Finals summary

(Doesn't include premidterm stuff)

1Biodiversity and regulation of the Earth system¶

Conditions required for life:

• Liquid water
• Elements for metabolism/reproduction
• Energy
• Suitable environment

Water most important

Goldilocks zone: Region of space around a star that's suitable for liquidwater/life

1.1The Gaia hypothesis¶

The hypothesis that the environment in which organisms live in is a self-aware and evolving system which self-regulates its climate and chemistry to be suitable for life

Mostly bullshit

For the past billion years, Earth's temperature has been comparatively stable, no more than 15 deg warmer or 5 deg colder

4.5-2.5 bya the sun was a lot fainter than today, but it wasn't heavily glaciated - "faint early sun paradox"
Greenhouse warming was in effect at the time, with gases such as methane, ammonia, CO2. The organic haze idea

Why didn't the planet overheat?

Warmer planet creates better conditions for phytoplankton/plant growth, removing CO2 from the atmosphere, a particular phytoplankton that produces dimethyl sulfide is responsive to changes in climate, creating a negative feedback loop that stabilises the temperature of the Earth's atmosphere.

1.2Daisy World¶

I'm a daisy girl, in the daisy world

James Lovelock/Andrew Watson (gaia guys) developed a mathematical model for temperature regulation facilitated by organisms interacting with the environment

• Black daisies decrease albedo, makes the earth warmer, white daisies increase albedo, makes the earth colder. Each species of daisies has an ideal temperature for growth, the birthrate falls off by the temp deviation from the ideal, squared.

• Black daisies absorb more radiant energy from the sun, and grows faster in colder temperatures. But more black daisies increase the earth's temperature. White daisies are suited for warmer temperatures, they will start growing when the earth becomes warmer, and their growth rival the black daisies. The two populations reach equilibrium, and so does the surface temperature.

This homeostatic balance is being changed by human activities. Multiplication of greenhouse gases may change Gaia's negative feedback loops into positive feedback loops. This could bring an accelerated global warming.

Extensions of daisy world simulation include other species, which led to a surprising finding that the larger number of species, the better temperature regulation.

2What drives extinction?¶

(Humans)

Humans population increased, diversity of megafauna species decreased.

What are the main drivers of extinction?

On land:

• Habitat change
• Climate change

In freshwater:

• Invasive species
• Habitat change
• Pollution

In oceans:

• Climate change
• Over exploitation

On islands:

• Invasive species

2.1Invasive species¶

Most extinctions occur on islands, caused by predation (hunting or infectious disease). Islands are biologically isolated and have endemic species

2.2Exploitation¶

Hunting historically is the most important human-induced cause of extinctions. Overfishing is more recent - In eastern canada, 60% of fish stocks have collapsed.

Killing large animals for meat is problematic - large, slower to produce. Ecology of animal, economic demand, habitat characteristics influence hunting vulnerability.

Some Andean species of Cedro (a tree) are now thought to be locally extinct - roads are being made so harvesting becomes easier

2.3Pollution - Acid rain¶

Caused by emissions of CO2, SO2, NO, lakes become acidified, diversity of fish/invertebrates decrease. Changes soil chemistry and damage to foliage kills trees

2.4Pollution - Eutrophication¶

Pollution increases nitrogen/phosphorous in water, increases phytoplankton, and algae bloom, algae dies and the decomposing matter creates anoxic conditions. Over 50 years, nitrogen levels double, phosphorous levels tripled.

2.5Climate change¶

When climate changes, species' range also changes. Researchers measure such range shifts in 2 ways:

• Climate envelopes
• Escalator effect

2.5.1Climate envelopes¶

Decreases the area for a species to live in because the region with the species' prefered climate shifts, the species can now only live in the overlap between the old range and the new range.
A drop in area decreases diversity according to $S = cA^z$

2.5.2Escalator effect¶

Species are pushed up mountains and north (or south)

• Plants move up alps at 4m/decade
• Butterfly species move upward and northward.

Invasive species can move up into the range of another species, causing the other species to die.
North/south areas of the world, and mountainous regions are most vulnerable.

2.6What is land use?¶

A lot of the world's land is being converted to cropland over time.
Agriculture uses a lot of world's land - 12% for crops, and 24% for pastures.

Forest area is decreasing rapidly, 55% -> 30%.

A lot of annual loss in brazil, a lot of annual gain in china. Tropical forests disappear at a rate of 1.8% each year.

A lot of deforestation in the amazon, mainly caused by agriculture/cattle ranges. 25% of current deforestation is occurring in the brazillian amazon.
Logged areas are more susceptible to fire.

2.7Why does this matter?¶

Pristine ecosystems are more biodiverse than conventional farming systems.

Deforestation increases atmospheric CO2.
Increasing of agriculture promotes eutrophication.
Disturbance (fire/eutrophication/fragmentation/grazing) can make areas more susceptible to species invasions.

2.8Some good news¶

Lifestyle/food choices can make a difference in land conversion. Using trees in small scale farming practises and agroforestry can improve soil quality/fertility, reduce erosion. These systems have higher biodiversity.

Forested watersheds provide cheap water purification services.

Reforestation in andean ecuador. Communities reforested watersheds with native trees.

3Biodiversity loss: past and present¶

All species go extinct

Different clades tend to dominate at different times.

Defining background extinction rates:

1. Number of species that normally go extinct over a given period of time.
2. Rate given in million species years
3. Species survival rate over time.

3.1Five mass extinctions¶

1. Ordovician 12% families 65% species, 445 mya caused by large glaciation/sea level fall
2. Devonian 14% families 72% species, 365 mya caused by asteroid
3. Permian 52% families 90% species, 250 mya caused by asteroid lead to global warming/low oxygen conditions
4. Triassic 12% families 65% species, 210 mya caused by asteroid
5. Cretaceous 11% families, 62% species, 65 mya caused by asteroid

Mass extinctions

A loss of over 75% of species (mean species extinction rate = 25% per millions of years, mean species lifespan = 4 mil)

• Number of extinct taxa is much higher than bg numbers
• Event happens very suddenly and quickly in geological time
• Affects several taxa, ecosystem, biomes
• Geographically wide reach, often global
• Causes differ qualitatively/quantitively from those background extinctions.
• Recovery proceeds by spreading of previously non-dominant taxa or of new taxa, or by restructuring of ecosystems.

Terrestrial causes of mass extinction

1. Plate tectonics. Big continents support less diversity than split up continents, because with different continents different species can fill the same niche but not outcompete each other.
2. Globally low sea-levels, animals living at depths of less than 1000 m run out of space when sea levels drop.
3. Rapid climate change, organisms tend to migrate (or extinct) rather than evolve
4. Lack of oxygen in the ocean. H2S forms in anoxic conditions, and it might be released in large quantities when the ocean is disturbed. Might have caused or contributed to the Ordovician-Silurian, devonian, Permian-triassic and triassic-jurassic extinctions. Trigger for those extinctions appear to be caused by a rise of CO2 levels to 1000 ppm.
   • Increased CO2 cause planet to warm
   • Warm planet stops ocean currents, lack of circulation makes the ocean lose oxygen
   • A bacteria takes over in these anoxic conditions, it produces H2S, when H2S is greater than 200 pmm, every animal is killed in the ocean
   • The H2S leaks into the atmosphere and animals/plants are killed

Extraterrestrial causes of mass extinction

1. Supernova explosions - occur every 50 years in milky way. No evidence that it influenced life on Earth
2. Impact of large asteroids/comets, nine mile-wide asteroid struck the earth on the tip of the yucatan peninsula, in the gulf of mexico. This would result in massive forest fires/severe storms, reduction in air quality, ocean to ocean tidal waves, cloud sunlight for longer than 6 months.

Alternative explanations for extinction of dinosaurs:

• Small brains
• Volcanism
• Stress
• Outcompeted by invertebrates for primary production

Causes of mass extinctions:
External causes: changes in habitat so rapid/major that organisms cannot migrate/adapt: terrestrial and extraterrestrial causes
Internal causes: Not probable, because many different phyla on land/sea must be vulnerable.

3.2Human impacts on biodiversity in prehistoric times¶

Humans had more impact in places further away from africa because the animals did not coevolve with humans.

3.3Mass extinctions vs bg extinctions¶

Background extinctions are typically continuous and low-level, caused by environmental factors or biological factors, species biology/ecology predict species vulnerabilities to background extinctions. Mass extinctions are rapid and severe.
Extinctions are more random during mass extinctions: extinction cascades, basal species P is removed, a cascade happens that lead to other higher trophic species being removed.

Are we about to enter a sixth mass extinction?

Methods of comparing present and past mass extinctions:

• Assess percentage loss of species
• Compare currently measured extinction rates to background rates assessed from fossil record
• Use various modelling techniques, including species-area relationships, to assess loss of species
• Compare currently measured extinction rates to mass-extinction rates
• Use molecular phylogenies to estimate extinction rate

Background rate: approx 1 extinction per MSY

3.4IUCN Thread categories¶

• Extinct. No reasonable doubt that the last individual has died.
• Extinct in the wild. Only survivors are in cultivation, captivity or naturalized population well outside the past range.
• Critically endangered. When the best available evidence indicates that it meets any of these criteria:
  • Reduction in pop size
  • Geographic range < 100 km², area of occupancy < 10 km²
  • Fewer than 250 mature individuals and declining
  • Fewer than 50 mature individuals
  • Quantitative analysis showing the probability of extinction in the wild is >50% within 10 years or 3 generations
• Endangered, same as above, but 5000 km2, 500 km2, 2500 mature individuals, 250 mature individuals, >20% within 20 years or 5 generations
• Vulnerable, same as above, but 20000 km2, 2000 km2, 10000 mature individuals, 1000 mature individuals, >10% within 100 years
• Near threatened, evaluated against the criteria, but does not qualify for the above 3, but is close to qualifying in the near future
• Least concern, none of the above

40% in least concern, 36% are threatened (CE, EN, VU)

Red List Index value

1.0 means all species in the group are LC, 0 means all species are extinct.

Corals have the most loss in diversity, amphibians has the lowest red list index value

Sometimes when a host species is endangered, the affiliate species are also endangered.

4Biodiversity loss: extinction drivers¶

• Habitat Destructions, currently biggest threat.
• Invasive species, mostly exotic species on islands causing extinctions to native species.
• Exploitation - hunting/harvesting
• Pollution. Acid rain and eutrophication
• Climate change

In developing world, impacts are largely local, in developed world, many impacts are exported.

Economic inequality aggravates biodiversity loss

Human impact on biodiversity, I:

$$ I=PAT $$

P = human population size
A = average per captita affluence or consumption
T = average environmental impact of the technologies and socioeconomic-political systems used to generate affluence

5Biodiversity loss: predicting species extinctions¶

At least 80 mammal extinctions since 1500, over 1200 species listed as threatened by IUCN.

Quantifying extinction risk

Extinction risk in mammals: the IUCN Red List

Criteria for Red Listing:

• Rapid population decline
• Small range + decline/fluctuation
• Small and declining population
• Very limited numbers
• Quantitative analysis

5: extinct/extinct in the wild
4: critically endangered
3: endangered
2: vulnerable/conservation dependent
1: near threatened
0: least concern

% risk differs among orders, and close relatives are more similar than expected by chance: primates are at 40% at risk, while rodents are at around 20%.

5.1Predictors of risk¶

Risk = Threat + Susceptibility + Susceptibility x Threat

What might help species to be bulletproof?

Fox: Large geographic range, high reproductive output, ecological generalist
Panda: Small geographic range, low reproductive rate, ecological specialist

For small animals, environment/human interaction terms are more signficant, while for large animals, life history is more important.

Factors for mammals:

• Life history: adult mass, weaning age, litter size, litters per year, gestation length
• Ecology: population density, geographical range size
• Environment: Precipitation, latitude, actual evapotransporation
• Human impact: Human population density
• Interactions: adult mass x latitude, geographical range x adult mass, geographical range size x human population density

For carnivores, geographic range size/gestation length are good predictors

5.2Measures of threat intensity¶

For species that has don't have a lot of people in its geographic range, geographic range size and population density is less important of a factor than species which have a lot of people in most of its geographic range. Those species with a lot of people in its geographic range also is influenced by gestation length in determining the risk.

As human popoulation increase, the importance of biology in determining extinction risk will also increase. Species of most concern have "poor" biology, and live in regions of rapid human population growth.

5.3Predicting future risk in carnivores¶

• Project human population density 25 years from now
• Identify species which move from low to high threat intensity
• Predict risk using model for high-threat intensity species

Species with highest predicted risk increase: African Linsang, Common gent, Uganda genet.

5.4Latent risk¶

Latent risk

Predicted risk - current risk.

Hotspots of latent risk: Northern canada and alaska, greenland, siberian tundra, south east asia, tasmania.

6Global conservation & the future of biodiversity¶

6.1Nine templates of global priorities¶

• Global biodiversity hotspots: A region must contain at least 1500 species of vascular plants as endemics, and have lost at least 70% of its original habitat.
  Myers, et al. (2000) listed 25 biodiversity hotspots.

  • Central/south america, mediterranean coast, southeast asia, new zealand.

• Crisis Ecoregions: Biomes and ecoregions where biological diversity and ecological function are at greatest risk because of habitat conversion and lack of protection

  • Highest risk regions: Mediterranean biomes, temperate grasslands

• Endemic Bird Areas: Proposed by Birdlife International, 50% of range restricted birds are threatened or vulnerable, 218 areas in range restricted birds, 4.5% area of Earth. Mostly forest, 77% located in tropics and subtropics

  • Indonesia, Mexico, Brazil, Peru, Colombia, Papua New Guinea, China, 70% overlap with areas with endemic plants

• Centers of Plant Diversity: Identified by WWF and IUCN. Rich in plant species or have high number of endemics, vary enormously in size, from extensive mountain systems, to island complexes and small areas. Mainland: more than 1000 species and 100 endemics, Islands: 10% endemics or 50 endemics. Other factors include importance to humans, and high devastation of habitat by humans.

  • South america, rockies, mediterranean.

• Megadiversity countries: World's top biodiversity-rich countries - countries with a high number of species. 17 countries have 66% of the world's known spp, 80% of the endangered spp found in these countries. To achieve best results, we concentrate on countries richest in diversity and endemism, and most severely threatened.

  • China, india, US, AUS, BR, Mexico

• Global 200 ecoregions: proposed by the WWF, analyzed marine/fresh water/terrestrial ecoregions for their uniqueness. Factors considered: endemic species, species richness. A total of 238 Global 200 ecoregions have been identified so far. 142 are terrestrial, 53 are freshwater, 43 are marine. 50% classed as endangered

  • South america, northern canada, southern states, central russia, southern china, mediterranean coast, southern africa, aus

• Last of the wild: Wildlife conservation society and center for international earth science information network @ Columbia University. 10% wildest areas of the terrestial planet. Mapped human influence, identified 569 wild areas, may be the easiest to conserve.

  • Northern Canada/alaska, amazon, northern african, northern siberia, western china, australia

• Frontier Forests: World's remaining large intact forests, proposed by world resources institute and global forest watch. Large ecologically intact, relatively undisturbed natural forests. Contribute large portion to ecological services such as watershed protection and climate stabilization.

  • Northern canada, amazon, northern siberia, south east asia.

6.2Limits to these methods¶

• Data limits
• Cost
• Climate change not considered
• Ignoring political/institutional capacity/will
• Only one considers aquatic ecosystems
• Invertibrates not considered directly
• Transition zones and benign zones that are important for speciation or refugia not considered

Congruence among conservation schemes

Reactive zones are in central america, southern brazil, central africa, mediterranean coast, southeast asia
Proactive zones are in northern south america, northern canada/greenland, north africa, northern aus, russia

7Future of biodiversity¶

7.1what are the effects of humans on speciation¶

Humans cause:

• Habitat loss
• Species invasions, agriculture, exploitation
• Climate change
• Pollution

We can use phylogeny as a record of speciation, to see the rate of speciation in history.

7.2Causes of speciation¶

• Geographic isolation: small populations, external barriers, parapatry
• Ecological speciation: environmental gradients, sympatry, host-shifts, ecomorphology
• Reproductive isolation: sexual traits, plumage, genital morphology, reinforcement
• Genome changes: ploidy, chromosome rearrangements, hybridisation

Are these likely to change??

7.3Habitat conversion¶

Reduction of the area of natural habitat, fragmentation of remaining natural habitat for organisms restricted to their natural habitat

Increase in area of modified matrix habitat, for organisms that colonise the newly formed habitat

7.3.1Reduction of the area of natural habitat¶

Extinction rates will increase due to smaller range and lower abundance. Speciation rates will decrease with smaller area because of the lower chance of encountering conditions promoting speciation, such as geographic isolation or heterogeneity of environments

• No speciation on islands < 80 km in diameter

7.3.2Fragmentation of remaining natural habitat¶

For species that survive the transition, what will be the effect on speciation rates?
Dispersal among patches: islands or metapopulation, environmental variation among patches. Speciation rates might increase due to isolation and divergence among patches, but might not if survivors are those able to disperse among fragments.

No evidence for higher speciation/extinction in more subdivided clade for Ilybius and Deronectes

7.3.3Increase in human-dominated matrix¶

Initial selectivity for gap/weedy organisms, later specialization. Large area but less biomass, different allocation among trophic levels. Ecological divergence between patch and matrix populations, but matrix biotically uniform among areas.
Potential for high speciation rates and diversification in lineages invading the matrix. Finches, foxes, squirrels

7.4Species invasions¶

New opportunities for speciation:
Invasives: allopatric divergence or hybridization
Natives: host shifts in plant feeding insects

Depends on if invasive populations are isolated from source populations, and how homogenized the environment is

7.5Climate change¶

Species are adapted to present/past environment

Scenario 1: Ecological shuffling

Species ranges shiftinto areas with suitable habitat, composition and relative abundances change. Assume no new combinations of environment and no restriction to dispersal

Scenario 2: evolutionary turnover

Widespread extinction with survival of a subset of species, survivors adapt to new environment and diversity into empty niches.

Fossil evidence indicates 5-10 MYA for scenario 2.

Climate change could lead to evolutionary turnover over timescales of millions of years.

7.6Effect of climate on evolutionary rates¶

Environmental energy increases mutation rates and decreases generation times, which increases evolutionary rates, which increases speciation rates. Prediction: Human effects on the environment might speed up evolutionary rates and increase potential biomass.

7.7Could/should conservation manage future speciation to mitigate the extinction crisis?¶

1. Maintain large as possible areas for speciation, manage land to promote desirable speciation events
2. Identify and conserve speciation hotspots, e.g. mountains.

Speciation would not yield benefits to millenia, extinction management is an immediate solution to an immediate problem