BOIEE 1780 1st Edition Exam #1 Study Guide1-28 (Tree-thinking I)There are currently around 9 million species (not including extinct ones) and each has 20-30,000 genes. The idea of how to deal with organizing these species is attributed to Darwin and his primitive phylogenetic tree from 1839ish. Ernst Haukel came up with his own version soon after. Phylogenetic trees exist on several levels: individuals, populations, species, phylogeny.1-30 (Tree-thinking II)Mammals are classified as having an amniotic egg because they have many similar structures to chickensand reptiles. Snakes are classified as having “legs” because they have remnants of femurs and pelvis. In order to use a certain character in determining a phylogeny, make sure it is 1)heritable, 2)slowly evolving, and 3)homologous. Synapomorphies define a clade, but it’s not necessary for all present day members of the clade to still show that character state (example: some ancestor evolved limbs, but snakes then devolved those legs… they are still considered part of that clade). 2-2 (Tree-thinking III)Molecular trees are different than what we’ve been discussing. Their tips represent current day alleles, not species, and their branch length reflects the number of mutations. Neutral theory states that most new mutations are not favored or disfavored. They arise at an average rate, and can therefore be used for dating. Coalescence is the point in which any two homologous chromosomes exist in the same ancestor. I doesn’t always line up with species phylogeny. Mitochondria only comes from the mom (we can trace back to a “mitochondrial Eve”).2-4 (Phylogeny and Diversity)Monophyletic groups are more closely related than paraphyletic groups. An outgroup can help determine the ancestral state of a clade and synapomorpies. Homoplasy is the result of convergent evolution, and evolutionary reversal can cause lineages to lose the traits that are common of the rest of their clade. Studying phylogeny is important because we can trace common traits and determine correlation, analyze epidemics, study coevolution, and show the sequence of colonization of islands. All organisms have DNA/RNA and cellular unity, meaning that we can trace these traits all the way back to LUCA (Last Universal Common Ancestor). Earth formed 4.6 billion years ago, with the earliest evidence oflife around 3.7 billion years ago and the earliest eukaryote around 1.8 billion years ago. Viruses cannot be included as “life” because they use no AATP, have no ribosomes, and have evidence of multiple origins. There are about 2 million described species, six of which are “model species,” including E. Coli, mice, and flies. Make sure you know the important taxa posted online.2-6 (Prokaryotes)There are 20,000 described species, and as many as 10^14 microbial cells are associated with an adult body, most being benign/useful. Bacterial walls contain peptidoglycan. The high level of atmospheric oxygen is caused by cyanobacteria. Algae contain chlorophyll a. Purple sulfur bacteria have bacteriochlorophyll and use H2S rather than H20, plus use a wavelength of light beyond the visible spectrum. Spirochetes, including chlamydia, are a corkscrew shape prokaryote discovered byLeeuwenhoek. Archaea (which include extremophiles) include halophiles and methanogens. Prokaryotescan reproduce through binary fission, conjucation, or phage conversion, and occasionally lateral gene transfer occurs, sometimes across entire domains.2-9 (Eukaryotes)Eukaryotes are a combination of archaea and bacteria, and are defined by a nuclear membrane. They contain several useful innovation including flexible call membranes, infolding, microtubules, digestive vacuoles, mitochondria (result of endosymbiosis of proteobacteria), and chloroplasts (result of endosymbiosis of cyanobacteria). In some cases, we can see evidence of secondary and tertiary endosymbiosis. Endosymbiosis is the acquisition of a complete organism (genome + cellular machinery). Protists are any eukaryotes that can’t be classified as animals, plants, or fungi. They include alveolates (which can be ciliates, dinoflagellates, or plasmodium), stramenopiles (including diatoms), excavates (which include euglena and trypanosomas), and amoebozoans (which include loboseans and slime molds).2-11 (Plants and other)Chloroplasts are the synapomorphy of all plantae. Chloroplasts have two membranes with peptidoglycanin between. Green plants have photosynthetic membranes stacked within their chloroplasts. The great oxidation event was the result of the evolution of photosynthesis. Glaucophytes have chloroplasts called cyanelles, membranes not stacked, and peptidoglycan. Red algae make up coral reefs and do not contain peptidoglycan. Green algae are paraphyletic and include “green plants,” which have chlorophyll a and b. Land plants had to develop a number of solutions to problems like dessication, physical support, movement of nutrients, increased UV radiation. Liverworts are the earliest land plants, live in moist habitats, and use alteration of generation. Mosses and vascular plants have stomata, cuticles, and also show alteration of generations.2-13 (More plants)Plants transitioned to land in the Silurian period, around 420 million years ago. They did so to get better access to light, reduce competition, access nutrient-rich soil, access CO2, grow taller, escape predators and escape aquatic pathogens. Lycophytes (club mosses) comprised huge forests in the Carboniferous Period. They have true branching roots, small vascularized leaves, and a vascular system. Horsetails is a small group of 15 species with a small gametophyte and large sporophyte. Their flagellated gametes must use water to swim. Ferns have flagellated gametes as well, and their gametophyte is photosynthetic. Their large leaves are called megaphylls. Gymnosperms have “naked seeds” and pollen, and include cycads, ginkgos, and conifers. Angiosperms make up 90% of plants and have the synapomorphies of fruits and flowers. In some species that grow in sibling groups, plants will not compete against the others they are related to.2-18 (Opisthokonts and Fungi)Fungi can live a saphrobes, parasites, predators, or as part of a mutualistic partnership. Fungi can be microsporidia (parasitic fungi originally not thought to be eukaryotes), dikarya (they two types are Ascomycota/sac fungi and basidiomycota/club fungi), chytrids (which are