First two major clades of the Eukarya

alveolata.md

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+# Alveolata
+

apicomplexa.md

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+# Apicomplexa
+
+- Members of the [[Alveolata]] [[pyhlum]] of the [[SAR Supergroup]]
+- Plasmodium Falciparum
+  - Causes malaria
+- Toxoplasma Gondii
+  - Normal cycle of infection revolves around mice and house cats
+  - Makes mice act arrogant around predators to transmit to cats
+  - Cat feces carries the parasite, which ends up being transmitted to mice
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Alveolata]: alveolata "Alveolata"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"
+

archaea.md

@@ -23,6 +23,7 @@
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
 [bacteria]: bacteria "Bacteria"
+[eukarya]: eukarya "Eukarya"
 [Lokiarchaeota]: lokiarchaeota "Lokiarchaeota"
 [TACK Supergroup]: tack-supergroup "TACK Supergroup"
 [Archaea]: archaea "Archaea"
@@ -30,4 +31,5 @@
 [Korarchaeota]: korarchaeota "Korarchaeota"
 [Thaumarchaeota]: thaumarchaeota "Thaumarchaeota"
 [Crenarchaeota]: crenarchaeota "Crenarchaeota"
+[Eukarya]: eukarya "Eukarya"
 [//end]: # "Autogenerated link references"

brown-algae.md

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+# Brown algae
+
+- Members of the [[Heterokonta]] [[phylum]] of the [[SAR Supergroup]]
+- Macrocystis Pyrifera
+  - Giant kelp
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Heterokonta]: heterokonta "Heterokonta"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"

ciliophora.md

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+# Ciliophora
+
+- Members of the [[Alveolata]] [[pyhlum]] of the [[SAR Supergroup]]
+- Have hundreds to thousands of cilia used for feeding and mobility
+- Abundant and diverse in most aquatic habitats
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Alveolata]: alveolata "Alveolata"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"

cyanobacteria.md

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 # Cyanobacteria
 
-- Responsible for The Great Oxygenation
+- Responsible for [[The Great Oxygenation]]
 - [[Spirulina]]: Highly nutritious
 - [[Rivularia]]: Classifies as multi-cellular, as it can regrow its
 photosynthetic filament
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[The Great Oxygenation]: the-great-oxygenation "The Great Oxygenation"
+[//end]: # "Autogenerated link references"

diatoms.md

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+# Diatoms
+
+- Members of the [[Heterokonta]] [[phylum]] of the [[SAR Supergroup]]
+- Photosynthetic algae, with silica-rich shells
+  - When diatomaceous earth is exposed, silica can be harvested from the
+  remains of diatoms
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Heterokonta]: heterokonta "Heterokonta"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"

dinoflagellata.md

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+# Dinoflagellata
+
+- Members of the [[Alveolata]] [[pyhlum]] of the [[SAR Supergroup]]
+- Associated with red tides
+  - Lingulodinium Polyedrum
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Alveolata]: alveolata "Alveolata"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"

diplomonadida.md

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+# Diplomonadida
+
+- Members of the [[Metamonada]] [[phylum]] of the [[Excavata]]
+- Giardia Intestinalis
+  - Relatively common in wildlife
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Metamonada]: metamonada "Metamonada"
+[Excavata]: excavata "Excavata"
+[//end]: # "Autogenerated link references"

endosymbiosis.md

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+# Endosymbiosis
+

euglenozoa.md

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+# Euglenozoa
+
+- Members of the [[Excavata]]
+- Euglena Gracilis
+  - Photosynthetic, free-living
+- Typanosoma Cruzi (Chagas Disease) and Trypanosoma Brucei (African Sleeping
+Sickness)
+  - Nonphotosynthetic, parasitic
+  - Transmitted by arthropod vectors
+  - Because they're eukaryotic and aerobic, they're hard to target with
+  medication
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Excavata]: excavata "Excavata"
+[//end]: # "Autogenerated link references"

eukarya.md

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+# Eukarya
+
+- There are two parts to the origin of eukaryotic cells:
+  - [[Endosymbiosis]]: Theorized by [[Lynn Margulis]], proposes that
+  mitochondria, along with other eukaryotic organelles, first existed as
+  independent organisms
+  - [[Endomembrane System]]: Documented by [[Christian de Duve]], the
+  endomembrane system involves parts of organelles specific to eukaryotic
+  organelles, such as the nuclear envelope
+- In eukaryotes, [[mitochondria]] have separate DNA from the nuclear genome,
+which is evidence for [[Endosymbiosis]]
+
+## Taxonomy
+
+- [[Eukarya]]
+  - Bikonta
+    - [[Excavata]]
+      - [[Euglenozoa]]
+      - [[Metamonada]]
+        - Trichozoa
+          - [[Diplomonadida]]
+          - [[Parabasalia]]
+    - Diaphoretickes
+      - [[SAR Supergroup]]
+        - Rhizaria
+          - Cercozoa
+          - Retaria
+            - Foraminifera
+            - Radiolaria
+        - Halvaria
+          - [[Alveolata]]
+            - [[Ciliophora]]
+            - Myzozoa
+              - [[Apicomplexa]]
+              - [[Dinoflagellata]]
+          - [[Heterokonta]] (Stramenopiles)
+            - [[Diatoms]]
+            - [[Oomycota]]
+            - [[Brown algae]]
+      - [[Archaeplastida]]
+        - Red algae
+        - Viridiplantae
+          - Chlorophyta
+          - Streptophyta
+            - Charophyta
+            - Embryophyta (land plants)
+  - [[Unikonta]]
+    - Amoebozoa
+      - Tubulinea
+      - Entamoeba
+      - Eumycetozoa (slime molds)
+    - Opisthokonta
+      - Holomycota
+        - Nucleariida
+        - Fungi
+      - Holozoa
+        - Choanoflagellatea
+        - Animalia
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Endosymbiosis]: endosymbiosis "Endosymbiosis"
+[mitochondria]: mitochondrion "mitochondrion"
+[Eukarya]: eukarya "Eukarya"
+[Excavata]: excavata "Excavata"
+[Euglenozoa]: euglenozoa "Euglenozoa"
+[Metamonada]: metamonada "Metamonada"
+[Diplomonadida]: diplomonadida "Diplomonadida"
+[Parabasalia]: parabasalia "Parabasalia"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[Alveolata]: alveolata "Alveolata"
+[Ciliophora]: ciliophora "Ciliophora"
+[Apicomplexa]: apicomplexa "Apicomplexa"
+[Dinoflagellata]: dinoflagellata "Dinoflagellata"
+[Heterokonta]: heterokonta "Heterokonta"
+[Diatoms]: diatoms "Diatoms"
+[Oomycota]: oomycota "Oomycota"
+[Brown algae]: brown-algae "Brown algae"
+[//end]: # "Autogenerated link references"

excavata.md

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+# Excavata
+

heterokonta.md

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+# Heterokonta
+
+- A [[phylum]] of the [[SAR Supergroup]] with two kinds of flagella
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"

metamonada.md

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+# Metamonada
+
+- A [[phylum]] of the [[Excavata]] which lacks [[mitochondria]]
+  - This means they're adapted to anaerobic environments
+- Includes  [[Diplomonadida]] and [[Parabasalia]]
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Excavata]: excavata "Excavata"
+[mitochondria]: mitochondrion "mitochondrion"
+[Diplomonadida]: diplomonadida "Diplomonadida"
+[Parabasalia]: parabasalia "Parabasalia"
+[//end]: # "Autogenerated link references"

mitochondria.md

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+# mitochondria
+

mitochondrion.md

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+# mitochondrion
+

oomycota.md

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+# Oomycota
+
+- Members of the [[Heterokonta]] [[phylum]] of the [[SAR Supergroup]]
+- Heterotrophic and fungus-like
+- Fish parasites
+- Phytophthora Infestans
+  - Cause of Irish Potato Famine
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Heterokonta]: heterokonta "Heterokonta"
+[SAR Supergroup]: sar-supergroup "SAR Supergroup"
+[//end]: # "Autogenerated link references"

parabasalia.md

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+# Parabasalia
+
+- Members of the [[Metamonada]] [[phylum]] of the [[Excavata]]
+- Flagellated anaerobes, living within anaerobic spaces within other animals
+- Mixotricha Paradoxa
+  - Found in the gut of termites
+  - Cellulose is not digestable by most animals
+  - Mixotricha Paradoxa can break down cellulose before the termite digests it
+    - Mixotricha Paradoxa doesn't produce cellulase
+    - Unclear whether the termite actually digests the Mixotricha Paradoxa or
+    lets it live
+  - Uses own flagellum as rudders, while [[spirochetes]] power the movement
+- Trichomonas Vaginalis
+  - Agent of STD in humans
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[Metamonada]: metamonada "Metamonada"
+[Excavata]: excavata "Excavata"
+[spirochetes]: spirochaeota "Spirochaeota"
+[//end]: # "Autogenerated link references"

sar-supergroup.md

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+# SAR Supergroup
+
+

the-great-oxygenation.md

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+# The Great Oxygenation
+
+- The diverity of [[bacteria]] exploded during the [[Archaean]], leading to the
+evolution of [[Cyanobacteria]]
+  - This does not mean that [[Spirulina]] existed during the [[Archaean]]: it
+  is a modern organism
+- There was almost no O₂ in the atmosphere before the
+[[Archaean]]-[[Proterozoic]] break
+  - No O₂ means no formation of peroxides
+  - Peroxides are dangerous to many cells as they rob electrons from
+  proteins, fatally altering them
+- Cells had to develop anti-oxidation defenses, including [[catalase]]
+- Cells had two ways to adapt to O₂
+  1. Become a strict anaerobe, and avoid oxygen-containing habitats
+  2. Tolerate O₂
+     - O₂ toleration can easily lead to aerobic metabolism
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[bacteria]: bacteria "Bacteria"
+[Archaean]: archaean "Archaean"
+[Cyanobacteria]: cyanobacteria "Cyanobacteria"
+[Proterozoic]: proterozoic "Proterozoic"
+[//end]: # "Autogenerated link references"