but this is not always easy, fast, or widespread Fungi terminology - polytomy - yeasts - Filaments - Hypha/hyphae - Mycelium/mycelia - chitin - septa - Saprophyte / saprophytic - Symbiont - Conidia - Dikaryotic stage - Plasmogamy - Karyogamy - one of the three major lineages of large, terrestrial Eukaryotes - functionally, fungi are very close to animals - often why fungal infections are more difficult to treat - few fossils, evolutionary history hard to study - first fungi (aquatic) ~800 to 1000 million years ago - colonized land ~500 million years ago (before plants) - key innovation - how to extract nutrients in a terrestrial environment? - 110 000 named species - taxonomy(s) mostly based on reproductive structures and DNA - very diverse - from single cells (yeast) to huge multicellular structures - fun fact - humungous fungus = 9 km^2 (potentially largest eukaryotic organism still alive today, thought to weigh tons and be thousands of years old) - the vast majority of fungus is mycelium (underground) - critical to ecosystem functioning - a wide range of human uses - disease (athlete's foot, yeast infections, jock itch, ringworm) - hard to treat, but humans tend to not die from them (maybe because we are warm-blooded) 1. structure - singled celled or made of filaments. no complex transport systems. cell walls (like plants) but contain chitin (more like animals) 1. yeasts - single cells 1. difference between yeast (membrane-bound nucleus → eukaryotic) and bacteria (no membrane-bound nucleus → prokaryotic) 2. mycelium - made of hyphae - long, thin filaments 3. hyphae usually separated by cross-walls called septa 4. septa have large pores that allow passage of nutrients (even nuclei) 5. hyphae are 100x thinner than the thinnest plant root 6. can pack together to form mushrooms 7. The shape of the mushroom is determined entirely due to turgor pressure 1. why do fungi occur mostly in moist habitats? - require lots of water 2. nutrition - absorb food directly from surroundings 1. implications of structure for nutrition 1. thin hyphae → waster absorbers (high SA to V ratio) 2. need for moisture → often symbiotic 2. plants photosynthesize, animals east things, fungi secrete digestive enzymes externally 1. saprophytes - eat dead stuff  2. symbionts - live symbiotically within other organisms 3. novel methods of absorbing nutrients drove fungi diversifications 4. key in N, C, P cycles (major nutrient cycles) 5. main decomposers of cellulose and lignin (most abundant molecules of earth) - often tangled together to form lignocellulose 1. lignin totally indigestible to animals 2. cellulose also difficult to digest 1. most famous symbiosis? 1. fungi and tree roots - mycorrhizae 1. 80% of angiosperms partner with fungi to get nutrients from soil 2. lack of mycorrhizae partners can limit plant species distributions 3. introduction of mycorrhizae; partners can enable invasion 4. lichens and fungi 1. fungi and algae or cyanobacteria 2. 20 000 species 3. 6% of earth’s surface - cover lots of arctic tundra 4. mutualism? - algae photosynthesize and provide nutrients, fungi provide structure/protection 1. more like the capture and farming of algae - algae cells can die in the process and can survive on their own, while fungi cannot 3. reproduction - sexual asexual, diverse 1. complicated - many species reproduce in multiple ways, sometimes during both haploid and diploid phases  1. asexual 1. fragmentation 2. during haploid phase 1. haploid cell - any cell that contains only 1 copy of an organism’s genetic information 3. vegetative spores (conidia) 4. produced on conidiophores 2. sexual 1. very different from sex in plants or animals 2. often only see sexual reproductive structures 1. eg. Ascomycetes and Basidiomycetes 4. dispersal - spores 1. unlike hyphae, spores tolerate dry conditions 2. important for dispersal 3. small size facilitates airborne dispersal 4. some species have ejection mechanisms (eg. puffballs)  5. some use animal dispersers (eg. stinkhorns) 6. Cordyceps species create zombies 1. eg. control ant behaviour to make them climb trees, and grow out of ant’s head, then disperse from higher up to spread spores further 2. each species specializes to control only one species of animal humans and fungi - edible mushrooms - breakdown of sugars → alcohols and CO2 - fungi critical for fermentation - alcohols (grains, fruits) - bread - soy sauce - cheese - mycotoxins - extract antibiotics and other medically useful compounds - penicillin - psychedelics - fungal diseases - model organisms in biology (yeast) - bioremediation (especially white rot fungus that devours lignin) - biocontrol of insect pests Microbes, Part 1 why care about microbes? - they make us sick - they make us not sick - bacteria in the gut microbiome help train our immune system and protect against pathogens - they have been evolving for billions of years - they have filled effectively every available niche on earth - they are essential for all global nutrient cycles (C, N, P) - they are continuing to evolve - see point 1 (eg. SARS-CO-V2) - they are great models for evolution history - Louis Pasteur (1870s) - invisible microbes are responsible for fermentation and infections - Koch’s postulates - the microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms - the microorganism must be isolated from a diseased organism and grown in pure culture  - the cultured microorganism should cause disease when introduced into a healthy organism - the microorganism must be re-isolated from the inoculated diseased experimental host and identified as being identical to the original specific causative agent - seeing the invisible world - microscopes - compound microscope first in 1590 - Jansen, improvements in 1650 - Hooke, more improvements in 1670 - van Leeuwenhoek - microscope of the 21st century - genome sequencing - DNA sequencing cost is decreasing rapidly (more than computer power is increasing) social lives of bacteria: symbiosis (”living together”) - eg. *Vibrio fischeri* bacteria colonize the bobtailed squid and provide a useful ‘camouflage’ function - there is a fine line between mutually beneficial relationships and pathogenesis - eg. Vibrio cholerae - symbiosis has played a major role in the evolution of life on Earth… - most plants and animals have a microbiome: microbial communities living in and on them - we humans are ~2% bacteria by mass - these bacteria are mostly in the gut, where there are ~100 common species - what is the balance between bacterial and human cells in our body? - about 1:1 (by cells), about 100:1 (by genes - because there are many different species of bacteria on/in the body, so they have much more genetic diversity) - bacteria have been evolving for billions of years - eg. stromatolites: mats of cyanobacteria, fossils or alive today - cyanobacteria were the first organisms to perform oxygenic photosynthesis - created banded iron formations (iron oxide) in rocks due to oxidation - bacteria as models of evolution - bacteria have a much higher generational rate (higher reproductive rate) which allows for easy use in experimental systems - infinite adaptation can possibly happen? Experiments have shown no fitness plateau… - bacteria as models of very rapid evolution - evolution of resistance against ‘evolution-proof’ antimicrobial peptides What is a microbe? - really small organisms - about half of all the kinds of things in the world are invisible advantages of being small - smaller cells can grow faster than big ones - small cells can absorb more nutrients per unit volume - less surface area as volume increases  - possibly - big cells take longer to replicate their DNA levels of biological organization unit mechanism process individual (eg. a cell) Metabolism and replication Requires continual input of energy and material to keep the cell out of thermodynamic equilibrium population (of related Variation and evolution Replication causes variation; cells) Reproduction causes competition. Mean fitness increases community (of Consumption and nutrient Populations are linked by different species) cycling consumption. Must be in mass and energy balance at level of ecosystem - the boundary of the cell is the plasma membrane - phospholipid bilayer - hydrophilic head group, hydrophobic tails - separates life (inside) from the environment (outside) - all traffic with the outside must take place across the membrane - dual system of the cell - membrane encloses two distinct biochemical systems - metabolism - cell generates or harvests energy and channels it to synthesize new biomass, including the components responsible for metabolism. Without a membrane, the products of metabolism would rapidly diffuse away from one another - information - cell stores the information necessary to synthesize the metabolic system. Without a membrane, the information system could not be permanently linked to the metabolic system - growth leads to reproduction - large cells are inefficient because volume increases faster than surface area) - once the cell has grown to a certain size it divides to form two daughter cells - both cells receive information and metabolic systems from their progenitor - reproduction involves the division of biomass and the replication of information - a more efficient metabolic system leads to more rapid growth and more rapid reproduction - if the information system is coupled with the metabolic system by being enclosed in the same membrane, the increased efficiency is heritable - information system that specifies a more efficient metabolic system will then be replicated more rapidly - this is called evolution by natural selection - genome stores information - a typical bacterial genome comprises about 2 million base pairs encoding about 2000 genes  - formed of a single molecule of DNA in a closed loop about 1.6 mm long - plasmids - small DNA molecules that occur in bacteria but are not essential for normal function - replicate at the same time at the chromosome but daughter cells don’t always receive equal numbers - Some plasmids encode conjugation that results in plasmid transfer from a donor to a recipient via a pilus - Plasmids may encode functions that benefit the host bacteria, but in some cases they are parasites - replication proceeds along a replication fork separating the two strands - follows the same basic scheme in prokaryotes and eukaryotes, but differs in many important details - a protein (DnaA) recognizes the origin of replication and unwinds DNA - origin-binding protein loads two helicases onto DNA - ATP hydrolysis moves helicase along chromosome, driving a wedge between the strands and forcing them apart - an RNA primer is synthesized on the single-stranded portion of DNA - multi-protein replication machine (replisome, consisting of DNA polymerase plus other elements) synthesizes both daughter strands at the same time - two replication forks meet at the termination site, the replisome is unloaded and the daughter chromosomes separate - replication results in two copies of the chromosome - proceeds with occasional errors - the error rate of replication in bacteria is very low: about 10^-10 per base pair per replication - amounts to about 10^-3 mutations per genome per replication - however, a 5-ml overnight culture of E. coli contains about 1010 cells, so every possible single-nucleotide mutation is likely to be present - chromosome replication and cell division are linked - differential reproduction leads to evolution by natural selection - in communities consisting of many species, there are trophic links between organisms with different kinds of metabolism - eg. photoautotroph vs heterotroph Microbes, Part 2 transcription and translation link information storage to metabolic pathways transcription ○ a working copy of RNA is produced from storage in DNA RNA polymerase synthesizes a single-stranded mRNA molecule from one strand (the ‘antisense’ strand) of the DNA, producing a working copy of the ‘sense’ strand - complementary base pairing transcription stops when a termination sequence is encountered translation  ○ the ribosome is a molecular machine that translates mRNA to protein consist of ribosomal RNA (rRNA) and protein there are about 10,000 ribosomes in a fast-growing bacterial cell - only 10-100 in a slow-growing cell there are ~1-15 copies of ribosomal genes in a bacterial genome the genetic code is redundant ○ number of amino acids to be specified < number of different nucleotides in mRNA, number of nucleotides per codon ○ A < N^L ○ amino acids (roughly 20) made of C, H, N, O, and S ○ two theories of why this system is the way it is a ‘frozen accident’ (Crick) - works the way it is, so it never evolved further optimal biochemistry in view of versatility, cost of synthesis, etc. redundancy can be adaptive - allows for some ‘silent’ mutations the history of life on earth mostly microbial happened only once in the universe (to our knowledge) ○ genome size doubles every ~400 million years how did this happen? ○ Most important attributes of living organisms are: 1. genetic - self-replication and heritability, because these alone confer evolvability 2. physiological - metabolism, and thus complexity ○ three theories: 1. special creation - outside the realm of science 2. panspermia 1. undirected panspermia - dispersal of microbes from planet to planet taken seriously because of the short interval between the appearance of permanent oceans and the first signs of life bacteria could be transported by meteors it seems likely that some would survive atmospheric heating and impact objections to undirected panspermia low local star density low probability of capture - probably quite a lot from Mars, etc. but this is not much help since Mars is the same age as Earth 2. directed panspermia - deliberate seeding of planets by aliens the advantage is that it incorporates an effective (intentional) dispersal mechanism  but there are many objections it has taken 4 billion years for intelligent life to evolve on Earth, and we still can’t travel to other stars. If it took 4 billion years elsewhere, then we are getting close to the age of the older stars. only a very few planets could have been seeded no convincing evidence for intelligent life anywhere else has yet been produced why did we only get bacteria? 3. misdirected panspermia - galactic pollution by spacecraft the NASA Viking landers are sterilized to exacting microbiological standards - specifies a maximum of 300 000 spores per spacecraft and 300 spores per square meter the attraction of this hypothesis is that we know it has probably already happened, perhaps other civilizations have been equally careless 3. spontaneous generation 1. flies, lice, and even mice were once supposed to arise spontaneously from putrefaction. Pasteur showed this to be wrong. but perhaps very simple creatures could arise spontaneously in the uninhabited early earth 2. this theory requires: Either that complex organisms such as bacteria should arise spontaneously by some natural process of self-organization (big jump) or that there is a continuous series of entities linking the unambiguously chemical with the indisputably living, with evolution through natural selection at some early point taking over from self-assembly 3. only the second version is taken seriously. It is a very difficult task, however, to reconstruct this chain of events. How can ordered complexity evolve from nothing? ○ History of life: hypothesis for a plausible origin of biomolecules 1. spontaneous generation 1. two chemical processes need to happen for life to be possible growth reproduction 2. for life to evolve from prebiotic chemistry we need one more process  inheritance - reproduction gives rise to products that resemble their parents more closely than they resemble random members of the same population 3. there are then two possible routes for the origin of life genetics (inheritance, information) first metabolism (growth, reproduction) first 2. Genetics First: the RNA world 1. no reasonable pathway leading directly from a dilute solution of small molecules to a full-fledged DNA-protein cell has ever been formed 2. RNA is replicated by RNA polymerases. small RNA replicators exist today as viruses 3. RNA molecules can replicate without cells when they are provided with raw materials and a replicase 4. RNA can also act as enzymes call ribozymes comparable to protein enzymes 5. ribozymes catalyze reactions, including reactions that modify the state of other RNA molecules 6. thus, RNA uniquely combines the capacity to replicate with the capacity to direct metabolism 3. this led to the theory of the RNA world: an early ocean populated by self-replicating RNA strands from which cells and eventually all living organisms descended 4. metabolism first 1. What metabolic strategies would have been possible on early Earth? potentially photosynthesis 2. a potential energy source - chemical disequilibrium at a hydrothermal vent 3. metabolism - fundamentally consists of redox reactions 4. the redox tower bacterial metabolism is based on pairing electron acceptors with electron donors if the oxidation of molecule A in the left column is above the reduction of molecule B in the right column, then the oxidation of A can be coupled to the reduction of B, yielding energy thus, arrows drawn between half-reactions yield energy if they run downward from left to right, and the length of the arrow indicates the amount of energy released 5. the evolution of metabolism  1. lightning, UV, CH2O (sugars), amino acids, and nucleotides allowed for: 6. glycolysis and fermentation - doesn’t yield a lot of energy 7. respiration - yields much more energy 8. glycolysis → 2 ATP, 2 NADH 1. pyruvate is transformed into acetyl group and attached to a carrier molecule of coenzyme A 9. citric acid cycle (TCA cycle, Krebs cycle) → 1 ATP, 3 NADH 10. electron transport chain → ~30 ATP 1. electrons can be passed along a series of molecules in this way, always ‘downhill’ from more electropositive to more electronegative (’electron-hungry’) molecules 2. the energy released by the fall in potential energy from high-energy to low-energy electrons can be harvested and made to do work in the cell Microbes, Part 3 - fermentation - plausible first form of metabolism - glucose + ADP + NAD+ → pyruvate + NADH + ATP - pyruvate + NADH → lactate + NAD+ (a redox reaction) - electron transport chain (ETC) - in the absence of oxygen, some bacteria can use other final electron acceptors to perform anaerobic respiration - chemiosmotic energy storage by membranes - lipid bilayer membranes are impermeable to ions: they separate the electrical charge inside from the outside - charge imbalance created by redox reactions of the ETC that pumps protons (H+) from inside to outside - these protons tend to return spontaneously because of the difference in concentration across the membrane - when they return, they pass through the ATP synthase channel, which turns and drives the oxidative phosphorylation of ADP to ATP - this creates a high-energy phosphate bond that can then be hydrolyzed to support biosynthesis - ATP synthase can be likened to a water mill (with hydrogen ions as the water) - moving from a higher potential energy state to a lower potential energy state - this process was created by bacteria! (done across the cell membrane instead of inside the mitochondria - the evolution of metabolism  - oxygenic (produces oxygen) vs anoxygenic (doesn’t produce oxygen) - aerobic (in the presence of/using oxygen) vs anaerobic (in the absence of/not using oxygen) - both oxygenic photosynthesis and aerobic respiration were evolved by cyanobacteria - Winogradsky column - simple method of separating and visualizing the diverse metabolic systems found in a community of prokaryotes - autotroph = gets C from CO2 - heterotroph = uses organic C - photo = light energy - chemo = chemical energy - eg. humans are chemoheterotrophs - the history of the Tree of Life - trees as a classification scheme (taxonomy) - Aristotle's Scala Naturae - Linnnaeus’ Systemae naturae - species are immutable - trees as a depiction of evolution (phylogeny) - Lamarck - adaptations are acquired - Darwin - adaptations via natural selection (On the origin of species) - molecular phylogenetics brings big surprises - a new Domain of Life - the extent of horizontal gene transfer (HGT) - molecular phylogenetics - Watson and Crick - “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” - Crick - suggests the idea of protein taxonomy - Pauling and Zuckerkandl - molecular clock - mutations accumulate at a roughly regular rate - based on haemoglobin protein sequences - phylogenetic methods - start with a sequence alignment - identify changes at homologous sites - choose a method - distance-based - compute a distance matrix between each pair of sequences, join the two most similar sequences as neighbours on the phylogenetic tree, repeat - parsimony - choose the tree structure that minimizes the total number of mutations (shown as x) - eg. in above example, take second as correct - molecular clock example - coronavirus - SARS-CoV-2 point mutations appear once every ~2 weeks  - this allows us to fit a molecular clock and build ‘time trees’ - bacteria are notoriously hard to classify - Linnaeus - “chaos” - Haeckel - Monera at the base of the tree, giving rise to more complex forms - Chatton - Prokaryotes vs Eukaryotes - morphology and metabolism have limited information - molecular phylogeny provides the perfect tool - Carl Woese - “not elegant science, but a big slog” - 16S ribosomal RNA - universally conserved (18S in eukaryotes) - requires culturing large amounts of bacteria - extract RNA, fragment, run on a gel to produce a “fingerprint” - one day, Woese’s lab fingerprints a methanogen to see where it would fall within the prokaryotes - found Archaea - where are the prokaryotes? - they are not monophyletic - monophyly - sharing a common ancestor that excludes other groups - phylogenies are like mobiles - the branches can rotate and it doesn’t change the meaning Microbes, Part 4 - for phylogenetic tree questions → more closely related = diverge more recently (common ancestor further from the root of the tree) clade - group on a phylogenetic tree - back to the tree of life… - Woese continues to add branches to the tree - halophilic bacteria and thermoacidophiles also turn out to be Archaea - the directness of Archaea is also supported by weird phospholipids - three-domains hypothesis - only one change - eocyte hypothesis - two changes - chemically, not more difficult - so, growing support for this hypothesis Are we basically archaea? - if so, which ones? - Asgard archaea superphylum was discovered by culture-independent DNA sequencing from deep-sea hydrothermal vents in the Arctic Sea: “Loki’s castle” - Lokiarchaeota, Thorarchaeota, Odinarchaeta, etc. - more genome sequences and latest phylogenetic methods place eukaryotes within the archaea - 12 years of enrichment culture later…were able to “re-create” these organisms (closest living relative) - co-culture of the Lokiarchaea Prometheoarchaeum syntrophicum with another archaean and a bacteria - no organelle-like structures, but complex morphology - syntrophy (cross-feeding) - these three organisms have interdependent metabolisms (provide each other with resources) - a possible model for the origin of eukaryotes - entangle - engulf - endogenize (to develop internally) - model of what the origin of eukaryotes could have been like - endosymbiotic theory - Lynn Margulis, 1970 - LUCA (the Last Universal Common Ancestor of all living organisms) *Last synonymous with Most Recent - all cells today descended from a single cell which lived in the ocean long ago - all the other cells then alive gave rise to lineages that subsequently became extinct and have left no descendants - LUCA divided to give rise to two daughter cells: - one was the ancestor of all living bacteria - the other was the ancestor of all living archaea - we can build bigger, better phylogenies - updating the tree of life - Ciccarelli et al. 2006 - 191 genomes included in the tree - based on an alignment of 31 genes (mostly ribosomal) present in 1 copy per gene - the expanded tree of life - Laura Hug et al. 2016, Jillian Banfield lab - 30 000 cultured genomes - +1011 metagenome-assembled genomes (uncultured) - discovered new bacteria - problems with the tree? - if a tree is based on ~100 genes, it may not represent the evolutionary history of the other ~2000 genes in a typical prokaryotic genome - endosymbiotic theory - “horizontal” processes (such as endosymbiosis) are not easily represented by a (vertical) tree - evidence for endosymbiotic theory - morphological similarity (Margulis’ microscopy) - DNA similarity (molecular phylogenetics) - Doolittle and Bonen compare cyanobacteria 16S rRNA with eukaryotic algae’s 18S rRNA  - algae: nuclear rRNA is eukaryotic, chloroplast is cyanobacterial - endosymbiotic theory and HGT - endosymbiosis is a special case of horizontal gene transfer (HGT) involving an entire genome - over time, some genes from the symbiont genome are transferred into the host genome (another form of HGT) - with more genome sequencing, the extent of HGT turns out to be much greater than expected… - viruses are a potential vector What is a virus? - a tiny protein package containing a DNA or RNA genome - not considered a cell (no cytoplasm, no ribosomes…) - not capable of replication without a host cell (obligate parasite) - all forms of life are infected by viruses - LUCA probably had viruses - all viruses use host resources (nucleotides, amino acids) to build more copies of themselves - some viruses are more virulent (killing) than others - example of a eukaryotic virus: Coronavirus - viral particle is made up of - genetic material single-stranded RNA - a protein coat (capsid) - lipid bilayer, 3 membrane proteins - spike - membrane - envelope - enters the host cell and replicates using host cell machinery - adaptation to one animal species can bring tradeoffs for infecting other - SARS-CoV-2 experimentally evolved in ferret or mink acquires a point mutation in the Spike protein - amino acid changes tyrosine to phenylalanine at position 453 - this mutation reduces the ability of the virus to infect human airway cells - viruses acquire mutations to make them better at infecting certain animals (and therefore, worse at infecting others) - a phage is a virus that infects bacteria or archaea - highly diverse (size, shape, gene content) - linear double-stranded DNA, 3000 to 500 000 base pairs - transducing phage quite rare, but due to the large number of phages, they can still be a vector of HGT - vibrio cholerae and phage - lytic cycle - selective pressure (resist or die) - HGT - the cholera toxin is a phage integrated into the bacterial genome - viruses are tiny but abundant - there are 10^30 viruses in the ocean, and 10^23 new infection events happen every second - phages are important in ecosystems - vectors of HGT - often target the most abundant bacteria and keep them in check (”kill the winner”) - eg. could they terminate Cyanobacteria blooms? - keep pathogens like V. cholerae under control? - coevolution - defined as mutually imposed selective pressures - the evolution of one affects the other, and vice versa - adaptation and counter-adaptation - first stage of infection: a phage must attach to a receptor protein on the bacterial surface - mutations in the receptor gene can confer resistance to the phage - phages are then under selection to bind to the mutated receptor - example of evolutionary consequences of intra-patient phage predation on microbial populations - bacteria evolved (via a mutation) to become resistant to phages, but this mutation in turn prevented them from being able to infect their host animal - would need a reverse mutation to complete the cycle Algae terminology - monophyletic - sister taxa/sister groups - Protist - Plantae - Archaeplastids - Opisthokonts - chloroplasts - endosymbiosis - secondary endosymbiosis - thallus - trophic cascade - Alternation of generations - Sporophyte - Gametophyte Monophyletic group - evolved from a common ancestor and includes all descendants of that common ancestor Sister groups - two groups that split from a common node (pairs of terminal taxa that are each other’s closest relatives) - sharing a common node means evolved from a common ancestor, not (necessarily) that one group evolved from the other - sister groups are always monophyletic Note about taxonomy and human bias - 1735 - Linnaeus creates his first classification system for nature with three kingdoms - animals, vegetables, and minerals (rocks) - 1969 - not all organisms are animals or vegetables - Whittaker proposed 5 kingdoms - Plantae (land plants), fungi, Animalia, protista, monera (bacteria) - 2005 - tree of life re-done with DNA evidence - protist is an outdated term → protists are not monophyletic - 2019 - 7 to 11 kingdoms - many more groups of species discovered/reclassified - photosynthesizers → archaeplastids (most), amoebozoans, haptista, stramenopiles, alleviates, rhizarians, discobids (some from all of rest) Origin of photosynthesis: - cyanobacteria = global game changers - oxygenic photosynthesis first evolved (2.5-3 BYA) - developed multicellularity and cell specialization (2.2-2.5 BYA) - around that time, oxygen appears in earth’s atmosphere (great oxidation event) - GOE → 1st mass extinction, but then made complex life possible - if photosynthesis evolved first in bacteria, how did so many eukaryotes get it? - clue 1 - both photosystems (PSI and PSII) evolved in bacteria - clue 2 - all photosynthetic eukaryotes use chloroplasts for photosynthesis - the capture of photosynthesis - endosymbiotic origin of chloroplasts - hypothesis - eukaryotic chloroplast originated when a single-celled eukaryotes (a ‘protist’) engulfed a cyanobacterium - evidence in support - chloroplasts similar to cyanobacteria and behave somewhat independently of cell - replicate by fission, independently of cell division - manufacture some of their own proteins  - have their own DNA, organized into circular molecule very similar to those in some cyanobacteria - peptidoglycan in the cell wall of some chloroplasts (like in bacteria) - chloroplasts have (at least) a double membrane - extant endosymbiotic cyanobacteria live in cells of some ‘protists’ and animals - how did chloroplasts spread to most eukaryote ‘supergroups’? - clues - all species in Plantae/archaeplastids have chloroplasts with double membranes - chloroplasts in other lineages have >2 membranes - possible explanations can be grouped into 4 options: - some eukaryotes evolve photosynthesis on their own? (ie. not by engulfing cyanobacteria) BUT all photosynthetic eukaryotes use chloroplasts and both PSI and PSII evolved in bacteria - single origin in eukaryotes but then was lost in many lineages? BUT roots of phylogeny don’t support a single common ancestor of all currently-photosynthetic lineages, and this hypothesis is quite complex - multiple eukaryotic lineages engulf cyanobacteria independently? Better, BUT doesn’t explain the different numbers of membranes - hypothesis - endosymbiosis leading to chloroplasts first occurred in the common ancestor of Plantae (primary endosymbiosis) - other groups acquired chloroplasts via secondary endosymbiosis - which photosynthesizers make the most oxygen today? - phytoplankton - single-celled photosynthetic organisms living in marine environments - ~50% of global photosynthesis - base of (almost) every ocean food web - phytoplankton is made up of: - photosynthetic bacteria - includes Cyanobacteria (’blue-green algae’) - responsible for half the ocean’s primary productivity - Single-celled photosynthetic eukaryotes - mostly Dinoflagellates and Diatoms (’algae in glass houses’) - brown algae (Phaeophytes) - chloroplasts with 4 membranes - 1500 to 2000 species - multicellular marine organisms - individual = thallus (no complex vascular system) - brownish colour from carotenoid pigment fucoxanthin used in photosynthesis - tallest tree in the world = redwood (max normal height is ~90 m - how tall is the tallest seaweed? → 80 m - Famous phaeophytes: kelp - >120 species  - fastest growth rate of any seaweed - max growth rate 3.5 m / week - final height up to 80 m - don’t have to fight against gravity when growing, so able to grow at a faster rate (compared to something like a redwood tree) - kelp forests - largest biogenic marine habitat - biodiverse: >100 000 mobile invertebrates / m^2 of kelp tissue - kelp forests in ecology: - keystone species, trophic cascades (sea otter/sea urchin/kelp - relationship example) - red algae - most diverse marine seaweeds (>7000 species) - both unicellular and multicellular species - can live at great depths - red colour from carotenoid pigment phycoerythrin used in photosynthesis - phycoerythrin absorbs blue light, which penetrates water deeper than any other wavelength - no flagella (ie. non-motile sperm) - alternation of generations (some species) - famous red algae → Nori, dulse - Coralline red algae - calcareous deposits in cell walls - max growth rate = 0.8 cm / year - help build coral reefs - attract coral larvae - patch up broken coral like a bandaid - reinforce coral skeletons - diversity nose-dived with the evolution of parrot fish - alternation of generations - kelp alternate between two multicellular life stages: multicellular haploid (n) form (gametophyte) and multicellular diploid (2n) form (sporophyte) - gametophytes produce gametes (n) by mitosis - sporophytes produce spores by meiosis - spore - single n cell, can grow into multicellular organism without fertilization - both the n and 2n life stages are multicellular (always) - the n and 2n life stages can be independent, free-living organisms (sometimes)