Phylogeny and Classification Viruses Bacteria Archaea Protists Fungi

Phylogeny and Classification Viruses, Bacteria, Archaea, Protists, Fungi

• Evolutionary theory is so important to modern biology that it is how biologist organize the modern world • • Phylogeny is the evolutionary history of a species or group of related species usually organized into a phylogenetic tree • • Phylogenetic trees and cladograms (also tree shaped) seek to arrange organisms based on common ancestry • phylogenetic trees and cladograms represent a hypothesis about evolutionary relationships and are ever-changing based on new evidence • Each branch point represents the divergence of two species • Sister taxa are groups that share an immediate common ancestor • A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree

What is the difference between a phylogenetic tree and a cladogram? • • Many biologists use these terms interchangeably • Both are based on ancestral relationships • Some scientists associate phylogenetic trees with true evolutionary history • Some scientists consider cladograms to represent hypotheses about a group of organisms’ ancestry • In phylogenetic trees branch lengths can represent the amount of genetic change or are proportional to time (most common) • • In cladograms the branch lengths are usually considered to be arbitrary Phylogenetic tree cladogram

What evidence is used when building a cladogram or a tree? • Morphologies, genes, and biochemistry of living organisms • • Organisms with similar morphologies or DNA sequences are likely to be more closely related • • Must distinguish whether a similarity is the result of homology or analogy • • Homology is similarity due to shared ancestry • • Analogy is similarity due to convergent evolution (shark/dolphin)

What We Can and Cannot Learn from Phylogenetic Trees • • Phylogenetic trees do show patterns of descent • • Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage • • It shouldn’t be assumed that a taxon evolved from the taxon next to it • • In this example, the lancelet is the outgroup. Why?

Look at the cladogram at the right. What conclusions can be drawn about the relationship between humans and chimps?

• This diagram shows a relationship between 4 relatives. These relatives share a common ancestor at the root of the tree. • • Note that this diagram is also a timeline. The ‘older’ (evolved earlier) organism is at the base (bottom) of the tree. • • The four descendants at the top of the tree are DIFFERENT species. This is called SPECIATION.

• Branches on the tree represent speciation • • The event that caused speciation is shown as a fork on the tree.

• A CLADE places species into groups that includes an ancestral species and all of its descendants. • • If you cut a branch of the tree you could remove all the organisms that make up a clade

Terms of a Cladogram

How trees show evolutionary history: Derived Character

Three trees, all depict same evolutionary history. (nodes can rotate!)

Dichotomous keys • tool used to help identify unknown organisms based on a key. The key has a series of choices that leads the user to correctly identify organism(s). • Dichotomous keys help scientists to classify organisms into different taxonomic levels (kingdom, phylum, family, etc. ) based off of their similar characteristics.

Classification of organisms • Taxonomy-Discipline of Bio that deals with identifying, naming, classifying, organisms • Linnaeus: Binomial nomenclature-2 word Latin name Ex. : Homo sapiens • Taxa: Domain, Kingdom, Phylum, Class, Order, Family, Genus, species • Old System: 5 Kingdoms • New System: 3 Domains, 6 Kingdoms Eubacteria Arachaebacteria Bacteria Arachaea Eukarya Plantae Animalia Fungi Protista

• Organisms are grouped in a hierarchy of different levels or TAXA based on similar characteristics: Domain Kingdom Phylum Class Order Family Genus Species Dear King Philip Come Over For Great Spagetti

Domain Eukarya Kingdom Animalia Chordata Phylum Mammalia Class Carnivora Order Family Felidae Genus Panthera Species leo

Bacteria

Bacteria Structure • Unicellular, prokaryotic organisms • Large circular chromosome • Plasmids in nucleoid region • Cell walls (peptidoglycan); Many secrete sticky substance that forms capsule outside wall. • Usually 1 -10 um long • Cell wall prevents osmotic rupture.

Prokaryotes are the foundation of life on earth!!!!!!! • Decompose dead organisms • Decomposers, saprobes, saprophytes • Perform nitrogen fixation • Live in our digestive system and are also used in the food industry • Cheese, yogurt, etc • Used to decompose waste in sewage • Disesase causing bacteria – Usually produce toxins. Exbacteria that causes botulism (paralyzes nerve cells)

Some Prokaryotes Cause Disease: Pathogens • Bacterial Examples: cholera, diphtheria, leprosy, Lyme disease, meningitis, the plague, pneumonia, syphilis, gonorrhea; tetanus, tuberculosis, strep throat. See book for more. • Antibiotics are the most effective means of fighting bacterial infections • Penicillin breaks down cell wall and allows rupture • **No known Archaea cause disease

Archaea

Major Groups of Archaea • Extremophiles-3 examples • Methanogens: are poisoned by oxygen • use CO 2 as the electron acceptor in respiration • produce methane as a waste product • Halophiles- lives in very saline places • Thermophiles (aka

Archaeabacteria vs eubacteria • Used to be grouped with bacteria and called Monerans • Now believed eukaryotes “split” from archaeal line of descent • Differences between Arch and Bac: • Archaea have “unusual” diverse lipids in membrane that allow them to live under extreme conditions • Cell walls composed of polysacc and some only are entirely protein. **A few recently discovered have no wall (not on test, just FYI) • Similarities between Arch and Euk: • Arch and Euk share some of the same r. RNA sequences and ribosomal proteins • Similar t. RNA • Some Archaea have introns; bacteria do not

Viruses

Viruses: What do they look like? • Made of protein coat (capsid) and nucleic acid (DNA or RNA) • 5 -300 nm (nm is a billionth of a meter) • Orders of MAGNITUDE smaller than cells • (not cells)

Viruses: What do they do? • Intracellular parasites • Virus attaches to host cell using their coat’s proteins and the host’s cell membrane receptors. • Viral genome (DNA or RNA) then enters host cell and uses cell’s enzymes to replicate itself

Virus Life Cycle – lytic or lysogenic

Fungi

What is a fungus? • Most are multicellular • Unicellular fungi: yeast • Multicellular: mushrooms, molds • Cell walls made of chitin. • Heterotrophic • Nonphotosynthetic • Digest food outside bodies (release enzymes and absorb nutrients • Some live off of dead organic matter • Decomposers AKA Saprotrophs

Fungi STRUCTURE • Most of the fungus is UNDERGROUND • Composed of tiny filaments called hyphae • Hyphae are long strings of cells. • Mycelium = mass of hyphae • Mushrooms are the fruiting bodies • Meaning it creates/releases the spores

Fungi Reproduction • Can reproduce asexually by releasing haploid spores • Can also reproduce sexually by fusing hyphae of neighbor fungi • (makes a 2 n organism, which then undergoes meiosis for 1 n spores)

Ecological Impacts of Fungi • Decomposers! Important nutrient recyclers • Some are pathogens, such as ringworm and athletes foot. • Ex: ringworm, athletes foot • Plant pathogens: Dutch elm disease, Chestnut blight • Some produce deadly toxins-ex-some species of mushrooms • We use them for their antibiotics-penicillium. • Produce enzymes that rupture bacterial cell walls

Lichens • Look similar to some species of moss, but are not! • Lichens are symbiotic associations between a fungus and a cyanobacteria (photosynthetic bacteria) • The fungus usually give bacteria “shelter” • Bacteria provides the fungus with food

Mycorrhizae (“fungus roots”) • Mutualistic associations of plant roots and fungi • Plant gives fungi SUGAR • Fungi gives plants NUTRIENTS • Almost all vascular plants have mycorrhizae!

Protista

Kingdom Protista • Very diverse group of organisms • Most are unicellular, some multi • Most are aerobic & use mitochondria for respiration • Some are autotrophs, some are heterotrophs • 3 types: ingestive, absorptive, photosynthetic. • Animal-like, Fungi-like, and Plant-like

Kingdom Protista • Some reproduce sexually, some reproduce asexually • The haploid stage is the main vegetative stage of most protists • Only the zygote is diploid. • Zygotes undergo meiosis and become haploid (see life cycle in book) • Can form cysts that survive harsh conditions • Most are aquatic (plankton). What adaptation prevents them from lysing in water?

Protozoa – animal-like protists • Heterotrophs (ingestive) • Motile (most). Classified by how they move. • 4 groups: Sarcodines: moves and ingests using pseudopodia ex: Amoeba Ciliates: move with cilia ex: Paramecium Flagellates: move with flagella Ex: Euglena Sporozoans: Don’t move. Are parasitic ex: Plasmodium (Malaria

Algae – the plant-like protists • Autotrophic • Currently, classified by the pigments they contain • Green Algae • Volvox (single cells, colonial) Golden-Brown Algae Diatoms

The Plant-Like Protists • Dinoflagellata • dinoflagellates – cause red tide (toxic to fish)

More Plant-Like Protists • P. Phaeophyta – the brown algae • -include the largest seaweeds, the kelps (**multicellular) • P. Rhodophyta – the red algae • -include the red seaweeds, some encrusted and common in coral reefs

The Fungus-Like Protists • Known as SLIME MOLDS and WATER MOLDS • Unicellular, heterotrophic, absorptive (usually feed on decaying matter) • Cell walls mainly made of cellulose (like plants). No chitin, which is found in true fungal walls

Protists are so diverse, they’re not a “real” group • Currently being phylogenetically reclassified based on common DNA sequences, proteins, and therefore common ancestors