Martin

Question 1

Indicators of past environments?

Answer 1

• Zircons (minerals)
o 4.1 Billion years old
o Contained in graphite, so therefore carbon is present
o Carbon-12 = lighter and therefore preferred organic carbon
o Carbon-13 and carbon-14 are heavier
o Presence of carbon-12 points to life

•	Oldest rocks
o	3.7 Billion years old
o	Isua, Greenland
o	Carbon bonded to nitrogen and phosphorus
o	Building blocks for DNA = presence?

•	Rocks ‘rust’ 
o	3.7 billion years ago
o	Presence of atmospheric oxygen
o	Must be produced
o	Photosynthesis?

Question 2

Factors affecting likelihood of fossilisation?

Answer 2

1. Decay: No tissue or outsides = if no shell = no fossil
2. Scarcity: If few of them, less chance of fossilisation
3. Sedimentation: On land less likely to be buried
4. Ecology: Where you live
5. Chemistry: CaCO3 dissolves
6. Digenesis
7. Metamorphism
8. Outcrop: Only see fossils at outcrops
9. Collection: Only recently have Chinese fossils been looked at by wider community = dinosaurs with feathers

Question 3

Organism Fossil Record?

Answer 3

1. Stromatolites - 3.7 Billion Years ago
   a. Trace fossils, first macroscopic fossils
2. Strelley Pool Formation – 3.43 Billion Years ago
   a. Cell Walls
   b. Sulphur-fixing bacteria
   c. First fossil organisms
3. China’s small carbonaceous fossils – 1.6 billion years ago
   a. Additional level of complexity
   b. Eukaryotes
4. Arctic Canada, Bangiomorpha pubescens - 1.05 billion years ago
   a. First sexually reproducing organism
5. Sponges
   a. First animals (Metazoans)
   b. Transformed oceans: took bacteria out of water and stopped algal bloom = oxygen can get in and life can diversify
   c. 750 million years ago - no fossil – biomarker used, molecule which is produced by sponges but could be produced by seaweed
   d. Fossils first found in Australia and Russia – moulds in sandstone –moldic preservation – 555 million years ago
6. Small shelly fossils – Cloudina – 545 million years ago
   a. Latest Precambrian – Ediacaran
7. Amber - 140 million years ago
   a. Tree resin = trees
   b. Cretaceous
8. Decapods – 135 million years ago
   a. Lobsters
   b. 3D preservation
9. Mammoths – 10,000 years
   a. Oldest ice = 1.2 million years by no fossils

Question 4

Missing intermediates?

Answer 4

• Extinction means that intermediate morphologies are not alive today
• Do not know what the common ancestor looks like
• Because the favoured characteristics are random, evolutionary history is full of dead ends with failed adaptations
• The fossil record is therefore narrow with few ancestral descendants
• Intermediate varieties are hidden within a huge ancestral tree littered with dead ends
• Further back you go, the less likely you are to find fossils with links to current living species

Question 5

‘Explosive Beginnings’?

Answer 5

• Sudden appearance of complex animal life at the base of the Phanerozoic, the “Era of Well Displayed Life”
o Few simpler precursors
• Relative rapid appearance of species in the lowest strata – Cambrian Explosion

Question 6

Fossil indicators of the Cambrian Explosion:

Answer 6

Small shelly fossils
• Low diversity Ediacaran communities (Cloudina)
• Contrasts with the rich diversity of the skeletonized taxa in the Cambrian

Small Carbonaceous Fossils
• Not mineralised
• Preserve many taxa similar to the small shelly fossils
• Again suggest a shift from simple to diverse and complex organisms

Phosphorites
• Turn flesh into stone
• Edicaran – no more complex than a sponge
• Cambrian – rich with animal embryos and juveniles

Burgess Shale preservation
• Organisms squashed flat
• Seaweed-grade organisms in the Ediacaran
• Exotic array of Cambrian animals

Ediacara-type preservation – only for Ediacaran period
• Sediment stabilised by microbial mats
• Perhaps also gelled by the precipitation of silica – extracted today by sponges – were present
• Preserves moulds of upper and lower surfaces of organisms
• Preserves impressions of fossils

Disk- and frond-like organisms
• Interpreted as jellyfish or seaweeds
• Lack morphological details to be supported
• Dwell in too deep of water to be photosynthetic plants
• Fractal branching surfaces seem to have been absorbing nutrients from the water – perhaps carbon or sulphur ions
• Not a living group – perhaps no living ancestors

• Some exceptions – Kimberella - constructed as a jellyfish, it was later assigned to the cubozoans (‘box jellies’), and has been cited as a clear instance of an extant animal lineage present before the Cambrian
• Edicaran
• Perhaps the base of the animal tree?

Burgess Shale preservation
• Contains representatives of almost all the modern animal phyla
• Clear explosion of diversity in the cambrian
• Hallucigenia – claws share construction similar to modern velvet worms
o Lacks adaptations for terrestrial life where modern ancestors live (rainforests)
o Shows the process of evolution

Question 7

Cause of Cambrian Explosion?

Answer 7

• Rise in atmospheric O2? – Geochemical proxies show that sea floor sediments lacked oxygen – Edicaran levels were 15-40% of present levels – enough for sponges and bilaterians
• Perhaps sponges pumped water and mixed the oceans, transporting oxygen to deeper waters
• Perhaps low levels of oxygen could support scavengers and herbivores, but increasing oxygen allowed for predators – increasing diversity
o No predators = low diversity
• Explosion was a positive feedback system – evolution led to a heterogeneous environment which allowed for further diversification

Question 8

Struggles of evolving to land?

Answer 8

Most fossils in the ocean – fossil record mostly marine life
Life presumed to have formed in the ocean – is this just fossil record bias?

Only three phyla have completely broken ties to the ocean
•	Arthropods, molluscs and vertebrates
Even today many species return to water like ponds – to feed or breed
Hard to leave the water – many challenges to terrestrial life:
•	Respiration
•	Food
•	Movement
•	Pressure difference
•	Temperature
•	Desiccation
•	Senses
•	Food
•	Gravity
•	Osmosis and gas exchange 
•	UV radiation
•	Reproduction

Question 9

Terrestrial Fossil Record?

Answer 9

1. Palaeosols – Fossil soils – 2760 million years ago
   a. Geochemical hints of microbial activity
   b. May just have been part of processes linked to an atmosphere with no oxygen
   c. Oxygen first available in substantial quantity 2200 million years ago
2. Concrete life evidence of life outside the oceans – 1060 million years ago
   a. Microfossils
   b. Nonesuch Shale – Northern USA
   c. Simple filaments and sacs – microbial life – in freshwater lakes
   d. Would require adaptations to live in freshwater
   e. Possible source of adaptations for desiccation leading to eventual life on just land
3. Increase in weathering on land – 850 million years ago
   a. Clay mineralogy show increase in weathering of regoliths
   b. Carbon isotope signatures suggest it was due to organic acids being produced by microbes
   c. Much uncertainty
4. Middle of Cambrian also saw depletion of phosphorus from the uppermost soil layers – probable indicator of fungal activity
5. Climactichnites - first evidence of animal life – 510 million years ago
   a. Tracks found on beach
6. First plant life – 460 million years
   a. Middle Ordovician - possible it was earlier but not as much evidence
   b. Trilete spores – formed in tetrads
   c. Each spore covered in a layer of sporopollenin – biopolymer with excellent fossilization potential – perhaps why the parent plant was not preserved
   d. Trilete marks – indicate they grew and developed in air, not water
7. First terrestrial organism – tortotubus – 444 million years ago
   a. Fungus – an underground network
   b. Decomposer – fertilised the soils
   c. Gave stability to soils – as was an underground network – accelerated the weathering of bedrock
   d. Increased wreathing showed by decreasing grain sizes
8. Land plants – 440 million years ago
   a. Early Silurian
   b. Thalloid organisms – “soggy cornflakes”
   c. Basic
9. Land plants – 430 million years ago
   a. Mid to late Silurian
   b. Increasing complexity
   c. Cooksonia – have vascualar tissue – xylem – active transport of water – beaten gravity - Tracheophytes
   d. Also have a waxy, impermeable cuticle – Stomata – transpiration system
10. Pneumodesmus – 428 million years ago
    a. Silurian
    b. Millipede
    c. First entirely terrestrial species
11. Another preservation caveat – Devonian 419 million years ago
    a. Rhynie Cherts near volcanic springs – whole exosystems including spiders and all
    b. Fossils of early plants
    c. Is this representative of all terrestrial ecosystems?
12. Devonian – 419 million years ago – plants firmly established – first trees establishing
13. Vertebrates – 380 million years ago
14. By Carboniferous – 358 million years ago – forests established

Question 10

Plants to trees?

Answer 10

• Eventually leads to need for roots for increased water uptake and stability
• More roots = holding riverbanks together = leads to meanders = slower rivers
• Deeper roots – more stable sources of groundwater – larger plants reinforced with lignin in xylem = trees
• Also begin to grow higher to release spore and compete for water
• Leads to tree evolution
• Devonian forests = first source of coal -
• Oxygen concentrations skyrocket – once it reached 13% in atmosphere fire was possible (by lightning strikes)
• Turned plants to charcoal – extra detail of plants preserved from the mid-Silurian onwards – follow the development of xylem and stomata through time

Question 11

Terrestrial and climactic transformation?

Answer 11

• Coal deposits transfer atmospheric carbon to the stratigraphic record
• Arctic Basin – extensive oil and gas reserves in Eocene rocks
• Shows a massive change in climate 49 million years ago
• Caused by freshwater fern, azolla
• 49 Million years ago – Arctic Ocean cut off from the North Atlantic
• Global temperatures were 10-15 degrees at the poles
• Rainfall and melting of winter snow brought freshwater
• A low-density nepheloid layer formed on the surface of the deep Arctic Ocean
• Inhibited mixing of the ocean basin
• Freshwater layer had nutrients deposited by continental weathering
• Azolla was in perfect growing conditions – could asexually reproduce in the 20-hour days of the arctic summer and double its biomass every three days = 8.4 x 1018 kg of biomass over the 800,000 summers
• Deep arctic ocean was anoxic because of the layer and it being cut off from the Atlantic = dead organic matter would sink but not decay and would be buried by clastic runoff
• Over 800,000 years it could have potentially sequestered more than 10,000 times the carbon than is in the atmosphere today
• Drop of CO2 levels from 3500 to 650ppm
• Change in climate from greenhouse in the cretaceous to icehouse seen with glacial dropstones being first seen after the Azolla event

Question 12

Outline of history of flight?

Answer 12

Unpowered flight is very common – example of convergent evolution
Powered flight is more interesting; it is metabolically expensive, and this cost must be balanced by access to otherwise unavailable resources or other benefits.
Insects got there first (396 Ma, Rhyniognatha?). [The upper size limit of flying insects is approximately the lower size limit of flying vertebrates – coincidence?]
Pterosaurs– 250 million years ago
• Flying reptiles
Within vertebrates, powered flight has evolved three times.
The wings of pterodactyls, birds and bats are homologous as appendages, but not homologous as wings – they representing convergently derived homoplasies
Archaeopteryx - The oldest bird (both geologically – 160 Ma – and historically, discovered in 1860 - was immediately recognised as intermediate in form between birds and dinosaurs, leading to a briefly accepted – and eventually rejected – theory that birds evolved from dinosaurs.

Question 13

Types of dino?

Answer 13

1. Theropods – Raptor like
2. Sauropods – Long neck like
3. Ornoithschians – “odd balls”

Question 14

Similarities between birds and theropods?

Answer 14

1. Jointing of the arms – fold up arms against their chest
2. Size of the brain – relatively large brains
   a. Good coordination + good sense (eye contact)
3. Furcula ‘wishbone’ – Strengthens ribcage
   a. Also have stiffened ribcage by small bones between
4. Tail (relict – fused)
   a. Vestigial on birds = squashed vertebrate = shrunken evolutionary from theropods

Question 15

Breathing in birds and dins?

Answer 15

The circulation of air through birds’ respiratory system incorporates flexible bellows-like reservoirs (‘air sacs’ pumping air through inflexible lungs. Space is created for ‘two breaths at once’ by hollowing out bones – the lungs and caudal sacs fill nearby ribs and vertebrae. Air sacs in tail and brain
Certain theropods (but not the most basal) exhibit equivalent chambers in equivalent bones
• Large number of air sacs in the body
• Hollow cavities (pre-adaptation to flight)
• In some theropods
• In progress of development

Question 16

Gene IDs?

Answer 16

Genes (coded by DNA) encode proteins (made up of sequences of animo acids). Protein – particularly the ‘connective tissue’ protein collagen – can preternaturally survive for at least 200 million years, allowing the reconstruction of the original genetic sequencing.
Carefully-handled (contaminant-free?) ornithischian protein sequences contain some crocodile characteristics, and some bird characteristics – as befits their phylogenetic position.
195 Ma – Sauropod – collagen ID

Question 17

Feathers?

Answer 17

The earliest dinosaur feathers were likely scales modified into little bristles to help with insulation or camouflage – bird feathers start life this way in early embryonic development.
Key taxa include Sinosauropteryx, discovered 1996, the first featured dinosaur – a theropod with more than a passing resemblance to Archaeopteryx, reviving the dinosaurs-as-birds theory – and Kulindadromeus, a feathered ornithischian that established feathers as a dinosaur-wide feature (not just the preserve of bird-like theropods).
Spectacular amber fossils reveal the three-dimensional structure of feathers down to micron-scale resolution. – China
Feathers = exaptation = “blind evolution” – feathers happened and then were later used for flight

Question 18

Wings and flight?

Answer 18

One day evolve into pennaceous feathers. Feathery wings are unique to a subgroup of theropods (one proposed name for this group is the Pennaraptora), but the earliest members of this group could not fly.
Uses of wings before flight:
• Wing-assisted incline running – Anchinornis – White and black regions = different colours caused by melanin
• Courtship – Ornithomimus
• Brood care – Oviraptor – Mothers caring for eggs – feathers to keep them warm – incubation – reason in adults and not in juveniles
All but one of these lineages to go extinct in the Creteceous–Palaeogene (K–Pg) mass extinction, removing ‘intermediate forms’ from the living biota and enlarging the gap between living birds and their closest relatives.
Beginning of Powered Flight
• Archaeopteryx (150 Ma) is the earliest good candidate for powered flight
• You could be forgiven for thinking that this great evolutionary innovation would pave the way for birds to access all sorts of previously unattainable niches and thus to diversify spectacularly. But no such radiation occurred. Instead, birds remained in the shadows until the K-Pg mas extinction. Perhaps this event cleared out the incumbent occupants of aerial niches (such as the pterodactyls, and perhaps large insects), creating gaps into which birds could radiate?
This reading of the fossil record opposes a Darwinian/Lyellian view of gradual change being the primary factor shaping the fossil record, instead reflecting the catastrophism espoused by Cuvier (in 1796). Had the orbit of that cataclysmic meteorite been just minutely different, pterodactls might still rule the skies; perhaps theropods’ trajectory to larger brains may have continued to this day…?
Occasional catastrophes give way to large changes in life
End of cretaceous period – 66 Ma – large organisms affected badly – extinction – small dinosaurs do well

Question 19

Permo-Triassic Extinction outline?

Answer 19

• 220-250 Million Years ago
• “Great Dying” – largest extinction event in history
• Loss of 17% of marine orders, 52% of families – by end of Permian
• Before 45000 – 24000 species
• After 1800 - 9600 species

Aftermath
The mass extinction heralded a new world order: with the demise of incumbent taxa, new groups (e.g. molluscs, echinoids) rose to prominence. The last remnants of the ‘Cambrian fauna’ (e.g. trilobites) disappeared, and the ‘Palaeozoic fauna’ (e.g. brachiopods, crinoids, corals) were displaced from their dominant ecological positions. 
•	Hard hit
o	Brachiopods
o	Crinoids
o	Bryozoans
o	Insects, tetrapod’s, plants

Geological strata are difficult to date accurately, except where they contain volcanic ashes. Only recently (China) have ash layers close to the extinction event been recovered; precise dates with the Uranium-Lead clock time the extinction with great precision.

Question 20

Potential mechanisms of extinction?

Answer 20

Temperature:
Monitoring systems:
• Vegetation patterns:
o Migration of warm water algae to Poles
o Peat deposits to jungle style plants below Southern tropic
• British climate to Africa
• Isotopic excursions
o δ 18O – temperature proxy
o High water temp implied
o 21 degrees to 36 degrees (mean surface temp)
Leads to shut down of overturning circulation
• No deep water – rich in nutrients – no upwellings

Continental weathering:
• Strontium ratios
o 87Sr (continental crust) + 86Sr (Mid-Ocean Ridges)
• 87Sr from weathering; 86Sr ‘constant’
• Spreading rate is constant
• More 87Sr= more crustal material in oceans = more weathering = eutrophication?
• Cause or consequence? Death of plants?

Primary productivity:
• Plankton – eukaryote-dominated to bacteria-dominated
• Eutrophication = starve animals
• Bacteria release toxins + are harder to digest

CO2:
• Increase rapidly = natural selection can’t accommodate fast enough
• Ocean acidification: carbonic acid: pH lowers, proved by Ca isotopes
• Hyercapnia: too much CO2 in the body – decreases growth, survival and reproduction
• If reproduction decreased by 1% then species doomed over century
• Impedes skeletonization as CaCO3 is dissolved
• Bad for corals, calcitic brachiopods = 81% genera extinct
• Good for molluscs, arthropods, chordates = 38% genera extinct
• = non-random extinction

Anoxia:
Evidence:
•	Demise of burrowing 
•	-  Organic & pyrite-rich horizons at P/Tr boundary, even in facies where oxygen typically plentiful 
Causes:

• Reduced ‘intake’ of O2 by oceans
• Increased respiration of O2 by organisms and decay

Respiratory challenges:
Ammonids – 74%
Strong bohr effect in living relatives
CO2 inhibits respiration
A −5–7 ‰ carbon isotope excursion at the P–T boundary indicates the rapid delivery of ‘light’ carbon into the oceans.
The release of a smaller amount of extremely negative clathrates (methane hydrates) could produce a similar effect.
Clathrates: change in pressure from sand movement
• Build up of methane
• Lowers the density of water

5-10 million year of recovery:
•	Low diversity
•	Small animals
•	Fewer biomineralisers
•	Coal gap
•	Reef gap

Question 21

Potential causes of extinction? (Bacterium)

Answer 21

Methanosarcina
• A bacterium that could have evolved a new nickel-based enzyme 240+-41 Ma
• Could convert organic matter (acetate) to methane (CH4), leading to a rise in temperature and as methane broke down, CO2

Verdict: the evidence is circumstantial – molecular clocks are imprecise (and inaccurate?); availability of nickel difficult to constrain (even if extra provided by volcanism); scale of activity difficult to constrain. Not proven guilty beyond reasonable doubt.

Question 22

Potential causes of extinction? (Impactor)

Answer 22

Impact of an extra-terrestrial object with land would disperse rock particles and soot (from burning vegetation), plunging the Earth into an ‘impact winter’ (like nuclear winter but worse). If the rock particles were gypsum, rock salt or limestone, these could cause acid rain to nucleate. This is not good for vegetation
Evidence
An impact is now almost universally agreed as the cause for the dino-killing Cretaceous-Palaeogene mass extinction 66 Ma; the same lines of evidence used to advance this cause have also been put forwards for the P–T event, if with less effect:
Iridium
The only major source of iridium is extra-terrestrial objects: all of Earth’s naturally occurring iridium is locked up in the core. There is an iridium-rich layer near the P–Tr boundary… but it doesn’t contain loads of iridium, and occurs below the actual boundary layer. That said, not all meteorites are iridium rich – the impactor needn’t necessarily have left an iridium signature.
The footprint of impact
The case for a bolide impact would be strengthened if there was evidence of the crater where it landed. Candidates so far are not quite the right age or shape.
6–15 cm thick layers of claystone breccias have been interpreted as representing material ejected during an impact. But other interpretations are possible…
And shocked quartz grains – interpreted as being ‘whacked’ by a rapid impact – are much rarer and smaller than their equivalents at the K-Pg extinction; the texture might
instead represent a tectonic overprint.
Verdict: No, how would it cause temp and CO2 spike

Question 23

Potential causes of extinction? (Traps)

Answer 23

Millions of cubic kilometres of lava flooded Siberia right at the time of the P–Tr extinction. Volcanism of this scale would release poisonous gasses, fuel acid rain, and emit carbon dioxide. If lava erupted onto permafrost, it could sublimate frozen clathrates; if onto coal deposits, it could start sooty fires. This modus operandi seems to match our observations. 
Geochemical measurements (mercury concentrations and isotopic compositions) in oceanic sediments support a volcanic input of mercury at the right time – and in shallow waters, an influx of mercury isotopes associated with biomass (dead vegetation?) and soil (denuded after vegetation death?) – consistent with a peak in siliciclastic input in marine deposits and a temporary switch from meandering to braided river deposits in the sedimentary record. 
Mercury: a proxy. Additional kill mechanism

Siberian traps
• Acid rain/ poison gas
• Climate change

Burning coal deposits
• Smog
• Acid rain
Burning permafrost = clathrates insides
There’s also evidence that surviving life was quite unhappy – spores, for example, failing to develop successfully. Perhaps halogen gasses emitted by volcanoes attacked the ozone layer (think CFCs) – allowing more UV to reach the surface.
The verdict: There’s good evidence that volcanism occurred at an unmatched scale at the right time, and it’s easy to link the consequences of volcanism to the effects observed – as well as suggesting a few more exotic kill mechanisms