evolution lectures 3&4 september 2013

Mini-summary of lectures 1 & 2

Monday, 30 September 13

Specific Questions/Comments

Geologists (Hutton, Lyell):Uniformitarianism: Changes in nature are gradual.

In 1800s, fossils showed species that no longer existed:

Some (e.g. Cuvier): Catastrophism: Fossils show extinct species (due to major, sudden, catastrophic events).


3 Schools of evolutionary thought

• Lamarck: characteristics acquired by an individual are passed on to offspring.

• Linneaus: each species was separately created.

• Darwin & Wallace: evolution as descent with modification.


Evolution by Natural Selection

• There is inherited variation within species.

• There is competition for survival within species.

• Genetically inherited traits affect reproduction or survival. Thus the frequencies of variants change.

(Not just numbers of offspring!)

Evolutionary fitness:A measure of the ability of genetic material to perpetuate itself in the course of evolution. Depends on the individual’s ability to survive, the rate of reproduction and the viability of offspring.


“Neo-Darwinism”or

“The Modern Synthesis”

The same thing... but with better understanding of how things work.

• Darwin’s Theory of Evolution by Natural Selection (1859)• Mendel’s Laws of Heredity (1866, 1900; see SBS 008)• Cytogenetics (1902, 1904 - )• Population Genetics (1908; see Lectures 7-12) • Molecular genetics (1970s- ; see SBS 633/210 and Lecture 6)

•More stuff since then (cultural evolution, epigenetics, etc...)


•Evolution also occurs by: • genetic drift• sexual selection• ...

Natural selection leads to adaptive change

•But environmental conditions change: What was advantageous yesterday may be a disadvantage today.

But not all change is adaptive!


Paperback 596 pages (11 Aug 2005)

Publisher : Oxford University Press


1. The Fossil Record

2. Comparative Anatomy

3. Comparative Embryology

4. Vestigial Structures

5. Domestication (artificial selection)

Darwin’s evidence for evolution


Geological times & continental drift


Today

1. Major transitions in evolution

2. Geological timescales

3. Major geological drivers of evolution

4. Recent major extinction events


Major transitions?1.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, indirect fitness...)

Maynard Smith and Szathmary 1995Monday, 30 September 13

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

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

Major transitions: early life

1953 Miller-Urey “primitive soup” experiment

350° vs 0°

➔ organic molecules



•Organic molecules ≠ Life•Early life:

•Hereditary replication•Compartmentalization

•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 sequencesMonday, 30 September 13


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

•Hereditary replication•Compartmentalization

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

+ Enzymatic activity.

•Amino-acids (initially as co-factors)•DNA (much more stable than RNA)•Linkage of replicators (chromosomes)


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 lectures Week 5.


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 2012Monday, 30 September 13

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




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

•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.

•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 ×

reduced by the coefficient of relatedness (r),


© 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


Today






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“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


Trilobites

Cambrian to late permian


50100150200250300350400450500 0542

0

1

2

3

4

5

Millions of Years Ago

Thou

sand

s of

Gen

era

Cm O S D C P T J K Pg N

Biodiversity during the PhanerozoicAll Genera

Well-Resolved Genera

Long-Term Trend

The “Big 5” Mass Extinctions

Other Extinction Events


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


Earth

Life

Eukaryotes

Homo sapiens: 5 m

eters

Whitechapel: Dinosaurs extinct

NH

M: first tetrapod

Ham

mersm

ith: Cam

brian explosion


Today







•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

GondwanaMonday, 30 September 13

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



Today







Pg

fraction of genera present in each time interval but extinct in

the following interval

KT: K

-Pg

Cre

tace

ous–

Paleo

gene

Triass

ic-Ju

rass

icPerm

ian-

Triass

ic

Late

Dev

onia

n

Ord

ovic

ian–

Silu

rian

Today


•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) extinction66 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.


•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 2012Monday, 30 September 13

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


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Week 3: Fossils, DNA and Molecules

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evolution lectures 3&4 september 2013

Education

major transitions

cultural evolution

course of evolution

darwinstheory of evolution

smaller entities

larger entities

hereditary information

genetic information