evolution week2

Schedule

1. Major transitions in evolution

2. Geological timescales

3. Major geological drivers of evolution

4. Recent major extinction events

Common properties of major transitions1. Smaller entities coming together to form larger entities. (e.g.

eukaryotes, multicellularity, colonies...)

2. Smaller entities become differentiated as part of larger entity. (e.g. organelles, anisogamy, tissues, castes...)

3. Smaller entities are often unable to replicate without the larger entity. (e.g. organelles, tissues, castes...).

4. The smaller entities can disrupt the development of the larger entity, (e.g. meiotic drive, parthenogenesis, cancer...)

5. New ways of transmitting information arise (e.g. DNA-protein, germline vs soma, indirect fitness...)

Maynard Smith and Szathmary 1995

http://en.wikipedia.org/wiki/Eukaryote

Major transitions: early life

1953 Miller-Urey “primitive soup” experiment

350° vs 0°

➔ organic molecules

Organic molecules from comets?

Fred Goesmann et al. Science 2015;349:aab0689


•Organic molecules ≠ Life•Early life:

•Hereditary replication•Compartments

•First hereditary information?

Phylogenetic Tree of Life

BacteriaGreen

FilamentousbacteriaSpirochetes

Grampositives

ProteobacteriaCyanobacteria

Planctomyces

BacteroidesCytophaga

Thermotoga

Aquifex

HalophilesMethanosarcina

MethanobacteriumMethanococcus

T. celerThermoproteus

Pyrodicticum

Entamoebae Slimemolds Animals

Fungi

PlantsCiliates

Flagellates

Trichomonads

Microsporidia

Diplomonads

Archaea Eukaryota

last universal common ancestor (LUCA)

Woese 1990 tree based on ribosomalRNA sequences

Which came first?

Enzymatic activity Encodes “copyable” genetic information

Protein Yes No

DNA No Yes

RNA Yes Yes


•Organic molecules ≠ Life•Early life of simple replicators:


•First hereditary information?•Probably RNA: Genetic information (that can be copied)

+ Enzymatic activity.

COMMENT Open Access

The RNA world hypothesis: the worst theory of theearly evolution of life (except for all the others)aHarold S Bernhardt

Abstract

The problems associated with the RNA world hypothesis are well known. In the following I discuss some of thesedifficulties, some of the alternative hypotheses that have been proposed, and some of the problems with thesealternative models. From a biosynthetic – as well as, arguably, evolutionary – perspective, DNA is a modified RNA,and so the chicken-and-egg dilemma of “which came first?” boils down to a choice between RNA and protein. Thisis not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such differenttypes of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example ofa ‘top down’ (or should it be ‘present back’?) approach to early evolution: how can we simplify modern biologicalsystems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNApossesses catalytic ability provides a potential solution: a single macromolecule could have originally carried outboth replication and catalysis. RNA – which constitutes the genome of RNA viruses, and catalyzes peptide synthesison the ribosome – could have been both the chicken and the egg! However, the following objections have beenraised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA isinherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalyticrepertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by ourand other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as ‘proteinsfirst’, which holds that proteins either preceded RNA in evolution, or – at the very least – that proteins and RNAcoevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that theRNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand thebackstory to contemporary biology.

Reviewers: This article was reviewed by Eugene Koonin, Anthony Poole and Michael Yarus (nominated byLaura Landweber).

Keywords: RNA world hypothesis, Proteins first, Acidic pH, tRNA introns, Small ribozymes

BackgroundThe problems associated with the RNA world hypothesisare well known, not least to its proponents [1,2]. In thefollowing, I discuss some of these difficulties, some ofthe alternative hypotheses that have been proposed (in-cluding the ‘proteins first’ hypothesis), and some of theproblems with these alternative models. As part of thediscussion, I highlight the support provided to the RNAworld concept by the discovery of some extremely smallribozymes. The activities of these provide support for

proposals we have made previously for the identity ofthe first tRNA [3], for the origin of coded ribosomal pro-tein synthesis [4], and for the evolution of an RNA worldat acidic pH [5] (see also [6]). I also revisit the proposalfor a replicase origin of the ribosome, and what has be-come the most commonly held model for the origin oftRNA.In modern biological systems, the components of

DNA are synthesized from RNA components [7], and ittherefore makes sense to view DNA as a modified RNA.Similarly, the ribosome – the universal cellular machinethat makes proteins – is composed mainly of RNA, andRNA is its active component, although there are indica-tions that proteins may be playing an increasing role in

Correspondence: [email protected] of Biochemistry, University of Otago, P.O. Box 56, Dunedin, NewZealand

© 2012 Bernhardt; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.

Bernhardt Biology Direct 2012, 7:23http://www.biology-direct.com/content/7/1/23

Major transitions: early life•Organic molecules ≠ Life•Early life of simple replicators:


•First hereditary information/replicators?•Probably RNA: Genetic information (that can be copied)

+ Enzymatic activity. • co-factors that would speed up reactions: Amino-acids (initially); other functions (later)

•Selection for stability •Selection for correct dosage AND reduced competition between replicators ➡Linkage of replicators (chromosomes):

➡DNA (much more stable than RNA)

Major transitions: Prokaryote to Eukaryote

Prokaryotic cell

Cell membrane infoldings

Cell membrane

Cytoplasm

Nucleoid(containing DNA)

Endomembrane system

Endoplasmic reticulumNuclear membrane

Nucleus

Proteobacterium

Mitochondria

Cyanobacterium

Chloroplasts

Mitochondrion

†

†

†

1 A prokaryote grows in size and develops infoldings in its cell membrane to increase itssurface area to volume ratio.

2 The infoldings eventually pinch off from the cell membrane, forming an early endomembrane system. It encloses the nucleoid, making a membrane-bound nucleus.This is the first eukaryote.

3

5 Some eukaryotes go on to acquire additional endosymbionts—the cyanobacteria, a group of bacteria capable of photosynthesis. They become chloroplasts.

Ancestor of plants and algæ

Ancestor of animals, fungi, and other heterotrophs

First eukaryote

The aerobe's ability to use oxygen to make energy be-comes an asset for the host, allowing it to thrive in an in-creasingly oxygen-rich environ-ment as the other eukaryotes go extinct. The proteobacterium is eventually assimilated and becomes a mitochondrion.

Some eukaryotes go on to ac-quire additional endosymbionts — the cyanobacteria, a group of bacteria capable of photosynthe-sis. They become chloroplasts.Anaerobic (oxygen using) proteo-

bacterium enters the eukaryote, either as prey or a parasite, and manages to avoid digestion. It becomes an endosymbiont, or a cell living inside another cell.

Major transitions: sex

•See later lectures Week X (?).

Major transitions: multicellularity

Major transitions: multicellularityGreen algae: Inspiration for what may have occurred: Volvocales

http://en.wikipedia.org/wiki/Volvocales

e.g.: artificial selection for multicellularity in S. cerevisiae yeast

Ratcliff et al 2012

VolvoxSomatic cells

Gonidia

Major transitions: eusociality

•Solitary lifestyle --> Eusociality1. Reproductive division of labor 2. Overlapping generations (older

offspring help younger offspring)3. Cooperative care of young

Eg: ants, bees, wasps, termites. But also: naked mole rats, a beetle, a shrimp...

Hamilton, 1964

Major transitions: eusociality• Hamilton’s rule: genes for altruism increase in frequency when:

indirect fitness benefits to the receiver (B) ,

B

exceeds costs to the altruist (C).

> Cr ₒ

reduced by the coefficient of relatedness (r) between altruist & receiver,

•General framework: Kin selection: can favor the reproductive success of an organism's relatives (ie. indirect fitness), even at a cost to the organism's own survival and reproduction.

Similar diversity of lifestyles!

© National Geographic

Atta leaf-cutter ants

Oecophylla Weaver ants

© ameisenforum.de

© ameisenforum.de

Fourmis tisserandes

© ameisenforum.de

Oecophylla Weaver ants

Tofilski et al 2008

Forelius pusillus

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Avant

Workers staying outside die« preventive self-sacrifice »

Tofilski et al 2008

Forelius pusillus hides the nest entrance at night

Dorylus driver ants: ants with no home

© BBC

Animal biomass (Brazilian rainforest)

from Fittkau & Klinge 1973

Other insects AmphibiansReptiles

Birds

Mammals

Earthworms

Spiders

Soil fauna excluding earthworms,

ants & termites

Ants & termites

Schedule





“Complexity of life” didn’t increase linearly.

2. Geological time scalesDefined by changes in flora and fauna (seen in fossil record).

Eon > Era > Period > Epoch

4550 Ma:

HominidsMammalsLand plantsAnimalsMulticellular lifeEukaryotesProkaryotes

Hadean

Arch

eanProterozoic

Paleozoic

Mesozoic

Cenozoic

4527 Ma:Formation of the Moon

4.6 Ga

4 Ga

3.8 Ga

3 Ga

2.5 Ga

2 Ga

1 Ga

542 M

a

251 Ma65 Ma ca. 4000 Ma: End of the

Late Heavy Bombardment;first life

ca. 3500 Ma:Photosynthesis starts

ca. 2300 Ma:Atmosphere becomes oxygen-rich;

750-635 Ma:Two Snowball Earths

ca. 530 Ma:Cambrian explosion

ca. 380 Ma:First vertebrate land animals

230-65 Ma:Dinosaurs

2 Ma:First Hominids

Ga = Billion years agoMa = Million years ago

Eon

Eon

Eon

EraEra

Era

Phaneroz

oic

Eon

Geological timescales: Eon > Era > Period > Epoch

End of Proterozoic biota

Dickinsonia

4550 Ma:


Hadean

Arch

eanProterozoic

Paleozoic

Mesozoic

Cenozoic


4.6 Ga

4 Ga

3.8 Ga

3 Ga

2.5 Ga

2 Ga

1 Ga

542 M

a








230-65 Ma:Dinosaurs

2 Ma:First Hominids


Eon

Eon

Eon

EraEra

Era

Phaneroz

oic

Eon


50100150200250300350400450500 0542

0

1

2

3

4

5

Millions of Years Ago

Th

ou

sa

nd

s o

f G

en

era

Cm O S D C P T J K Pg N

Biodiversity during the Phanerozoic

All Genera

Well-Resolved Genera

Long-Term Trend

The “Big 5” Mass Extinctions

Other Extinction Events

Cambrian

Trilobites

Cambrian to late permian17,000 known species!

50100150200250300350400450500 0542

0

1

2

3

4

5

Millions of Years Ago

Th

ou

sa

nd

s o

f G

en

era

Cm O S D C P T J K Pg N

Biodiversity during the Phanerozoic

All Genera

Well-Resolved Genera

Long-Term Trend

The “Big 5” Mass Extinctions

Other Extinction Events

Cambrian

Permian Triassic Jurassic

4550 Ma:


Hadean

Arch

eanProterozoic

Paleozoic

Mesozoic

Cenozoic


4.6 Ga

4 Ga

3.8 Ga

3 Ga

2.5 Ga

2 Ga

1 Ga

542 M

a








230-65 Ma:Dinosaurs

2 Ma:First Hominids


Eon

Eon

Eon

EraEra

Era

Phaneroz

oic

Eon


Dimetrodon(sub-class Synapsida = “mammal-like reptiles”)

Early Permian mammal-like reptiles

4550 Ma:


Hadean

Arch

eanProterozoic

Paleozoic

Mesozoic

Cenozoic


4.6 Ga

4 Ga

3.8 Ga

3 Ga

2.5 Ga

2 Ga

1 Ga

542 M

a








230-65 Ma:Dinosaurs

2 Ma:First Hominids


Eon

Eon

Eon

EraEra

Era

Phaneroz

oic

Eon


Earth

Life

Eukaryotes

Homo sapiens: 5 meters

Whitechapel: Dinosaurs extinct

NHM

: first tetrapod

Ham

mersm

ith: Cam

brian explosion

Schedule






•Tectonic movement (of continental plates)

•Vulcanism

•Climate change

•Meteorites

Conditions on earth change.

Plate tectonics

12

354

Crustal plates and continental drift

Recent continental movements...

TETHYS SEA

LAURASIA

GONDWANA

EquatorTriassic 200 Mya

Pangaea - single supercontinent

Fossil distribution

Gondwana

Earthquakes

•Some tectonic movement is violent.

•E.g. 2004 Sumatra earthquake & tsunami...

Vulcanism•Local climate change (e.g. thermal vents, hot springs...)

•Global climate change: Emission of gasses & particles.

•New geological barriers (migration...)

•New islands (“Malay archipelago”, Galapagos... Hawaii... )

Deccan traps

Eyjafjallajokull

Climate change(since Cambrian)


•Tectonic movement (of continental plates)

•Vulcanism

•Climate change

•Meteorites

Conditions on earth change.

Vulcanism

Tectonic movement

Meteorite impact

Climate change?

?

Consequences: • Large scale migrations• Speciation• Mass extinctions• Adaptive radiations



Pg

fraction of genera present in each time interval but extinct in

the following interval

KT: K

-Pg

Creta

ceou

s–Pa

leoge

ne

Trias

sic-Ju

rassi

cPerm

ian-T

riass

ic

Late

Dev

onia

n

Ord

ovic

ian–

Silu

rian

Toda

y

•Oxygen levels.• Tetrapods and early amniotes.• Tropical conditions around equatorial landmasses.• Damp forests: tall trees & lush undergrowth: giant club mosses, lycopods, ferns & seed ferns.• Decaying undergrowth forms coal.• Good habitats for terrestrial invertebrates including spiders, millipedes and insects (e.g. giant dragonflies).

Pangaea - single supercontinent

Carboniferous/Permian

Dimetrodon(sub-class Synapsida = “mammal-like reptiles”)

Early Permian mammal-like reptiles

Climate change(since Cambrian)

Permian-Triassic Extinction

Sun et al Science 2012

Went extinct: •Up to 96% of marine species & 70% of terrestrial vertebrates•21 terrestrial tetrapod families (63%)• 7 orders of insects

Jurassic &Cretaceous

•Mammal-like reptiles were replaced as dominant land vertebrates by reptiles (dinosaurs).

• Lizards, modern amphibians and early birds appear.

• The conifer- and fern-dominated vegetation of the Late Triassic continued into the Jurassic.

Cretaceous–Paleogene (KT) extinction 66 million years ago

Subsequently, many adaptive radiations to fill newly vacant niches.eg. mammals, fish, many insects

AmmoniteMosasaur

(marine reptile) Non-bird dinosaurs

Most Plant-eating insects

75% of all species became extinct (50% of genera). Including:

http://www.scotese.com/earth.htm)


Evidence for Chixulub impact

Magnetic field near siteCrater : 180km diameter; bolide: 10km.

12

•Bolide impact at Chixulub. •huge tsunamis•cloud of dust and water vapour, blocking sun.•plants & phytoplankton die (bottom of food chain) --> animals starve

•dramatic climate & temperature changes are difficult (easier for warm-blooded?)

•Additional causes? •Some groups were ALREADY in decline •Additional impacts?•Deccan traps (India) - 30,000 years of volcanic activity (lava/gas release)


Diprotodon, Australia, extinct 40,000 ya

Dodo, Mauritius, extinct since 1662

Ongoing Anthropocene extinction•Hunting•Habitat destruction, modification & fragmentation

Passenger PigeonNorth America; extinct since 1914.

Glyptodon, Americas, extinct ~12000 years ago

Ongoing Anthropocene extinction•Hunting•Habitat destruction, modification & fragmentation•Pollution/Overexploitation•Spread of invasive species - & new pathogens•Climate change

Rainforest loss in Sumatra

Margono et al 2012

Summary.

•The history of the earth is divided into geological time periods

• These are defined by characteristic flora and fauna

•Large-scale changes in biodiversity (mass extinctions) were triggered by continental movement and catastrophic events

evolution week2

Education