1. CHAPTER 26 Early Earth and the Origin of Life
Figure A painting of early Earth showing volcanic activity and photosynthetic prokaryotes in dense mats
CHAPTER 26 Early Earth and the Origin of Life
Time line: Introduction to the History of Life
1. Life on Earth originated between 3.5 and 4.0 billion years ago
2. Prokaryotes dominated evolutionary history from 3.5 to 2.0 billion years ago
3. Oxygen began accumulating in the atmosphere about 2.7 billion years ago
4. Eukaryote life began by 2.1 billion years ago
5. Multicellular eukaryotes evolved by 1.2 billion years ago
6. Animal diversity exploded during the early Cambrian period
7. Plants, fungi, and animals colonized the land about 500 million years ago

2. Figure 26 Volcanic activity and lightning associated with the birth of the island of Surtsey near Iceland; terrestrial life began colonizing Surtsey soon after its birth
Geologic events that alter environments have changed the course of biological evolution.
For example, the formation and subsequent breakup of the supercontinent Pangea has a tremendous impact on the diversity of life.
Conversely, life has changed the planet it inhabits.
The evolution of photosynthetic organisms that release oxygen into the air had a dramatic impact on Earth’s atmosphere.
Much more recently, the emergence of Homo sapiens has changed the land, water, and air on a scale and on a rate unprecedented for a single species.
Historical study of any sort is an inexact discipline that depends on the preservation, reliability, and interpretation of past records.
The fossil record of past life is generally less and less complete the farther into the past we delve.
Fortunately, each organism alive today carries traces of its evolutionary history in its molecules, metabolism, and anatomy.
Still, the evolutionary episodes of greatest antiquity are the generally most obscure.

3. Phylogenetic trees: Timeline and order of events that shaped evolution of life. Branch points show derived characteristics unique to each group/clade.
Life is a continuum extending from the earliest organisms through various phylogenetic branches to the great variety of forms alive today.
The diversification of life on Earth began over 3.8 billion ago.
Fig. 26.1

4. Alternatively, we can view these episodes with a clock analogy.
Fig. 26.2

5. Origin of life (4 billion - 3.5 billion years ago)
Earth formation billion years ago - hostile to life - asteroids, volcanoes, water vaporized
Oldest fossils - Australia billion years old (bacteria like); evidence of earth cooling to a temp. when liquid water persisted.
For the first three-quarters of evolutionary history, Earth’s only organisms were microscopic and mostly unicellular.
The Earth formed about 4.5 billion years ago, but rock bodies left over from the origin of the solar system bombarded the surface for the first few hundred million years, making it unlikely that life could survive.
No clear fossils have been found in the oldest surviving Earth rocks, from 3.8 billion years ago.
The oldest fossils that have been uncovered were embedded in rocks from western Australia that are 3.5 billion years ago.
The presence of these fossils, resembling bacteria, would imply that life originated much earlier.
This may have been as early as 3.9 billion years ago, when Earth began to cool to a temper- ature at which liquid water could exist.

6. First living organisms - prokaryotes (3.5 - 2 million years ago)
The fossil record supports the hypothesis that the earliest organisms were prokaryotes.
Relatively early, prokaryotes diverged into two main evolutionary branches, the bacteria and the archaea.
Representatives from both groups thrive in various environments today.
This indicates that the metabolism of prokaryotes was already diverse over 3 billion years ago.
Proof: Prokaryote fossils - stromatolites (fossilized layered microbial mats) and sediments from ancient hydrothermal vent (deep ocean vents) habitats.

7. Figure 26.4 Bacterial mats and stromatolites

8. Figure 26.4x Stromatolites in Northern Canada

10. Early life did not use light/split water - they were chemoautotrophs
1. Photoautotrophs
2. Photoheterotrophs- obtains organic carbon, uses light to generate ATP.
3. Chemoautotroph- needs CO2 as carbon source and obtains energy by oxidizing inorganic compounds ( H2S, NH3, and Fe++
4. Chemoheterotroph- most bacteria are this.
Chemistry and life in unique environments:
1. What if you have NO organic molecules and NO sunlight?
--Oxidizing Fe--
In mine tailings (which are very acidic), iron-oxidizing bacteria--Thiobacillus ferrooxidans--thrive.
2. What if you have NO sunlight, NO organic molecules and NO acidic?
--Hydgrogen Reducing--
Fe + H2O ---> Hydrogen gas
6H2 + 2O2 + CO2 ---->CH2O + 5H2O + Energy
(where 6H2 is hydrogen gas)
Hydrogen gas comes from the oxidation of Iron by the groundwater located deep within the Columbia River Basalts.
This hydrogen gas is then used by the bacteria living at more than 1 km below the surface to convert dissolved inorganic carbon into energy.
Unlike the Thiobacillus ferrooxidans, acidic conditions are not necessary to slow down the iron oxidation.
This is an ecosystem that can exist without sunlight, or organically processed carbon. The bacteria exist completely independent of surface life. This ecosystem is referred to as being autotrophic (needing neither organic sources of carbon or photosynthesis to survive).
Would the bacteria in this example survive a great asteroidal impact?
Probably. Because their survival is not predicated on the Earth's surface viability.
*Both #1 & #2, are examples of bacteria that obtain their energy by oxidizing iron.
Some other examples of alternative energy for biota:
3. Sulfate based bacteria:
H2SO4 + 4H2 ----> H2S + 4H2O
(where H2SO4 is sulphate and 4H2 is hydrogen gas)
4. Methanogenic bacteria can use:
CO2 + 4H2 ----> CH4 + 2H2O
OR:
4CO + 2H2O ---->CH4 +3CO2
5. Acetalyne based bacteria:
2CO2 + 4H2 ----> CH3COOH + 2H2O
6. Iron-reducing bacteria or Hydrogen-oxidizing bacteria
2Fe+3 + H2 ----> 2Fe+2 +2H+
An interesting example of an iron-reducing bacteria (or hydrogen-oxidizing) are the hyperthermophilic species. These bacteria thrive in extremely hot environments such as 80°--125°C water. They can be found at mid-ocean vents or in hot springs like the ones in Yellowstone, WY (both locations associated with past or recent volcanic activity).
The bacteria that live in mid-ocean spreading areas get their carbon from the seawater, but their major source of energy is the atmospheric CO2 that has dissolved in the oceans (recall the CO2 feedback cycle). The CO2 is from inorganic sources; photosynthesis is not used. The bacteria in this environment are thus referred to as chemoautotrophs.
The bacteria that live in hot springs, such as the ones in Yellowstone Park displays itself in vivid colors. These bacteria are photosynthetic.
Energy for synthesis of organic compounds came from chemicals - iron, H2S, NH3
H2S > 2H+ + S

11. Oxygen began accumulating 2.7 billion years ago
Photosynthesis probably evolved very early in prokaryotic history.
Cyanobacteria, photosynthetic organisms that split water and produce O2 as a byproduct, evolved over 2.7 billion years ago.
Bacteria in yellow stone…. This early oxygen initially reacted with dissolved iron to form the precipitate iron oxide.
This can be seen today in banded iron formations.
About 2.7 billion years ago oxygen began accumulating in the atmosphere and terrestrial rocks with iron began oxidizing.

12. Figure 26.5 Banded iron formations are evidence of the vintage of oxygenic photosynthesis

13. 
Cyanobacteria
cyanobacteria

14. This “corrosive” O2 had an enormous impact on life, dooming many prokaryote groups. (OXYGEN KILLS!)
Some species survived by remaining anaerobic.
Others evolved mechanisms to use O2 in cellular respiration - DO or DIE!
While oxygen accumulation was gradual between 2.7 and 2.2 billion years ago, it shot up to 10% of current values shortly afterward.

15. Eukaryotic life began by 2.1 billion years ago
Eukaryotic cells are generally larger and more complex than prokaryotic cells.
This is due to the “endosymbiotic prokaryotes” that evolved into mitochondria and chloroplasts - major event in eukaryotic evolution
While there is some evidence of earlier eukaryotic fossils, the first clear eukaryote appeared about 2.1 billion years ago.
Other evidence places the origin of eukaryotes to as early as 2.7 billion years ago.
This places the earliest eukaryotes at the same time as the oxygen revolution that changed the Earth’s environment so dramatically.
The evolution of chloroplasts may be part of the explanation for this temporal correlation.
Another eukaryotic organelle, the mitochondrion, turned the accumulating O2 to metabolic advantage through cellular respiration.
In the above diagram taken from Gilson’s et al paper in PNAS, you can see the process that led to what is known as the nucleomorph of the chlorarachniophyte (uf…).
In a nutshell, an eukariotic cell (Euk 1) engulfed a prokaryotic photosynthesising cell establishing a symbiotic relationship (1 endosymbiosis), the common one among plants and algae. A second eukaryote (Euk2) swallowed this first endosymbiont leaving a cell with two nucleus (Nu1 and Nm) and a prokaryotic chromosome (within Pl). Well, what was Nu1 is the nucleomorph (Nm) and has undergone massive genome reduction.
In the aforementioned paper, they sequenced the Nm of Bigelowiella natans (a chlorarachniophyte), and they found that it was only 373,000 bp. which is smaller than the smallest sequenced prokaryote. The funny thing is that this tiny genome belongs to what once was a free-living organism, now most of the genes have been either lost or transfered to the main nucleus.
It is hypothesised that with the time the main nucleus (Nu2) will end up acquiring all the genes needed to maintain the plasmid, which is really what matters!. By that time the nucleomorph might end up being lost and we could find plastids with three or four membranes. This might explain why some groups such as dinoflagellates, euglenoids, haptophytes, diatoms, brown algae, chrysophytes and apicomplexan have these “multimembraned” plastids; maybe they underwent secondary endosymbioses and “got rid” of the nucleomorph.
So, we are now, to our evolutionary delight, in an intermediate stage of this reductive process.

16. Multicellular eukaryotes evolved by 1.2 billion years ago
Multicellular organisms, differentiated from a single-celled precursor.
Snowball hypothesis - earth covered in ice from 750 to 570 million years ago; prevented eukaryotic diversification in that period
Life stayed in parts where ice did not reach - deep sea vents/hot springs
Late Precambrian/Early Cambrian - diversification of eukaryotes started (thawing of snowball!)
A great range of eukaryotic unicellular forms evolved into the diversity of present-day “protists.”
Geologic evidence for a severe ice age (“snowball Earth” hypothesis) from 750 to 570 million years ago may be responsible for the limited diversity and distribution of multicellular eukaryotes until the very late Precambrian.
During this period, most life would have been confined to deep-sea vents and hot springs or those few locations where enough ice melted for sunlight to penetrate the surface waters of the sea.
The first major diversification of multicellular eukaryotic organisms corresponds to the time of the thawing of snowball Earth.
A second radiation of eukaryotic forms produced most of the major groups of animals during the early Cambrian period.
Cnidarians (the phylum that includes jellies) and poriferans (sponges) were already present in the late Precambrian.
Fig. 26.6

17. China - beautifully preserved animal embryos.
Recent fossil finds from China have produced a diversity of algae and animals from 570 million years ago, including beautifully preserved embryos.
Fig. 26.7

18. Animal diversity exploded during Cambrian period
However, most of the major groups (phyla) of animals make their first fossil appearances during the relatively short span of the Cambrian period’s first 20 million years.

19. Plants, fungi, and animals colonized the land about 500 million years ago
Colonization of land - important event in evolution - plants (with fungi) moved onto land and animals followed
Cyanobacteria and other photosynthetic prokaryotes coated damp terrestrial surfaces well over a billion years ago.
Terrestrial adaptations for land dwelling (later)
There is fossil evidence that cyanobacteria and other photosynthetic prokaryotes coated damp terrestrial surfaces well over a billion years ago.
However, macroscopic life in the form of plants, fungi, and animals did not colonize land until about 500 million years ago, during the early Paleozoic era.
The gradual evolution from aquatic to terrestrial habitats required adaptations to prevent dehydration and to reproduce on land.
For example, plants evolved a waterproof coating of wax on the leaves to slow the loss of water.
Plants colonized land in association with fungi.
Fungi aid the absorption of water and nutrients from the soil.
The fungi obtain organic nutrients from the plant.
This ancient symbiotic association is evident in some of the oldest fossilized roots.

20. Land Plants ----> herbivores ---> carnivores
Most diverse award: Arthropods (including insects and spiders) and certain vertebrates (including amphibians, reptiles, birds, and mammals).
Modern mammals, including primates, appeared million years ago.
Humans diverged from other primates only 5 million years ago
TETRAPODS
Plants created new opportunities for all life, including herbivorous (plant-eating) animals and their predators.
The most widespread and diverse terrestrial animals are certain arthropods (including insects and spiders) and certain vertebrates (including amphibians, reptiles, birds, and mammals).
Most orders of modern mammals, including primates, appeared million years ago.
Humans diverged from other primates only 5 million years ago
The terrestrial vertebrates, called tetrapods because of their four walking limbs, evolved from fishes, based on an extensive fossil record.
Reptiles evolved from amphibians; both birds and mammals evolved from reptiles.

21. Evolution of the first cells: chicken or egg problem
Nonliving materials became ordered into aggregates that were capable of self-replication and metabolism.
Greeks - spontaneous generation (life from nonlife); not correct!
The first cells may have originated by chemical evolution on a young Earth: an overview
Most scientists favor the hypothesis that life on Earth developed from nonliving materials that became ordered into aggregates that were capable of self-replication and metabolism.
From the time of the Greeks until the 19th century, it was common “knowledge” that life could arise from nonliving matter, an idea called spontaneous generation.
While this idea had been rejected by the late Renaissance for macroscopic life, it persisted as an explanation for the rapid growth of microorganisms in spoiled foods.
Observation: Every year in the spring, the Nile River flooded areas of Egypt along the river, leaving behind nutrient-rich mud that enabled the people to grow that year’s crop of food. However, along with the muddy soil, large numbers of frogs appeared that weren’t around in drier times.
Conclusion: It was perfectly obvious to people back then that muddy soil gave rise to the frogs.
Observation: In many parts of Europe, medieval farmers stored grain in barns with thatched roofs (like Shakespeare’s house). As a roof aged, it was not uncommon for it to start leaking. This could lead to spoiled or moldy grain, and of course there were lots of mice around.
Conclusion: It was obvious to them that the mice came from the moldy grain.
Observation: In the cities, there were no sewers, no garbage trucks, no electricity, and no refrigeration. Sewage flowed in the gutters along the streets, and the sidewalks were raised above the streets to give people a place to walk. In the intersections, raised stepping stones were strategically placed to allow pedestrians to cross the intersection, yet were spaced such that carriage wheels could pass between them. In the morning, the contents of the chamber pots were tossed out the nearest window. Food was purchased and prepared on a daily basis, and when people were done eating a meal, the bones and left-overs were tossed out the window, too. A chivalrous gentleman always walked closest to the street when escorting a woman, so if a horse and carriage came by and splashed up the filth flowing in the gutters, it would land on him, and not the lady’s expensive silk gown (many of these gowns were so ornately embroidered that they were not easily washable, and neither washing machines nor dry cleaners existed). Many cities also had major rat problems. People back then may or may not have not connected the presence of rats with the spread of Bubonic Plague (Black Death, a dreaded and fatal disease), but they were probably bothered by the rats chewing on things and by the rat fleas biting them (just as cat/dog owners, even now, are bitten by the offspring of their pet’s fleas). People may not have realized that the Plague was spread by the bites of those fleas, but I imagine they knew that if only they could get rid of the rats, the pesky fleas would soon disappear, too — hence the story of the Pied Piper of Hamelin, Germany, leading all the rats out of town.
Conclusion: Obviously, all the sewage and garbage turned into the rats.
Observation: Since there were no refrigerators, the mandatory, daily trip to the butcher shop, especially in summer, meant battling the flies around the carcasses. Typically, carcasses were “hung by their heels,” and customers selected which chunk the butcher would carve off for them.
Conclusion: Obviously, the rotting meat that had been hanging in the sun all day was the source of the flies.

22. 1862, Louis Pasteur - experiments that rejected spontaneous generation even for microbes.
A sterile broth would “spoil” only if microorganisms could invade from the environment.
Fig. 26.9

23. NOW - Principle of biogenesis - life from life.
Early earth - different conditions - remember NO OXYGEN to attack complex aggregates of molecules + Energy sources, such as lightning, volcanic activity, and ultraviolet sunlight, were more intense than what we experience today.
SOOOOO, spontaneous generation was possible in early earth only
All life today arises only by the reproduction of preexisting life, the principle of biogenesis.
Although there is no evidence that spontaneous generation occurs today, conditions on the early Earth were very different.
There was very little atmospheric oxygen to attack complex molecules.
Energy sources, such as lightning, volcanic activity, and ultraviolet sunlight, were more intense than what we experience today.

25. Evolution of first cell: Four stages:
(1) The abiotic synthesis of small organic molecules;
(2) The joining these small molecules into polymers:
(3) The origin of self-replicating molecules;
(4) The packaging of these molecules into “protobionts.”
This hypothesis can be tested in the laboratory.
One credible hypothesis is that chemical and physical processes in Earth’s primordial environment eventually produced simple cells.
Under one hypothetical scenario this occurred in four stages:
(1) The abiotic synthesis of small organic molecules;
(2) The joining these small molecules into polymers:
(3) The origin of self-replicating molecules;
(4) The packaging of these molecules into “protobionts.”
This hypothesis leads to predictions that can be tested in the laboratory.

26. 1) Abiotic synthesis of organic monomers
Stanely Miller - simulated conditions on early Earth (no oxygen, reducing environment with inorganic gases like H2, CO2, NH3, CH4; lightning/UV with no ozone. Favored the synthesis of organic compounds from inorganic precursors.
They reasoned that this cannot happen today because high levels of oxygen in the atmosphere attack chemical bonds.
The reducing environment in the early atmosphere would have promoted the joining of simple molecules to form more complex ones.
The considerable energy required to make organic molecules could be provided by lightning and the intense UV radiation that penetrated the primitive atmosphere.
Young suns emit more UV radiation and the lack of an ozone layer in the early atmosphere would have allowed this radiation to reach the Earth.
In 1953, Stanley Miller and Harold Urey tested the Oparin-Haldane hypothesis by creating, in the laboratory, the conditions that had been postulated for early Earth.
They discharged sparks in an “atmosphere” of gases and water vapor
The atmosphere in the Miller-Urey model consisted of H2O, H2, CH4, and NH3, probably a more strongly reducing environment than is currently believed to have existed on early Earth
. The Miller-Urey experiments still stimulate debate on the origin of Earth’s early stockpile of organic ingredients.
Alternate sites proposed for the synthesis of organic molecules include submerged volcanoes and deep-sea vents where hot water and minerals gush into the deep ocean.
Another possible source for organic monomers on Earth is from space, including via meteorites containing organic molecules that crashed to Earth.
The Miller-Urey experiments produced a variety of amino acids and other organic molecules.

27. 2) Laboratory simulation of early-Earth conditions produced organic polymers
Abiotic origin hypothesis - monomers should link to form polymers without enzymes and other cellular equipment.
Researchers have produced polymers, including polypeptides, after dripping solutions of monomers onto hot sand, clay, or rock.
Similar conditions likely existed on the early Earth when dilute solutions of monomers splashed onto fresh lava or at deep-sea vents

28. 3) RNA may have been the first genetic material (important)
Life = reproduction = inheritance.
First hereditary material was RNA, not DNA.
Because RNA can also function as an enzyme, it helps resolve the paradox of which came first, genes or enzymes.
Life is defined partly by inheritance.
Today, cells store their genetic information as DNA, transcribe select sections into RNA, and translate the RNA messages into enzymes and other proteins.
Many researchers have proposed that the first hereditary material was RNA, not DNA.
Because RNA can also function as an enzyme, it helps resolve the paradox of which came first, genes or enzymes.

29. 3) SELF-REPLICATING RNA: Short polymers of ribonucleotides can be synthesized abiotically in the laboratory.
If these polymers are added to a solution of ribonucleotide monomers, sequences up to 10 bases long are copied from the template according to the base-pairing rules.
If zinc is added, the copied sequences may reach 40 nucleotides with less than 1% error.
RNA is acting as a self-replicating enzyme - Ribozyme! (remember sNRNPs in spliceosome!!)
In the 1980s Thomas Cech discovered that RNA molecules are important catalysts in modern cells.
RNA catalysts, called ribozymes, remove introns from RNA.
Ribozymes also help catalyze the synthesis of new RNA polymers.
In the pre-biotic world, RNA molecules may have been fully capable of ribozyme-catalyzed replication.
Fig

30. 3) Natural selection of the ‘fittest RNA’:
RNA sequences evolve in abiotic conditions.
RNA molecules - genotype (nucleotide sequence) - phenotype (three-dimensional shape) that interacts with surrounding molecules.
Some RNA sequences are more stable and replicate faster and with fewer errors - selected
Occasional copying errors create mutations and selection screens these mutations for the most stable or the best at self-replication.

31. RNA-directed protein synthesis - weak binding of specific amino acids to bases along RNA molecules, (rRNA today in ribosomes).
If RNA synthesized a short polypeptide that behaved as an enzyme ahhhhh…
RNA-directed protein synthesis may have begun as weak binding of specific amino acids to bases along RNA molecules, which functioned as simple templates holding a few amino acids together long enough for them to be linked.
This is one function of rRNA today in ribosomes.
If RNA synthesized a short polypeptide that behaved as an enzyme helping RNA replication, then early chemical dynamics would include molecular cooperation as well as competition.

32. 4) Protobionts can form by self-assembly
Protobionts - aggregates of abiotically produced molecules (RNA and macromolecules) enclosed in a membrane (separate internal environment).
Metabolism and excitability - properties of life.
Living cells may have been preceded by protobionts, aggregates of abiotically produced molecules.
Protobionts do not reproduce precisely, but they do maintain an internal chemical environment different from their surroundings and may show some properties associated with life, including metabolism and excitability.
In the laboratory, droplets of abiotically produced organic compounds, called liposomes, form when lipids are included in the mix.
The lipids form a molecular bilayer at the droplet surface, much like the lipid bilayer of a membrane.
These droplets can undergo osmotic swelling or shrinking in different salt concentrations.
They also store energy as a membrane potential, a voltage cross the surface.
If enzymes are included among the ingredients, they are incorporated into the droplets.
The protobionts are then able to absorb substrates from their surroundings and release the products of the reactions catalyzed by the enzymes.
Unlike some laboratory models, protobionts that formed in the ancient seas would not have possessed refined enzymes, the products of inherited instructions
However, some molecules produced abiotically do have weak catalytic capacities.
There could well have been protobioints that had a rudimentary metabolism that allowed them to modify substances they took in across their membranes.

33. Liposomes behave dynamically, growing by engulfing smaller liposomes or “giving birth” to smaller liposomes.
Fig a

34. 4)Natural selection could refine protobionts containing hereditary information
Most successful protobiont - reproduces and passes on its traits: RNA genes and their polypeptide products; eventually RNA replaced by DNA.
Molecular cooperation could be refined because favorable components were concentrated together, rather than spread throughout the surroundings. As an example: suppose that an RNA molecule ordered amino acids into a primitive enzyme that extracted energy from inorganic sulfur compounds taken up from the surroundings
This energy could be used for other reactions within the protobiont, including the replication of RNA.
Natural selection would favor such a gene only if its products were kept close by, rather than being shared with competing RNA sequences in the environment.
The most successful protobionts would grow and split, distributing copies of their genes to offspring.
Even if only one such protobiont arose initially by the abiotic processes that have been described, its descendants would vary because of mutation, errors in copying RNA. Evolution via differential reproductive success of varied individuals presumably refined primitive metabolism and inheritance.
One refinement was the replacement of RNA as the repository of genetic information by DNA, a more stable molecule.
Once DNA appeared, RNA molecules wold have begun to take on their modern roles as intermediates in translation of genetic programs.
Fig

35. The five-kingdom system reflected increased knowledge of life’s diversity
Past - Kingdom was the highest taxonomic category. NOW - DOMAIN!
Old system - only two kingdoms of life - animal or plant.
Bacteria, with rigid cell walls, were placed with plants.
Even fungi, not photosynthetic and sharing little with green plants, were considered in the plant kingdom.
Photosynthetic, mobile microbes were claimed by both botanists and zoologists.

36. Recognizes Prokaryotes and eukaryotes
In 1969, R.H Whittaker argued for a five-kingdom system: Monera, Protista, Plantae, Fungi, and Animalia.
Recognizes Prokaryotes and eukaryotes
The five-kingdom system recognizes that there are two fundamentally different types of cells: prokaryotic (the kingdom Monera) and eukaryotic (the other four kingdoms).
Three kingdoms of multicellular eukaryotes were distinguished by nutrition, in part.
Plant are autotrophic, making organic food by photosynthesis.
Most fungi are decomposers with extracellular digestion.
Most animals digest food within specialized cavities.
Plants - autotrophs;
Fungi- decomposers/extracelluar digestion; Animals - heterotrophs with digestive cavities
Fig

37. Problems with 5 Kingdom system:
Protista consisted of all eukaryotes that did not fit the definition of plants, fungi, or animals - it was not monophyletic.
Most protists are unicellular.
However, some multicellular organisms, such as seaweeds, were included in the Protista because of their relationships to specific unicellular protists.
The five-kingdom system prevailed in biology for over 20 years.

38. 3 Domain System
Three-domain system: Bacteria, Archaea, and Eukarya, as superkingdoms/domains.
During the last three decades, systematists applying cladistic analysis, including the construction of cladograms based on molecular data, have been identifying problems with the five-kingdom system.
One challenge has been evidence that there are two distinct lineages of prokaryotes.
Many microbiologists have divided the two prokaryotic domains into multiple kingdoms based on cladistic analysis of molecular data.

39. A second challenge to the five kingdom system comes from systematists who are sorting out the phylogeny of the former members of the kingdom Protista.
Molecular systematics and cladistics have shown that the Protista is not monophyletic.
Some of these organisms have been split among five or more new kingdoms.
Others have been assigned to the Plantae, Fungi, or Animalia.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

40. Clearly, taxonomy at the highest level is a work in progress.
It may seem ironic that systematists are generally more confident in their groupings of species into lower tax than they are about evolutionary relationships among the major groups of organisms.
Tracing phylogeny at the kingdom level takes us back to the evolutionary branching that occurred in Precambrian seas a billion or more years ago.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

41. There will be much more research before there is anything close to a new consensus for how the three domains of life are related and how many kingdoms there are.
New data will undoubtedly lead to further taxonomic modeling.
Keep in mind that phylogenetic trees and taxonomic groupings are hypotheses that fit the best available data.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings