Early Cellular EvolutionMolecular & Cell Biology

Evolution Lecture 2

© 2004

Prof. David Fitch

Department of Biology

New York University

david.fitch@nyu.edu

Precellular evolution• "Prebiotic synthesis"

– Hypothesis: The molecules of life can be formed spontaneously under"prebiotic conditions"

– Assumptions: Prebiotic conditions, "uniformitarianism"

– Predictions• Amino acids and purines from prebiotic mixtures (Harold & Urey 1953)

• Ribose from formaldehyde ("formose" reaction; Butlerow 1861)

• Polymerization of "activated" nucleoside monomers without proteins

• The "RNA World"– Hypothesis: RNA preceded proteins and DNA as a primordial, information-

bearing, catalytic molecule

– Assumptions: Heredity, uniformitarianism

– Predictions:• Conserved roles for RNA in fundamental machinery of life

• At least some RNAs should demonstrate elementary catalytic activity

• Role for RNA as precursor to DNA may be conserved

RNA genome

• Early RNA genome could probably self-replicate– Template-dependent synthesis, ligation

• Self-splicing would have allowed rapid evolution– Different combinations of sequences and thus functions

= "exon shuffling"

• Early protein synthesis was directed by RNAs– tRNAs, rRNA

• Evolution of the Genetic Code– Order to codon groupings suggests a possible stepwise adoption

of codon assignments

– Once the codons began to be set up, and complexity of the codeincreased, it would be difficult to change (historical constraint)

Self-assembly of cell-like compartments• Order and complexity result from self-assembly

• Novel microenvironments allow:– Selective permeability via lipid or proteinoid "membranes"

– Novel (high) concentrations and enhancement of interactions

– Chained reactions (concentrated products available as substrates)

– Localized precipitation and organization (compartmentalization)

– Entropy can decrease in subsystems (not a violation of the 2ndLaw of Thermodynamics)

Conclusions about origin(s?) of life

• Under a variety of possible conditions representing earlyearth,– Building blocks of common, fundamental organic monomers and

polymers could have arisen spontaneously (as in extant systems)

– Self-sustaining, heritable RNA-based systems (= life) could havearisen from these building blocks

– Compartmentalization into cell-like structures could haveoccurred by self-assembly (as in extant systems)

• Once heritability and variation exist,– Diversification could result from such variation as sequence

duplications and "shuffling" (as in extant systems)

– Natural selection could produce novel functions (and complexity)by modification of pre-existing sequences (as in extant systems)

• Thus, "design" is not required to explain the origin of...

The Progenote(s?)• "The earliest cell" that was the ancestor of all extant life;

but consider...– A stepwise process led to cellular life, not a sudden event

– Probably not the only cell "species" existing at the time of theprogenote, but few lineages survive to reproduce during evolution

– "Endosymbiosis" could have integrated different genomes (called"reticulated evolution")

• Possibly not a single cell was ancestral, but a population of cells

How do we reconstruct cell history?

• Fossils?– Not much information!

How do we reconstruct cell history?

• and more fossils?– Not much information!

• The repository of inheritedinformation: i.e., genomes– Because of the fidelity of

inheritance, change is rare

– Lots of information!

– Do not need ancestors (fossils) toreconstruct genomic history: justuse extant genetic information

but how...?

Systematics

• Science of determining therelationships among "taxa"– A taxon can be a gene, an

individual, a population, aspecies, etc.

– These relationships are notarbitrary and reflect uniquehistory (genealogy)

– Taxonomy is the science ofdescribing taxa and applyingnames to groups (which isarbitrary)

• Relationships are depictedas "trees"– Phylogeny

Fossils not needed!

• Although fossils can be included, they are not needed toreconstruct phylogeny– Fossils of still existing groups are often more closely related

– Can provide indications of diversity of previous forms

– But because of biased sampling, fossils may also be misleading forphylogenetic reconstruction

• Eye-witness accounts not needed (or even possible)– Circumstantial evidence (e.g., DNA evidence) is often more

accurate than "eye-witness" accounts (e.g., 350 documented casesof misidentification due to eye-witness testimony in 10 years ofcriminal convictions)

– If nobody was there to see it, did it happen?

– Nearly all scientific facts are inferences about the unseen!

• Methods of phylogenetic estimation– Phenetic methods

– Cladistic methods

Phenetic methods• Assumptions

– Characters (features, sequences) compared are HOMOLOGOUS

– The most similar taxa are the most closely related

– Rate of change is fairly constant (or can be modeled)

• Example

Alignment positionsTaxa 1 2 3 4 5 6 7 8 9 10v A C C C G G G T T Aw A A C C G G G T T Ax A A A C G G G T T Ty A G A A A A G T T Tz T T A A A A A A A A

Taxa v w x yw 0.1x 0.3 0.2y 0.6 0.6 0.4z 0.9 0.9 0.9 0.6

v w x y z

Cladistic methods

• Assumptions– Characters (features, sequences) compared are HOMOLOGOUS

– Shared states are more likely to be shared by common ancestrythan by independent evolution (i.e., heredity works)

• Criterion to distinguish alternative hypotheses– Parsimony: the most likely is the tree with fewest changes

• Example...

Cladistic method

Alignment positionsTaxa 1 2 3 4 5 6 7 8 9 10v A C C C G G G T T Aw A A C C G G G T T Ax A A A C G G G T T Ty A G A A A A G T T Tz T T A A A A A A A A

x y v w z v w x y z

Hypothesis 1 Hypothesis 2

Total changes: 13 16

Application oftaxonomy

• Giving a name to a group– Arbitrary (but perhaps

useful?)

– Ernst Haeckel proposed 3main groups

– Later groups proposeddifferent numbers ofKingdoms...

Some recent taxonomiesLumpers vs Splitters

• Altman & Dittmer 1972: 2 Kingdoms– Plantae (incl. bacteria), Animalia (incl. protozoa)

• Several 3-Kingdom systems (e.g., Woese et al. 1990)– Bacteria, Archaea, Eukarya

• Copeland 1956: 4 Kingdoms– Monera, Protoctista (protozoa, algae, fungi), Plantae, Animalia

• Whittaker & Margulis 1978, 1992: 5 Kingdoms– Monera, Protoctista, Fungi, Plantae, Animalia

• Edwards 1976: 8 Kingdoms– Cyanochlorobionta, Erythrobionta, Chlorobionta, Myxobionta,

Fungi1, Fungi2, Chromobionta, Animalia

• Leedale 1974: 13 Kingdoms– Monera, Red algae, Plantae, Euglenoids, Myxomycetes, Fungi,

Heterokonts, Eustigmatophyta, Haptophyta, Cryptomonads,Dinoflagellates, Mesozoans, Animalia

SSU rRNA gene phylogeny

• Conclusions– One phylogeny

– Threephylogenetic"domains"

– Unrooted

– Origin of cellscontainingmitochondria canbe pinpointed (?)

– But OTHERgenomes alsoencode rRNA:plastids &mitochondria...

Tree of life with plastids and mitochondria

Origin of plastids and mitochondria

• Direct Filiation hypothesis– Organelles arise from within eukaryotic cells

– Prediction:

• Serial Endosymbiosis (SET) hypothesis– Organelles arise from other than eukaryotic cells

– Prediction:

Eukaryotic nuclear rRNA gene

mt rRNA gene

Bacterial rRNA gene

Eukaryotic nuclear rRNA gene

mt rRNA gene

Bacterial rRNA gene

Tree of life with plastids and mitochondria

Root?

How to root the tree of life?• Gene duplications that occurred earlier than the

"progenote" can root the tree– e.g., Iwabe et al. 1989, PNAS 86:9357

Eubacteria

Eukaryota

ArchaebacteriaArchaebacteriaEukaryota

Eubacteria

Eubacteria

Eubacteria

Eukaryota

Eukaryota

Archaebacteria

Gene evolution

• Gene lineages are assumed to follow species lineages ifthey are used to infer species phylogenies– This may not always be the case

– So we use several (many) genetic loci

• Evolution of genes themselves can be traced by phylogeny– For example, were introns...

• RECENT (and gained in eukaryotes)or

• ANCIENT (and lost in prokaryotes)?

• Evidence mainly supports INTRONS ANCIENT hypothesis– Intron positions have been anciently conserved

– Introns can be lost (as inferred from phylogenetic analysis)

Intron positions have been conservedANCIENTLY

500 MYA

800 MYA

1000 MYA

Introns have been lostRECENTLY

Why were introns kept in eukaryotes?• Observation: they generally separate "functional domains"

Speculations

• Introns were retained by "stabilizing selection" for afunction?– e.g., perhaps to allow differential splicing?

• Introns are a historical legacy (vestigial)?– Perhaps they are non-functional and just left over from the time

when self-splicing of RNA domains was occurring to formprimordial genomes?

• Introns were lost in most bacterial genes in response toselective pressure for replication efficiency?– e.g., to utilize ephemeral resources efficiently (or other mechanism

to maximize population growth rate)?

Origins of cells

• RNA cores of modern ribosomes are still-functionalDESCENDANTS from the RNA World

• Mitochondria and plastids are highly modifiedDESCENDANTS of eubacterial endosymbionts

• Intron-Exon structure of genes is probably DESCENDANTfrom an early RNA genome– Self-splicing introns allowed the construction of multi-domain genes

In conclusion

There is a high degree of LEGACY and CONSTRAINT in livingsystems because of the UNIQUE HISTORY that we sharewith ALL other living forms on this unique planet.

Nevertheless, variation continuously allows the evolution ofnew forms.

Because of heredity, not all of life is explained by functionalteleology.

Instead, much of life's patterns is explained by historicalrelationships.

"Nothing in biology makes sense, except in the light of evolution."

—Theodosius Dobzhansky