AP Biology, Chapter 28
The Origins of Eukaryotic Diversity

Summary
Introduction

INTRODUCTION TO THE PROTISTS
	Introduction
	Systematists have split protists into many kingdoms
		1. Explain the historical and current difficulties in classifying members of the kingdom 
		Protista.
			a. Historical
				i. Motile heterotrophs were put in Animalia
				ii. Sessile with a cell wall were put in Plantae
			b. Current difficulties
				i. Kingdom Protista was paraphyletic
				ii. Now split into as many as 20
	Protists are the most diverse of all eukaryotes
		2. Explain why protistan cells are not analogous to a single cell from a multicellular 
		organism.
			a. Multicellular cells are specialized
			b. Many protistan cell show elaborate adaptations for performing all life  
			functions 
		3. Describe the different nutritional strategies of protists.	
			a. Most are aerobic with mitochondria
			b. Some are heterotrophs, some autotrophs, some mixotrophs
		4. Describe the three ecological categories of protists. Explain why the terms "protozoa" 
		and "algae" have little usefulness.
			a. Categories
				i. Ingestive protozoa with a variety of means of locomotion
				ii. Absorptive, like fungi
				iii. Photosynthetic algae with a variety of pigments
			b. Both protozoa and algae are non-clade designations
		5. Distinguish between prokaryotic and eukaryotic flagella.
			a. Prokaryotic
				i. Stiff, helical, proteinaceous
				ii. Attached to cell surface by a proton-driven rotor
			b. Eukaryotic
				i. Flexible with 9+2 microtubules and covered by a membrane
				ii. Generates force internally using ATP
		6. Describe the general protistan life cycles and habitats.
			a. Life cycles
				i. Most can reproduce asexually; many also sexually
				ii. Haploids are the main vegetative stage in most
				iii. Many form cysts in harsh conditions
			b. Habitats
				i. Most are aquatic as free-living bottom dwellers or plankton
				ii. Many are symbionts

THE ORIGIN AND DIVERSIFICATION OF EUKARYOTES
	Introduction
	Endomembranes contributed to larger, more complex cells
		7. Describe three evolutionary trends that occurred as some prokaryotic groups became 
		increasingly complex.
			a. Multicellularity as in cyanobacteria
			b. Complex communities of mutualistic prokaryotes
			c. Intracellular compartmentalization of function
	The eukaryotic cell is a chimera of prokaryotic ancestors
		8. Describe the evidence that supports the theory that mitochondria and plastids 
		evolved by serial endosymbiosis. Explain what living organisms are the likely relatives of 
		the prokaryotes that gave rise to mitochondria and plastids.
			a. Modern endosymbiotic relationships
			b. Similarities between bacteria and mitochondria and chloroplasts
				i. Cell / organelle size
				ii. Prokaryote-type membrane components
				iii. Replication by binary fission
				iv. Single, circular DNA without histones
				v. Similar transcriptional and translational apparatus
			c. Mitochondria most resemble proteobacteria; plastids cyanobacteria
		9. Given the endosymbiosis theory, explain the modern collaboration between the 
		genome of the organelles and nucleus.
			a. Genes have been transferred from the organelle to the nucleus
			b. Transfer is common among prokaryotes
	Secondary endosymbiosis increased the diversity of algae
		10. Explain the diversity of plastids and the phylogenetic discontinuity of photosynthesis 
		among protists.
			a. Multiple endosymbiotic fusions
			b. Explains >2 membranes around some algal plastids
			c. Vestigial evidence in cryptomonad plastids
				i. Nucleomorph is vestigial nucleus
				ii. Retains cytoplasmic and plastid ribosomes
		11. Explain why the evolutionary origin of the eukaryotic cell doesn't easily fit within the 
		traditional model of an evolutionary tree. Describe the reasons for the new weblike 
		phylogeny and the problem of assigning groups to kingdoms and phyla.
			a. Gene transfer is pervasive
				i. All are chimeras
				ii. All braches show results of horizontal genetic transfer
			b. Reasons for weblike phylogeny
				i. Gene transfer into nuclei not just from mitochonria/chloroplasts
				ii. No single common ancestor but an ancestral community 

A SAMPLE OF PROTISTAN DIVERSITY
	Diplomonadida and Parabasala: Diplomonads and parabasalids lack mitochondria
		12. Describe the current hypothesis for the lack of mitochondria in diplomonads and 
		parabasalids.
			a. Had them once but lost them
			b. They have mitochondrial sequences in the nucleus
		13. Describe the structure, ecology, and human impact of diplomonads, parabasalids, 
		euglenoids, kinetoplastids, dinoflagellates, apicomplexans, ciliates, stramenopiles, 
		heterokont algae, oomycotes, bacillariophytes, chrysophytes, phaeophytes, 
		rhodophytes, and chlorophytes.
			a. Structure suggests doubled cells
				i. Multiple flagella
				ii. Two separate nuclei
				iii. Simple cytoskeleton
				iv. No plastids
			b. Ecology
				i. Diplomonads are intestinal parasites (Giardia)
				ii. Parasabalids can be infectious and sexually transmitted 
				(Trichomonas)
	Euglenozoa: The euglenozoa includes both autotrophic and heterotrophic 
	flagellates
			a. Structure
				i. Euglenoids
					.Flagellated from an anterior pocket
					.Glucose stored as paramylon
					.Pigments are similar to green algae and plants
				ii. Kinetoplastids
					.One large mitochondrion associated with a kinetoplast
			b. Ecology and human impact
				i. Euglenoids; free-living and mixotrophic
				ii. Kinetoplastids
					.Some are symbiotic
					.Some parasitic: Trypanosoma, sleeping sickness and Chagas' 
					disease 
	Alveolata: The alveolates are unicellular protists with subsurface cavities (alveoli)			a. Structure
				i. Superficial membrane-bound cavities form a pellicle or armor
				ii. Characteristic flagella or cilia; tubular cristae
			b. Ecology and human impact
				i. Dinoflagellata
					.Important unicellular phytoplankton
					.Cellulose armor plates with flagella in a groove
					.Blooms = red tides; produce toxins (Pfiestreria)
					.Some are bioluminescent
					.Some mutualistic associations with coral		
				ii. Apicomplexa (formerly Sporozoa)
					.Parasites  Plasmodium causes malaria
					.Haploid sporozoites spread to humans by mosquito
					.Infect the liver and divide to form merozoites
					.Merozoites infect and destroy RBCs
					.Develop into male and female gametes
					.Fertilization and meiosis take place back in the mosquito
				iii. Ciliophora
					.Mainly ciliated freshwater unicellular heterotrophs
					.Divide by binary fission, not mitosis
					.Complex sexual cycle = conjugation
						.One somatic macro-, one or more regenerative 
							micronuclei
						.Compatible cells fuse
						.Micronuclei undergo meiosis
						.Cells swap haploid micronuclei, then they fuse
						.Diploid micronuleus divides by mitosis
						.Macronucleus is replaced
					.Complex cell structures: contractile vacuole, oral groove
	Stramenopila: The stramenopile clade includes the water molds and the heterokont 
	algae
			a. Structure
				i. Stramen (flagella), pilos (hair)  hairy flagella
				ii. Mainly paired with a smooth flagella  heterokont
				iii. Zoospores only in most
				iv. Heterokont plastids have four membranes
			b. Ecology and human impact
				i. Oomycota
					.Unicellular or mycelial heterotrophs
					.Coenocytic = one cytoplasm, many nuclei
					.Cellulose cells walls
					.Large oogonium on mycelium
					.Mainly decomposers; water molds
					.Plant diseases: downy mildew, potato blight
				ii. Bacillariophyta (Diatoms)
					.Yellow or brown, silica cell walls
					.Store food as laminarin or oil
					.Important as phytoplankton; large deposits are mined
				iii. Chrysophyta (Golden Algae)
					.Two flagella at one end of the cell
					.Mainly are phytoplankton, some are mixotrophs
				iv. Phaeophyta (Brown Algae)
					.Multicellular, mostly marine
					.Common large brown seaweeds
	Structural and biochemical adaptations help seaweeds survive and reproduce at the 
	ocean's margins
					.Thallus: holdfast, stipe, blades
					.Mainly coastal
					.Harvested for food, food additives, etc.
	Some algae have life cycles with alternating multicellular haploid and diploid 
	generations
		14. Describe a life cycle including an alternation of multicellular generations.
			a. Diploid sporophyte makes haploid zoospores
			b. Haploid gametophyte makes gametes
			c. Zygote gives rise to sporophyte 
	Rhodophyta: Red algae lack flagella
			a. Structure
				i. No flagellated stage
				ii. Most are multicellular
				ii. Red pigment is phycoerythrin
			b. Ecology and human impact
				i. Pigments ratios are adapted for depth
				ii. Marine, freshwater and soils
				iii. Harvested for food
	Chlorophyta: Green algae and plants evolved from a common photoautotrophic 
	ancestor
			a. Structure
				i. Chloroplasts by primary endocytosis as in plants
				ii. Forms and examples
					.Unicellular flagellated Chlamydomonas 
					.Colonial Volvox
					.Multicellular Ulva
			b. Ecology
				i. Freshwater and marine
				ii. Lichens = green algae + fungi
	A diversity of protists use pseudopodia for movement and feeding
		15. Describe the similarities and distinct characteristics of the rhizopods, actinopods, 
		and foraminifera.
			a. Phylogeny
				i. Pseudopodia do not define a clade
				ii. Relation of the following groups is in question
			b. Rhizopoda (Amoebas)
				i. Unicellular amoebae; ex., Amoeba proteus
				ii. Some have a protein shell
				iii. Habitats: freshwater, marine, soil, parasitic (Entamoeba histolytica)
			c. Actinopoda (Heliozoans and Radiolarians)
				i. Name means "ray foot"; thin, pointy, radial pseudopodia
				ii. Silica or chitinous shells
				ii. Habitat: mostly planktonic
			d. Foraminifera (Forams)
				i. Multichambered, coiled, calcium carbonate shells with tiny holes
				ii. Habitats: marine, some with symbiotic algae
				iii. Very important standards in the fossil record
	Mycetozoa: Slime molds have structural adaptations and life cycles that enhance 
	their ecological role as decomposers
		16. Describe the adaptations of Mycetozoa that facilitate their role as decomposers.
			a. Heterotrophs moving and feeding using pseudopods
			b. Molecular data: closer to fungi and animals than other former protists
		17. Compare the life cycles and ecology of plasmodial and cellular slime molds.
			a. Myxogastrida (Plasmodial Slime Molds) (formerly Myxomycota)
				i. Large (up to 100cm?) multinucleate cell
				ii. Synchronous mitosis without cytokinesis
				iii. In harsh conditions erects fruiting bodies (sporangia)
				iv. Meiosis in sporangium gives amoboid or flagellated hapoid cells
				v. Syngamy yeilds zygote  plasmodium
			b. Dictyostelida (Cellular Slime Molds)
				i. Feed as individual haploid, uninucleate amoebae
				ii. In harsh conditions they aggregate to form a migrating slug
				iii. Slug attaches and form asexual fruiting body
				iv. Haploid amoebae can fuse, followed by meiosis
	Multicellularity originated independently many times