Knoll Chapters 8 and 9

Merezhkovsky (1905) hypothesis

Algae and plant cells are chimeras of two independent organisms united in an obligatory and permanent partnership.

Chloroplast origin (Merezhkovsky)

Proposed that the chloroplast originated as a cyanobacterium swallowed by a protozoan.

A.F.W. Schimper's botanical observation

Noticed that chloroplasts grow and divide independently of the surrounding cells.

Schimper's rule of chloroplast generation

Chloroplasts spring always and only from other chloroplasts, and cannot be generated anew by the host cell.

Endosymbiosis

Two cells yoked in a mutually beneficial partnership, with one cell nested inside the other.

Lynn Margulis (1967)

Reinvented and championed the endosymbiotic hypothesis for eukaryotic cell origins in a paper that was initially rejected 15 times.

Margulis's addition to endosymbiotic theory

Proposed that mitochondria were also descended from free-living, respiring bacteria.

Darwinian evolution vs. Margulis's view

Darwin focused on branches diverging; Margulis argued for evolutionary novelty emerging as branches fused.

Electron microscopy support for endosymbiosis

Revealed that chloroplasts and cyanobacteria share a nearly identical common structural organization.

Biochemical support for endosymbiosis

Demonstrated that cyanobacteria and chloroplasts are nearly identical in the molecular details of photosynthesis.

Antibiotic response of chloroplasts

They respond to antibiotics exactly like bacteria do, unlike the host cell's nucleus and cytoplasm.

Molecular machinery of chloroplasts

They contain their own DNA, RNA, and ribosomes, allowing independent cellular growth and replication.

Membrane structure of red and green algal chloroplasts

They are uniquely surrounded by two membranes.

Outer chloroplast membrane origin

Synthesized by the surrounding cytoplasm following instructions from the host's nucleus.

Inner chloroplast membrane origin

Made by the chloroplast itself.

Eukaryotic endomembrane system

A dynamic continuity between the bounding cell membrane, the nuclear membrane, and internal cytoplasmic membranes.

Topological position of chloroplasts and mitochondria

They lie completely outside the enclosed space defined by the eukaryotic endomembrane system.

Genetic test of endosymbiosis

Gene sequence comparisons place chloroplast DNA clustered with cyanobacteria on the Tree of Life, not with plant nuclear genes.

First hurdle of endosymbiosis

The engulfing host cell must be prevented from digesting its bacterial guest.

Cyanobacterial symbiont's survival tactic

Leaked photosynthetic sugar to the host, which chemically inhibited the release of the host's digestive enzymes.

Host cell's contribution to the symbiont

Ensured a steady, localized supply of carbon dioxide and essential nutrients.

Coral bleaching

An ecological phenomenon that occurs when corals lose their endosymbiotic algae due to environmental stress like rising temperatures.

Genetic impoverishment of chloroplasts

Modern organelles contain less than 10 percent of the DNA found in free-living cyanobacteria.

Organelle functioning with lost genes

Chloroplasts rely on proteins that are encoded by the host nucleus, synthesized in the cytoplasm, and imported inside.

Chaperone proteins

Ancient molecules that initially helped proteins fold properly, but were later co-opted to ferry molecules across chloroplast membranes.

Chloroplast gene migration

Over evolutionary time, some functional chloroplast genes physically migrated into the host's nucleus.

Spread of photosynthesis across the eukaryotic tree

Gene tree comparisons show photosynthesis was acquired half a dozen separate times via repeated, distinct symbioses.

Cryptophytes

Small, temperate and high-latitude single-celled algae whose chloroplasts are uniquely surrounded by four membranes.

Nucleomorph

A small, DNA-containing dark body lying between the inner and outer membrane pairs of cryptophyte chloroplasts.

Sarah Gibbs's cryptophyte hypothesis

They gained photosynthesis via secondary endosymbiosis by swallowing an already-photosynthetic eukaryotic alga.

Gibbs's inner two membrane interpretation

They represent the two original chloroplast membranes of the engulfed algal symbiont.

Gibbs's outer two membrane interpretation

They represent the symbiont's outer cell membrane and the enveloping membrane synthesized by the captor.

Genetic affinity of the nucleomorph

Sequence testing proves its genes branch directly with the nuclear genes of red algae.

Primary endosymbiosis

The direct incorporation of a cyanobacterium by a eukaryotic cell (seen in red and green algae).

Secondary endosymbiosis

The incorporation of a photosynthetic eukaryote by another eukaryote (seen in cryptophytes and others).

Tertiary endosymbiosis

A host engulfing a secondary endosymbiont, observed in the evolutionary history of dinoflagellates.

Dinoflagellates

Common marine plankton and coral symbionts that acquired photosynthesis via complex tertiary endosymbiosis.

Lichens

Symbiotic, sometimes inseparable associations between fungi and green algae or cyanobacteria.

Tridacna

The giant tropical clam that successfully farms microscopic algal symbionts within its tissues.

Vertebrate symbiotic limitation

Animals with backbones do not seem capable of forming internal symbioses with photosynthetic microorganisms.

Mitochondria

The compartmentalized sites of aerobic respiration in eukaryotic cells.

Proteobacteria

The specific bacterial clade that shares deep structural, genetic, and biochemical similarities with mitochondria.

Ivan Wallin (1925)

Anatomist who correctly proposed mitochondria are bacterial, though he falsely claimed he could culture them independently in a lab.

Metabolic exchange of mitochondria

The host supplied sugar; the protomitochondrion returned massive amounts of energy as ATP.

Metabolic limitation of eukaryotes

They are generally restricted to photosynthesis, aerobic respiration, or fermentation, utilizing hijacked bacterial pathways.

Defining feature of eukaryotes

A membrane-bounded nucleus containing the cell's genes.

Eukaryotic chromosomes

Long strands of DNA wound tightly around tiny proteinaceous beads, linear rather than circular.

Golgi apparatus

Flattened sacs in eukaryotic cells involved in intracellular transport and cellular secretion.

Cytoskeleton

A highly dynamic internal cellular scaffolding built from filaments of actin and other proteins.

Evolutionary advantage of the cytoskeleton

Enabled early cells to dynamically change shape, capture prey, and engulf particles, making endosymbiosis mechanically possible.

Classical endosymbiotic prediction

The earliest eukaryotic branches on the Tree of Life should contain nucleated cells lacking mitochondria.

Mitchell Sogin

Biologist who pioneered the use of ribosomal RNA genes to map early eukaryotic phylogeny in the 1980s.

Giardia lamblia

A simple, mitochondria-free intestinal parasite initially thought to be a perfect model for primitive early eukaryotic cells.

Problem with using Giardia as a primitive model

Its highly simplified biology might simply be a secondary adaptation for parasitism rather than true ancient simplicity.

Entamoeba histolytica

An anaerobic parasite that lacks mitochondria but was found to contain nuclear genes of undeniable mitochondrial origin.

cpn60

The chaperone protein gene found in Entamoeba's nucleus, definitively proving it once possessed mitochondria and later lost them.

Ubiquity of early bacterial symbiosis

All known eukaryotic lineages, even those currently without mitochondria, show nuclear evidence of early proteobacterial symbiosis.

William Martin and Miklos Müller hypothesis (1998)

Eukaryotes originated from a primordial symbiosis between a methanogenic archaean and a fermenting/respiring proteobacterium.

Martin-Müller metabolic cycle

The methanogen produced organic molecules for the proteobacterium, which in turn provided hydrogen and CO2 back to the methanogen.

Martin-Müller explanation for the cytoskeleton

It evolved as a necessary internal stabilizer when the archaean methanogen shed its rigid cell walls to fully engulf its bacterial partner.

Derivation of eukaryotic genes (Martin-Müller)

Bacterially derived genes tend to control metabolism; archaeally derived genes tend to control transcription and translation.

Hydrogenosome

A specialized, DNA-free organelle that directs anaerobic metabolism in some mitochondria-free eukaryotes.

Miklos Müller's hydrogenosome hypothesis

Proposed they are highly reduced, gene-free organelles derived from ancient bacterial symbioses.

Trichomonas

A parasite whose nuclear genome contains translocated proteobacterial genes that encode proteins functioning specifically in its hydrogenosome.

Hydrogenosome's closest relative

Sequence comparisons of its telltale translocated nuclear genes show it is most closely related to mitochondria.

Hyman Hartman and Alexei Fedorov

Identified hundreds of eukaryotic signature genes absent in bacteria/archaea, suggesting a third, now-extinct aboriginal partner cell.

Microsporidia

Tiny parasites whose rapid mutation rates pushed them to the very base of early RNA trees, though total genome sequencing proves they actually nest higher up with fungi.

Guizhou Province, China

Location of modern phosphate mines containing exquisite, 3D-preserved late Proterozoic eukaryotic fossils.

Significance of Guizhou fossils

They definitively document the era when nucleated organisms finally broke the 2-billion-year ecological hegemony of bacteria.

Yangtze Gorges basal rocks

Red sandstones formed by meandering streams, firmly dated by a layer of volcanic ash to 748 million years old.

Nantuo Tillite

A poorly sorted mixture of boulders, sand, and silt lying directly above the red sandstones in southern China.

Evidence for Nantuo Tillite's glacial origin

The intimate mixing of vastly different sized particles, striated/scratched pebbles, and the presence of dropstones.

Dropstones

Isolated pebbles and cobbles plunged into finely laminated muds, dropped by melting icebergs rafting over the ancient ocean.

Doushantuo Formation

A roughly 590-600 million-year-old rock formation in China containing incredibly preserved, diverse eukaryotic fossils.

Age estimation of Doushantuo rocks

590 to 600 million years, calculated using radioactive uranium and lutetium locked inside phosphate crystals.

Problem with sizing Proterozoic fossils

Intermediate microfossil sizes commonly encountered in rocks strongly overlap between large bacteria and small eukaryotes, making size a poor diagnostic tool.

Bitter Springs Formation

830-810-million-year-old Australian rocks containing hollow spheres and "black spot" fossils originally misidentified.

Misinterpretation of "black spots"

Originally thought to be preserved eukaryotic nuclei, but taphonomy proves they are actually just shriveled balls of decaying organic cytoplasm.

Most reliable indicator of eukaryotic microfossils

Distinctive morphology and flamboyant, complex ornamentation that is simply not produced by bacteria.

Doushantuo upper chert microfossils

Large (up to 600 microns) spherical fossils uniquely decorated with flamboyant arms, spines, flanges, or knobs.

Probable identity of Doushantuo spiny microfossils

Reconstructed as the discarded, resting spore coats of eukaryotic algae.

Fate of the Doushantuo spiny microfossils

Disappeared entirely in one of Earth's earliest-known mass extinctions, possibly linked to climate shifts.

Chen Menge (1990)

Chinese paleontologist who discovered large, macroscopic eukaryotic fossils preserved as organic compressions in Doushantuo black shales.

Miaohephyton

A Doushantuo compression fossil reconstructed as a grass-like, branching seaweed that formed dense lawns on the ancient seafloor.

Preservation mechanism of Miaohe compressions

Rapid burial in fine clay that tightly excluded oxygen and adsorbed the destructive decay enzymes of bacteria.

Burgess Shale

The famous Middle Cambrian deposit known for complex animal compressions, postdating the Doushantuo beds by 50-85 million years.

Key absence in Doushantuo compressions

Despite a perfect preservational window, they show absolutely no evidence of the complex animal anatomies found in the Burgess Shale.

Zhang Yun

Paleontologist who pioneered the collection and study of Doushantuo multicellular algal fossils from Guizhou phosphate mines.

Guizhou phosphate preservation mechanism

Biological remains were coated almost instantly by calcium phosphate crystals, perfectly preserving internal 3D cellular anatomy.

Cell fountain

An anatomical organization of thick-walled cells arranged in rows fanning outward, characteristic of red algae and found perfectly preserved in Doushantuo phosphates.

Significance of Doushantuo algal fossils

They prove that complex, tissue-forming multicellularity in algae was well established before the rise of large animals.

Weng'an balls

400-500 micron uniform spherical fossils in Doushantuo phosphate containing distinct, geometric cell divisions.

Shuhai Xiao's identification of Weng'an balls

Successfully recognized them as animal eggs and embryos captured in early stages of cell cleavage.

Closest modern analogue to Weng'an cleavage patterns

Arthropods and related invertebrates.

Evolutionary status during Doushantuo time

Animal evolution was just beginning with simple embryos and sponges, but the true "age of animals" was still tens of millions of years away.

Oldest definitive green algae fossils

700-800-million-year-old Spitsbergen microfossils closely related to the extant branching genus Cladophora.

Somerset Island fossils

1.2 billion-year-old Canadian chert fossils discovered by Nick Butterfield, representing the oldest confident, complex eukaryotic fossils.

Morphology of Somerset Island fossils

Filaments of aspirin-shaped cells featuring specialized holdfasts and pie-wedge reproductive bodies, linking them definitively to red algae.

Lakhanda Formation fossils

Simple branching filaments older than 1 billion years from Siberia that strongly resemble modern heterokont Vaucheria algae.

Grand Canyon biomarkers (750 Ma)

Extracted lipid molecules that preserve chemical signatures specifically for dinoflagellates and ciliate protozoans.