Origins of Life and Other Revolutions

Key Events in Evolution of Life on Earth

• Origins of life• Oxygen revolution• Eukaryotes (Endosymbiogenesis)• Multicellularity • Cambrian Explosion• Major Habitat Transitions

– Invasion of land

Millions of years ago (mya)

1.2 bya:First multicellular eukaryotes

2.1 bya:First eukaryotes (single-celled)

3.5 billion years ago (bya):First prokaryotes (single-celled)

535–525 mya:Cambrian explosion(great increasein diversity ofanimal forms)

500 mya:Colonizationof land byfungi, plantsand animals

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0Key Events in Evolution of Life on Earth

Outline

• Origins of life

• Evolution of Eukaryotes

• Evolution of Animals

• Major Habitat Transitions

Outline

• Origins of life

• Evolution of Eukaryotes

• Evolution of Animals

• Major Habitat Transitions

Fig. 26-21

Fungi

EUKARYA

Trypanosomes

Green algaeLand plants

Red algae

ForamsCiliates

Dinoflagellates

Diatoms

Animals

AmoebasCellular slime molds

Leishmania

Euglena

Green nonsulfur bacteriaThermophiles

Halophiles

Methanobacterium

Sulfolobus

ARCHAEA

COMMONANCESTOR

OF ALLLIFE

BACTERIA

(Plastids, includingchloroplasts)

Greensulfur bacteria

(Mitochondrion)

Cyanobacteria

ChlamydiaSpirochetes

The 3 Domains of Life

• Phylogenetic relationships based on 18S rRNA sequences, showing clade separation of bacteria, archaea, and eukaryotes.

Eukarya

The Earth was formed ~4.6 billion years ago

Earth’s early atmosphere likely contained water vapor and chemicals released by volcanic eruptions (nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, hydrogen, hydrogen sulfide)

Origins of Life (Herron & Freeman, Chapter 17)

• What were the earliest life forms?

• Prokaryotes are the earliest life forms we know of, but what might have preceded them?

Fig. 25-3

(a) Simple reproduction by liposomes (b) Simple metabolism

Phosphate

Maltose

Phosphatase

MaltoseAmylase

Starch

Glucose-phosphate

Glucose-phosphate

20 µm

Protobionts are aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure

Protobionts exhibit simple reproduction and metabolism and maintain an internal chemical environment

Protobionts

Protobionts

• Replication and metabolism are key properties of life

• Experiments demonstrate that protobionts could have formed spontaneously from abiotically produced organic compounds

• For example, small membrane-bounded droplets called liposomes can form when lipids or other organic molecules are added to water

Self-Replicating RNA and the Dawn of Natural Selection

• The early genetic material might have formed an “RNA world”

• The first genetic material was probably RNA, not DNA

• Early life forms might have consisted of protobionts with RNA as the genetic code

• Early protobionts with self-replicating, catalytic RNA would have been more effective at using resources and would have increased in number through natural selection

RNA World• RNA can both serve as the genetic code

(hereditary material) and also perform enzymatic functions (ribozymes)

• RNA molecules called ribozymes have been found to catalyze many different reactions– For example, ribozymes can make

complementary copies of short stretches of their own sequence or other short pieces of RNA

– Natural selection in the laboratory has produced ribozymes capable of self-replication (Herron& Freeman written prior to this discovery)http://www.rsc.org/chemistryworld/News/2009/January/09010901.asp

Self-Replicating RNA and the Dawn of Natural Selection

Ribozymes (= RNA enzyme or catalytic RNA)

RNA that can catalyze chemical reactions. Many natural ribozymes catalyze either the breaking or synthesis of phosphoester bonds in DNA or RNA. Such capacity would enable the capacity to self replicate and propagate life.

The functional part of the ribosome, the molecular machine that translates RNA into proteins, is fundamentally a ribozyme

RNA World• RNA can both serve as the genetic code

and also perform enzymatic functions (ribozymes)

• But, can RNA self replicate? If so, it would have all components to be considered “life”

Synthetic Life• Humans can now create synthetic life, by

constructing a genome on the computer, synthesizing the DNA and injecting the genetic code into a cell

• http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/overview/

• http://www.sciencemag.org/content/328/5981/958.summary

The First Single-Celled Organisms

• Stromatolites date back 3.5 billion years ago

• Prokaryotes were Earth’s sole inhabitants from 3.5 to about 2.1 billion years ago

Prokaryotes

Billions

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1 The oldest known fossils are stromatolites, rock-like structures composed of many layers of bacteria and sediment

The oldest known fossils are of cyanobacteria from Archaean rocks of western Australia, dated 3.5 billion years old

Stromatolites

Prokaryotes

• Prokaryote:

– No internal membranes, organelles, nucleus

– Bacteria + Archaea, not a Eukaryote

– Not a coherent category

– Archaea and Bacteria are not closer to each other than to Eukaryotes

Fungi

EUKARYA

Trypanosomes

Green algaeLand plants

Red algae

ForamsCiliates

Dinoflagellates

Diatoms

Animals

AmoebasCellular slime molds

Leishmania

Euglena

Green nonsulfur bacteriaThermophiles

Halophiles

Methanobacterium

Sulfolobus

ARCHAEA

COMMONANCESTOR

OF ALLLIFE

BACTERIA

(Plastids, includingchloroplasts)

Greensulfur bacteria

(Mitochondrion)

Cyanobacteria

ChlamydiaSpirochetes

Incredible Metabolic Diversity• Some can use inorganic chemicals as the electron donor in the

redox reaction of making ATP (respiration)(animals use organic carbon, food, as the electron donor)

• Eukaryotes can use only oxygen as the terminal electron acceptor when making ATP in the electron transport chain (aerobic respiration)

• Prokaryotes can use NO3-, NO2

-2, SO4-2, etc. (anaerobic respiration)

• Some are photosynthetic

• Some can fix nitrogen, converting atmospheric N2 NH3

Outline

• Origins of life

• Evolution of Eukaryotes

• Evolution of Animals

• Major Habitat Transitions

– O2 in the atmosphere was generated by photosynthetic activity of cyanobacteria

– Cyanobacteria were the first organisms to use H2O (instead of H2S or other compounds) as a source of electrons and hydrogen for fixing CO2

– Photosynthesis: 6 CO2 + 6 H2O + photons → C6H12O6 + 6 O2

Oxygen Revolution

Atmosphericoxygen

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1 “Oxygen revolution” from 2.7 to 2.2 billion yrs ago

– O2 allows the production of more energy and more efficient metabolism

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O, ΔG = -2880 kJ per mole of C6H12O6

• Aerobic metabolism: 36 ATP molecules per glucose

• Anaerobic metabolism: 2 ATP molecules per glucose

• Aerobic and anaerobic metabolism share the initial pathway of glycolysis but aerobic metabolism continues with the Krebs cycle and oxidative phosphorylation.

– However, Oxygen is also Toxic• Oxygen is highly toxic to many species

• Electrons that escape from the electron transport chain can bind to oxygen and produce reactive oxygen species

• Reactive oxygen species (H2O2, O2−) can damage DNA and other

molecules

Oxygen Revolution

Evolutionary History dictates type of Metabolism

• The fact that much of prokaryotic life evolved BEFORE the oxygen revolution is reflected in the diverse forms of anaerobic metabolism – Most bacteria do not require oxygen, and for many it is toxic– Most bacteria use other molecules as the terminal electron

acceptor when making ATP

• The fact eukaryotic life evolved AFTER the oxygen revolution is reflected in the fact that all eukaryotes use aerobic metabolism– They use oxygen as the terminal electron acceptor in energy

production

• Certain organelles originated as free-living bacteria that were taken inside another cell as endosymbionts.

• Mitochondria developed from proteobacteria (in particular, Rickettsiales or close relatives) and chloroplasts from cyanobacteria

• Both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (in being circular in shape, its size, and DNA composition)

Endosymbiotic TheoryLynn Margulis

Wrote the seminal paper“The Origin of Mitosing Eukaryotic Cells”1966

The organelles (mitochondria and chloroplasts) greatly aid in energy production in eukaryotes.

Probably Archaea

Covered in Chapter 15, Freeman and Herron

Given the evolutionary history of endosymbiosis (or endosymbiogenesis) leading to eukaryotes, eukaryotes will inevitably share traits with both archaea and bacteria

Outline

• Origins of life

• Evolution of Eukaryotes

• Evolution of Animals

• Major Habitat Transitions

65 mya: Cretaceous Extinction(dinosaurs go extinct)

230 mya: Permian Extinction

570 mya: Cambrian Explosion

Burgess Shale

(3) Origins of Animal PhylaCambrian Explosion (570 MYA)

Radiations:Evolution of hard body partsDiversification of body formsRadiation of Invertebrates

Extinctions????

(1) Precambrian-Paleozoic (570 MYA) Boundary

Cambrian Explosion

What is an Animal?

Multicellular (metazoan)Heterotrophic (eat, not photo or chemosynthetic)

Eukaryote

No Cell Walls, have collagenNervous tissue, muscle tissue

Particular Life History-developmental patterns (this lecture)

What is an Animal?

Origins of Multicellularity

It is thought that metazoans arose from Colonial flagellate protists

Oxygen Revolution: allow higher metabolic ratelarger body sizepowered motion

Cells of sponges are similar to flagellate protists

Doushantuo formation Southern China

Fossilized metazoan embryo at the 256 cell stage

• 570 million years ago• Clusters of cells (embryos?)• Sponges

Burgess Shale Fossils

Marrella

Canadia

Aysheaia

Hallucigenea

WHY?

Ecological arms race?Increase in oxygen?(higher energy, larger animals possible)

The Paleozoic Sea

When?

Are Genetic Distancesand fossil recordroughly congruent?

Was the Cambrian Explosion an Explosion?

Geology: YESSudden Appearance of Animal Fossils

Genetics: NODNA Divergences Predate Cambrian

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nCambrian

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Million Years Ago

Wray et al. 1996

Based on phylogeny of animals based on DNA sequence data, the radiation of animals predates the geological record of the Cambrian Explosion

Fossil Record vs Molecular Clock

• Molecular clock and fossil record are not always congruent– Fossil record is incomplete, and soft bodied species are

usually not preserved– Mutation rates can vary among species (depending on

generation time, replication error, mismatch repair)

• But they provide complementary information– Fossil record contains extinct species, while molecular data

is based on extant taxa– Major events in fossil record could be used to calibrate the

molecular clock

Fossil Record vs Molecular Clock

• So it’s highly likely that the divergence of animal lineages (phyla) was more gradual than the fossil record would suggest and that the time of divergence happened earlier

Evolution of Animal Body Plans

• True Tissues• Tissue Layers (Diplo vs Triploblasts)• Body Symmetry• Evolution of body cavity (Coelom)• Evolution of Development

Cambrian Explosion

But major body plans evolved within a short period of time

Of course, evolution continued after the Cambrian Explosion

How could this happen? (genetic mechanism?)

• We talked about how selection and drift could result in speciation

• The formation of novel body plans calls for changes (mutation, selection, drift) at loci that cause fundamental morphological changes

Genetic Mechanisms?

The Evolution of Development(Freeman& Herron, Chapter 19)

• The tremendous increase in diversity during the Cambrian explosion appears to have been caused by evolution of developmental genes

• Changes in developmental genes can result in radically new morphological forms

• Developmental genes control the rate, timing, and spatial pattern of changes in an organism’s form as it develops into an adult

Changes in a few regulatory genes could have big impacts

• Most new features of multicellular organisms arise when preexisting cell types appear at new locations or new times in the embryo.

• Changes in the specification of cell fates is a major mechanism for the evolution of different organismal forms.

• Hox genes are a class of homeotic genes that provide positional information during development

• If Hox genes are expressed in the wrong location, body parts can be produced in the wrong location

• For example, in crustaceans, a swimming appendage can be produced in a segment instead of a feeding appendage

Example of Evolution Developmental Genes that could result in radically new body forms

Mutations in a Hox gene causing legs to grow out of the head

In this case, the identity of one head segment has been changed to that of a thoracic segment.

Hox Clusters

• Gene family formed by gene duplication events

• Hox genes, usually found clustered next to each other along animal chromosomes

• Hox gene products are regulatory proteins that bind to DNA and control the transcription of other genes

Christiane Nüsslein-Volhard and Sean Carroll

• Hox genes specify the developmental fate of individual regions within the body (modules), and usually the genes are activated and expressed in the body in the same order as their position in the cluster

• These genes regulate timing and location of gene expression during development

Hox Clusters

Example: Hox Genes

Evolution of Hox clusters

• HOX-clusters undergo essential rearrangements in evolution of main taxa

• Duplication, deletion, divergence of the genes lead to differentiation in body plans

• Other regulatory genes/gene families are also important

Animal body plans

Evolutionary changes in Hox Genes

• New morphological forms likely come from gene duplication events that produce new developmental genes

• A possible mechanism for the evolution of six-legged insects from a many-legged crustacean ancestor has been demonstrated in lab experiments

• Specific changes in the Ubx gene have been identified that can “turn off” leg development

Hox gene 6 Hox gene 7 Hox gene 8

About 400 mya

Drosophila Artemia

Ubx

Differences in Hox gene expression distinguish the various arthropod segmentation patterns

• Evolution of vertebrates from invertebrate animals was associated with alterations in Hox genes

• Two duplications of Hox genes are thought to have occurred in the vertebrate lineage

• These duplications may have been important in the evolution of new vertebrate characteristics

Evolution of Vertebrates (Phylum Chordata)

• Polyploidization is probably the single most important mechanism for the evolution of major lineages and for speciation in plants

Multiple rounds of polyploidization might have occurred during the early evolution of vertebrates

Vertebrates (with jaws)with four Hox clusters

Hypothetical earlyvertebrates (jawless)with two Hox clusters

Hypothetical vertebrateancestor (invertebrate)with a single Hox cluster

Second Hox duplication

First Hox duplication

Outline

• Origins of life

• Evolution of Eukaryotes

• Evolution of Animals

• Major Habitat Transitions

Habitat Transitions

• Freshwater invasions

• Invasion of Land

• Key innovations with the invasion of land

• Geological record of timing of terrestrial invasions

Transitions between

Saltwater Freshwater and

Water Land

Constitute Major Evolutionary

Transitions in the History of Life

Example of extraordinary environmental change:

Sea Fresh LandProtista X XPorifera X XCnideria X XCtenophora XPlatyhelminthes X X XNemertea X X XRotifera X XGastrotricha X XKinorhyncha XNematoda X XNematomorpha X XEntoprocta X XAnnelida X X XMollusca X X XPhoronida XBryozoa X XBrachiopoda X Sipunculida XEchiuroida XPriapulida XTardigrada X XOnychophora XArthropoda X X XEchinodermata XChaetognatha XPogonophora XHemichordata XChordata X X X

Life evolved in the sea, and freshwater and terrestrial habitats impose profound physiological challenges for most taxa (Hutchinson 1957; Lee & Bell 1999)

Of ~40 Animal Phyla, only 16 invaded fresh water, and only 7 invaded land

Sea Fresh water Soil LandProtista X X XPorifera X XCnideria X XCtenophora XPlatyhelminthes X X X XNemertea X X XRotifera X X XGastrotricha X XKinorhyncha XNematoda X X XNematomorpha X XEntoprocta X XAnnelida X X X XMollusca X X X XPhoronida X

Habitat Invasions

Sea Fresh water Soil LandBryozoa X XBrachiopoda X Sipunculida XEchiuroida XPriapulida XTardigrada X X XOnychophora X XArthropoda X X X XEchinodermata XChaetognatha XPogonophora XHemichordata XChordata X X X X

Habitat Invasions

Osmoregulation

• The regulation of water and ions poses among the greatest challenges for surviving in different habitats.

• Marine habitats pose the least challenge, while terrestrial habitats pose the most. In terrestrial habitats must seek both water and ions (food).

• In Freshwater habitats, ions are limiting while water is not.

The invasion of land occurred relatively recently (late in the history of life on earth)

The Colonization of Land• Precambrian: colonization of land by bacteria

• Late Ordovician–Late Devonian: Terrestrial ecosystems of plants, fungi, arthropods and eventually vertebrates

• Late Silurian: vascular plants

• Devonian: evidence of interactions among groups (fungal-plant symbiosis, arthropod herbivory)

• Late Devonian: Two major megaclades that were major participants in the Cambrian explosion appear on land

– The lophotrochozoans: gastropod and bivalve mollusks, oligochaete annelids, rotifers, etc.

– The ecdysozoans: arthropods, nematodes, etc.• Invasion of land by crustaceans origin of insects (Hexapods)

• Early Carboniferous: radiation of tetrapods (vertebrates with 4 legs)

Major Transitions of the Paleozoic

The invasion of land by crustaceans(terrestrial crustaceans = insects)

Questions• What are some of the key biological revolutions that occurred during the history of life on earth,

and how did they come about?

• Why is it hypothesized that early life on earth was in the form of RNA?

• How did the Oxygen Revolution come about?

• What are the implications of a high oxygen atmosphere for organismal physiology?

• How were Eukaryotes created?

• What are animals?

• About when did animals evolve? Is there congruence between fossil estimates versus molecular clock estimates of the timing?

• How did animals diversify (Cambrian Explosion)?

• Where did life evolve (land, sea)?

• About when did organisms begin to live on land?

• What are some challenges of living on land (relative to the sea)?

1. Which of the following is MOST likely to be true regarding evolutionary relationships among the major domains of life?

(A) Bacteria and Archaea are both grouped into the category of “Prokaryotes” because they are more closely related to each other than to Eukaryotes

(B) Archaea are ancestral to all other forms of Life

(C) The Oxygen Revolution defines the emergence of life on Earth

(D) Eukaryotes arose from a symbiotic relationship among prokaryotes

(E) Eukaryotes evolved from Prokaryotes through Horizontal Gene Transfer

2. Which of the following is Least likely to be true regarding Prokaryotic Metabolism and the Oxygen Revolution?

(A) The oxygen revolution led to the proliferation of diverse types of prokaryotic metabolism

(B) The oxygen revolution enabled the preponderance of more efficient metabolism that could produce more ATP per unit glucose

(C) The oxygen revolution altered the atmosphere of the Earth

(D) The oxygen revolution created an inhospitable habitat for many classes of prokaryotes that use molecules other than oxygen as their terminal electronic acceptor for energy production

(E) The oxygen revolution was caused as a byproduct of photosynthetic activity of cyanobacteria

3. Which of the following does NOT make RNA a good candidate for early life on earth?

(a) RNA could act as an enzyme(b) RNA could serve as the genetic code(c) RNA is much more stable than DNA in our

current atmosphere(d) RNA can catalyze chemical reactions that break

or synthesize phosphodiester bonds in RNA or DNA

(e) Recent studies suggest that RNA is capable of self replication

4. Which is the following is NOT a consequence of the Oxygen Revolution?

(a) The ability of organisms to metabolically produce more ATP by using oxygen as the terminal electron acceptor during respiration

(b) Eukaryotes, which evolved after the Oxygen Revolution, all use aerobic metabolism

(c) The transformation of the earth's atmosphere ~2.5 billion years ago from one that was chemically reducing to one that is oxidizing

(d) The heightened risk of DNA and cellular damage in organisms through oxygen free radicals

(e) The proliferation of bacteria that use oxygen as the terminal electron acceptor during respiration, such that nearly all bacterial species are aerobic

Answers

• 1D• 2A• 3C• 4E