Fungi and Animals

Fungi and Animals

• Fungi and animals fall within the larger eukaryotic clade called Opisthokonta.
• Both groups share a common ancestor, making them each other's closest relatives.
• Within Opisthokonta, fungi are closest to protists called nucleariids.
• Animals are closest to organisms like choanoflagellates and ichthyosporea.

Fungal Metabolism

• Fungi are heterotrophs (chemoheterotrophs) that absorb food rather than ingest it.
• They use strong enzymes to break down macromolecules in the environment before absorption.

Fungal Structures

• Chitin is a long chain polymer of N Acetylglucosamine.
• Hyphae are composed of chitin and form the network threads of mycelium.
• Mycelium is a thread-like network of hyphae.
• Yeast is unicellular.

Fungal Reproduction

• Mushrooms primarily function in reproduction and mostly consist of mycelium.
• Saccharomyces cerevisiae is a yeast used in bread making and beer production.
• It produces bread by consuming sugar and releasing CO2 through fermentation.
• Absorptive nutrition involves organisms obtaining nutrients by absorbing them, often using digestive enzymes.
• Ingestive nutrition involves actively taking in food through a mouth, then digesting it internally

Ecological Roles of Fungi

• Fungi play vital roles as decomposers, parasites/pathogens, and mutualistic symbionts.
• Lichens are hybrid colonies of algae/cyanobacteria living symbiotically among fungi/yeasts/bacteria, embedded in the skin of the lichen.
• In lichen symbiosis, fungi receive nutrients from algae/cyanobacteria.
• Algae/cyanobacteria get shelter and access to water and minerals from the fungus.
• This symbiosis is important to fungus and alga for living on a rock face in the desert.

Mycorrhizae and The Wood Wide Web

• Mycorrhizae are symbiotic associations where fungi around plant roots help plants absorb water and nutrients.
• Plants provide carbs to the mycorrhizae fungi.
• This is important in natural ecosystems and agriculture.
• The "Wood Wide Web" refers to roots swapping information and food between plants using a fungal network.

Ant-Fungus Mutualism

• Leafcutter ants create nests of chewed leaves and excrement to grow fungi for food.
• The fungus turns the leaves, which are indigestible for ants, into food.

Asexual Fungal Reproduction Forms

• Fragmentation occurs when hyphae break up and become independent organisms.
• Spore formation involves asexual production of haploid spores through mitosis.
• Budding is when a small outgrowth detaches from a parent cell to form a new individual, common in yeasts.
• Most fungal tissue is haploid but needs to be diploid for meiosis.
• For sexual reproduction, haploid cells fuse, forming a heterokaryotic cell, which is considered a diploid cell.
• Fungal spores can be produced both sexually and asexually.

Heterokaryotic Cells

• Heterokaryotic cells result from the fusion of two haploid cells.
• This creates a condition where a single fungal cell contains multiple, genetically distinct nuclei.

Glomeromycetes and Ascomycetes

• Glomeromycetes engage in mycorrhizal mutualism with plants.
• Ascomycetes are the most diverse and common clade of fungi, often called "cup fungi."
• Fungi are important for antibiotic development because fungus produces spores and molds that created penicillin.
• Conidia are asexual pores whose asexual reproduction created penicillin.
• Edible fungi like truffles come from Ascomycota.

Basidiomycetes and Fungal Infections

• Basidiomycetes, known as "club fungi," comprise around 30,000 species.
• Members include mushrooms, shelf fungi, puffballs, and jelly fungi.
• Most edible mushrooms come from Basidiomycota (mushroom, shiitake), and ascomycota (truffles).
• Mycosis is a fungal infection.
• Tinea causes athlete's foot, ringworm, and jock itch.
• Candida causes thrush, vaginal yeast infections, skin infections, and UTIs.
• Plants are the most common hosts for fungal infections.

Cordyceps and Pathogens of Amphibians and Snakes

• Cordyceps is a parasitic fungus that infects the brains of ants and grows out of their heads, with each species specialized.
• Chytrid fungi is a pathogen of amphibians that infects skin and affects osmoregulation, causing death.
• White-nose syndrome is an invasive fungal pathogen that kills and decimates hibernating bat populations.
• Snake fungal disease is affecting snakes in the eastern USA
• Humans are generally protected by being warm-blooded.
• Climate change might allow fungi to match human body temperature and attack us.

Fungi Health Risks

• Candida auris and valley fever pose particular health risks to humans.

Phylogenies

• Darwin’s "On the Origin of Species" used a phylogeny as the single figure.
• Phylogenetic tree and cladogram are terms used for phylogenetic tree.
• Phylogenetic trees are "pipes” containing gene pools of populations flowing through time.
• Branching points in a phylogeny represent speciation, while branches represent populations.
• Chimpanzees and humans did not become different species immediately; evolution occurred over long periods.
• A node (branch point) in a phylogeny shows lineage divergence and represents a common ancestor.
• Phylogenies illustrate the flow of gene pools through time.
• A clade is a group of organisms including a common ancestor and all its descendants.

Taxonomy terminology

• Synapomorphy is a shared (2 or more taxa) derived character.
• Symplesiomorphy is a shared ancestral trait.
• Sister taxa are groups of organisms classified together based on shared characteristics and are most closely related.
• A polytomy indicates an unresolved pattern of divergence.Taxonomy
• Linnaeus grouped organisms based on overall similarity, while current taxonomy aims to reflect phylogeny.

Phylogenies Data and Homology

• Phylogenies are constructed using data like DNA, anatomy, behavior, fossil data, and character states of living taxa.
• Homology is phenotypic and genetic similarities due to shared ancestry, such as skeletal systems or DNA sequences. Homologous, Vestigial Features
• Homologous characteristics indicate evolution, with shared ancestors using similar embryological patterns.
• Vestigial structures are anatomical features that don't seem to have a purpose in the current form of the organism, showing homology because they indicate a shared, functional ancestry.

Embryology and Evolution

• Embryology shows homology; organisms with different adult forms can have similar embryos, revealing shared embryological patterns inherited from ancestors.
• Convergent evolution is the process where unrelated organisms independently evolve similar traits due to similar environments.
• Convergent evolution occurs as organisms in similar environments independently evolve similar traits as adaptations.
• Homoplasy is a character shared by species but not present in their common ancestor.
• Analogy is a synonym of homoplasy.
• Examples of homoplasy include wings of butterflies, bats, and birds.
• Homology is more reliable for inferring phylogenetic relationships than homoplasy.
• This is because homology directly reflects shared evolutionary history while homoplasy involves independent adaptations.

Taxonomy

• Monophyletic includes a common ancestor and all descendants (e.g., mammalia).
• Paraphyletic includes a common ancestor and some, but not all descendants (e.g., reptilia).
• Polyphyletic includes groups of species with multiple ancestors (e.g., warm-blooded animals, including birds ).
• Taxonomic categories should be monophyletic to ensure accurate representation of evolutionary relationships.
• Taxonomic classification should reflect evolutionary history; new data can lead to revisions of phylogenetic hypotheses and classification.

Prokaryotic Biodiversity and Archaea

• Metagenomics is the study of genetic material directly recovered from environmental samples, aiding the discovery of prokaryotic biodiversity.
• Domain Archaea was discovered in the 1970s by Carl Woese using molecular techniques.
• Archaea are considered extremophiles due to their discovery in oxygen-lacking, extremely hot, acidic, or salty environments.
• Methanogenic archaea produce methane.
• Methanogens live in anaerobic swamps, the guts of grazing animals, and the human microbiome.
• Cattle produce a large amount of methane: leading to concerns about their impact on global climate change.
• Nitrogen (78%) comes from bacteria for plant use.
• Oxygen (21%) produced by photosynthetic organisms such as cyanobacteria.
• CO2 (0.04%) is produced by chemoheterotrophs and photoautotrophs.

LECA, Eukaryotes, and Endosymbiosis

• LECA stands for Last Eukaryote Common Ancestor.
• Proteobacteria and cyanobacteria are important in eukaryote evolution due to the endosymbiosis theory.
• Endosymbiosis says mitochondria evolved from engulfed aerobic bacteria (proteobacteria), and plastids evolved from cyanobacteria.
• The endosymbiosis theory proposes that mitochondria and plastids were formerly small prokaryotes inside larger cells, becoming mutually beneficial.
• Mitochondrial DNA is more similar to proteobacteria DNA, while chloroplast DNA is more similar to cyanobacterial DNA than to eukaryotic nuclear genome.
• Key eukaryote features include a nuclear envelope, cytoskeleton, endoplasmic reticulum, membrane-bound organelles, and chloroplasts
• Some eukaryotes do not have mitochondria, having lost or degenerated them due to adaption to anaerobic conditions
• Microsomes and hydrogenosomes evolved from reduced mitochondria.
• Multicellularity evolved more than 30 times in single-celled eukaryotes.
• Multicellularity allows survival in rough places since important parts are more protected within cells unlike cooperative colonial organisms.
• Euglena moves with flagella.
• Mixotrophs combine photosynthesis and heterotrophic nutrition.
• Trichomonas vaginalis is from the Excavata clade and causes trichomoniasis (STI). Mitosomes
• Mitosomes of Giardia are reduced mitochondria not for ATP synthesis but for maturation of iron-sulfur proteins.
• Naegleria fowleri is a brain-eating amoeba in freshwater that penetrates nasal mucus, causing severe, untreatable infection
• Straminopiles include diatoms, golden algae, and brown algae.
• Diatoms' "homes" are made of glass-like silicon in an organic matrix, creating a strong structure.
• Diatoms are a major source of oil, a fossil fuel.
• Kelp is special because it ate red algae and became photosynthetic.
• Paramecium belongs to the SAR clade and moves via cilia.
• Dinoflagellates are mixotrophic "algae" that spin through water with two flagella.

Dinoflagellates, Slime Molds, Tree of Life Domains and Prokaryotes

• Dinoflagellates can cause toxic red tides but are important symbiotic mutualists with reef-building corals.
• Loss of dinoflagellates results in coral bleaching and death.
• Plasmodium is a big deal because it causes malaria.
• Forams are in the Rhizarians supergroup.
• Paleontologists study forams.
• This is because they are crucial for understanding the fossil record due to their small size, abundance, and unique shells.
• Amoebas move and ingest using pseudopodia, similar to white blood cells (neutrophils).
• Slime molds are amoebozoans, traditionally fungi; they form multicellular reproductive structures and are decomposers.
• Slime molds are similar to fungi because they are decomposers.
• The three domains of life are Bacteria, Archaea, and Eukarya.
• The stromatolite is the oldest fossil evidence for life on earth (~3.5 billion years ago).
• Prokaryotes do not form a clade relative to eukaryotes, since Prokaryotes include two distinct groups: Bacteria and Archaea, so they aren't closely related.

Prokaryotes

• Prokaryotes thrive in diverse habitats, and are the most numerous organisms on earth.
• They are important due to their ecological roles.
• Prokaryotes lack nuclei, membrane-enclosed organelles, and cytoskeletons.
• Their chromosomes are circular.
• Most prokaryotes are cocci, bacilli, or spiral shaped.
• Most motile bacteria propel themselves by flagella.
• All domains of life have members with flagella, but bacterial flagella differ structurally and functionally from eukaryotic flagella.
• Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides, which Archaea lack.

Gram Staining and Capsules

• Gram staining identifies bacteria based on peptidoglycan content.
• Gram-positive bacteria trap crystal violet stain due to a thick peptidoglycan layer.
• Gram-negative bacteria do not.
• A capsule (polysaccharide or protein layer) covers some prokaryotes and protects the cell from consumption and dehydration.
• Prokaryotes reproduce via binary fission (asexual).
• Offspring cells are generally identical with short generation times.
• Rapid reproduction rates and short generation times enable quick mutation accumulation, leading to rapid evolution.
• Prokaryotes are more metabolically diverse than eukaryotes, allowing for diverse adaptations.

Metabolism and Facultative Anaerobes

• Aerobic organisms require oxygen.
• Anaerobic organisms require the absence of oxygen.
• Autotrophs use CO2 as a carbon source. Heterotrophs
• Heterotrophs require organic nutrient to make organic compounds.
• Phototrophs obtain energy from light.
• Chemotrophs obtain energy from chemicals.
• Facultative anaerobes can survive with or without O2.
• Aerotolerant organisms are not affected by the presence of O2.
• Photoautotrophs include cyanobacteria.
• Chemoheterotrophs include most bacteria, including decomposers and parasites.

Oxygen Revolution and Plasmids

• The evolution of oxygenic photosynthesis, led to the Oxygen Revolution.
• It was likely started by cyanobacteria and was one of the important events of all time.
• The "Oxygen Revolution" occurred approximately 2.3 billion years ago, evidenced by rusting iron-rich rocks.
• The "Oxygen Revolution" is also called the Oxygen Crisis because O2 is very reactive, causing extinction of many prokaryote groups.
• After the Oxygen Revolution, evolutionary changes occurred in organisms, leading to using O2 for cellular respiration.
• A plasmid, it is a small circle of DNA with few genes.

Transformation and Transduction

• Transformation is used in bacterial cloning in the laboratory and transduction moves bacterial DNA via a phage vector.
• In 1978, recombinant technology using bacterial transformation was used to meet the increasing U.S. demand for the drug insulin
• Bacterial conjugation involves the construction of pili and the transfer of genetic material via an F factor.
• Endotoxins are lipopolysaccharides released when bacteria lyse (burst open).
• Exotoxins are proteins secreted by living bacteria instead.
• Spirochetes, such as Borrelia cause Lyme disease.

Bacterial Pathogens and Antibiotics

• Xylella fasticiosa attacks plants.
• Opportunistic bacteria cause respiratory infections in Saiga Antelopes.
• Many antibiotics target peptidoglycan and damage bacterial cell walls
• Genes for traits like antibiotic resistance can be transferred between bacteria through conjugation.
• Gram-negative bacteria and bacteria and Bacteria with thick cell walls are also resistant to many antibiotics
• Prokaryotes are ecologically important for nutrient cycling and decomposing.

Symbiosis

• Symbiosis is an ecological relationship where two species live in close contact.
• Mutualism: both benefit.
• Commensalism: one benefits, the other is neither harmed nor helped.
• Parasitism: one harms but does not kill its host.
• SCOBY is Symbiotic Community Of Bacteria and Yeast.
• Nitrogen-fixing bacteria convert atmospheric nitrogen (N2) into ammonia (NH3).
• Rhizobium in legume root nodules has a mutualistic relationship with the legume.
• The human microbiome is the amount of microorganisms found in a human body.
• The ratio of bacteria to human cells is about 1 to 1, with about 30-40 trillion cells.

The Human Microbiome and Its Impact

• The human microbiome affects the fitness of the holobiont.
• Genes + microbe genes + environment impact health.
• Holobiont refers to a host organism plus all symbiotic microbiota, transient and stable.
• A large organism is a biological community.
• All animals and plants comprise holobionts.

Darwin's Postulates and the Medium Ground Finch

• Peter and Rosemary applied Darwin’s to the Medium Ground Finch in 1977
• Variation: traits, such as bill depth, varying among individuals.
• Heritability: parents with thick beaks having offspring with thicker beaks and parents with thin beaks having offspring with thinner beaks.
• Competition: the finch population dropping by 84% following a 1977 drought, indicating competition for survival.
• Non-random survival: birds with deeper (thicker) bills surviving the drought and succeeding in non-random reproduction.
• Thus Thicker-billed birds were better able to crack the remaining larger seeds.

Natural Selection, Sexual Dimorphism and Selection

• Natural selection acts on individuals, but it's the population that changes, evolving across generations.
• Sexual dimorphism: significant differences between males and females in size, coloration, traits, and calls.
• Sexual dimorphism happens due to natural selection not being able to explain it and raises questions of how traits evolve without selection.
• Sexual selection comes from female asymmetrical reproduction, with females investing time and resources and can lead to conflicts and selective pressures for gender
• Females typically invest more resources such as eggs, pregnancy, and feeding into offspring than sperm producing males.
• Asymmetry sets up males for matings to increase reproductive success and select females for their matings to ensure offspring
• With higher access to female mates, males compete for females competing or choosing mates to breed
• Males competing via fighting challenging others for female access, using sperm to complete mating and sperm plugs, and infanticide.

Sexually Selected Characters and Mate Choices

• More elaborate traits on males such as body size or horns/antlers means to out-compete other males and mate.
• For example, larger elephant seals attract females, thus more offspring.
• Females chose mates with strong traits.
• Females choose males with elaborate traits because the traits signal strong genetics (male fitness).

Evolutionary Trade-Offs and Evolution Forces

• A trade-off between individual survival and sexual selection: The survival risk between male calling frogs with "chuck" calls being favorable to females and risk to frog eating bats
• Five forces of evolution are:
• natural selection
• drift
• mutation
• rules for mating
• migration (gene flow)

Speciation

• Speciation describes the emergence of new and increased life species.
• The three ingredients needed for speciation are geographic isolation, time, reproductive isolation.
• Allopatric speciation occurs when individuals are separated physically by a physical barrier for significant ammounts of time.
• Snapping shrimp splitting between the Pacific and Caribbean from Panama is an allopatric speciation example.
• Earth's change of geological surface, like seas, and canyons, isolating physical populations lead to genetic divergence over time affecting allopatric differentiation on the planet.
• Gene flow barriers prevent gene from divering genetically with speciation.
• Sympatric speciation is when different populations diverge without physical location separation with selection.

Hybrid Speciation

• Hybrid speciation describes when parent species form new, polyploid species.
• Neither time or location prevent rapid isolation.
• Prezygotic barriers prevent reproduction.
• They include habitat, temporal, behavioral,and Isolation.
• Postzygotic barrierrs reduces offpsring breakdown.
• With reduced location, the earth has various geographical conditions that prevent flow.

Reproduction

• Isolated organisms through courtship maintain genetic isolation.
• Behavior prevents genetic isolation.
• With various pollen, organism prevent genetic isolation.
  • They have specific pollen.
• The time of the cycle can prevent genetic isolation.
  • Eastern and western skunks breed at different times for isolatioon.
• Molecular components can do the same.
  • With proteins.
• Sterile Offpsring commonly for postygotic isolation.
  • Mules.
• Interbreeding leads to natural species in the biological setting.
• Since grolar bears aren the same from not being sterlie, they are united with gene expression.
  • Hybrids.
  • In the grolar bear, hyrbidization is different with grolar bears and mules from forming different specie.
  • Genetics and crossings relate with different traits.

Fungi and animals are in the Opisthokonta clade and share a common ancestor. Fungi are closest to nucleariids, while animals are close to choanoflagellates. Fungi are heterotrophs that absorb their food using enzymes.