| Color Key | |
| Important key words or phrases. | |
| Important concepts or main ideas. | |
1. Large Blue Butterflies - ants - sheep story
- U.K. - populations of large blue butterflies declined due to habitat loss - e.g., urbanization, afforestation, over-collecting, pesticides, weather
- Extinction forecast starting in 1880s - set up a reserve in the 1970s and removed the resident domestic sheep >> butterflies disappeared
- Real reason more complicated
- Depends on sheep and ants

- Bottom lines:
- Species within an ecosystem interact
- Interactions are often unpredictable based on current knowledge
- Human are part of most (all?) ecosystems, and human activities affect ecosystems
- Humans can make things worse accidentally, even when trying to help >>> Fallacy of Benign Interference
- When interacting with the environment, proceed cautiously and humbly
Ecology encompasses population biology, community ecology, population genetics, ecosystem ecology >>> all central to conservation biology.
Biodiversity
- Species and diversity of species
- αdiversity
- Genetic makeup of species is raw materials
for
- evolution
- new crops
- modifying crops
- transgenics
- Composition of communities across a landscape
- β and γ diversity
- Biotic and abiotic environment and processes that support
the biotic community
- competition, predation, symbiosis
- cycling of nutrients, rainfall, temperature
Species: a collection of populations that actually or potentially interbreed under natural conditions and that are reproductively isolated from other such groups. Arise through evolution
Evolution: a change in the genetic makeup (allele frequencies) of a population in successive generations = central focus for all of biology. The primary mechanisms of evolution are adaptation through natural selection, and drift (random loss of alleles across generations).
Evolution is the key to:
- Adaptation to a changing environment
- Local adaptations
- Development of antibiotic and pesticide resistance
- Disease re-emergence
- Diseases affecting host behavior to increase disease spread
- Creating and maintaining crops
- Creating transgenic species
2. Species Extinctions
Natural - 5 mass extinctions, and extinctions in between
- Ordovician-Silurian (439 ybp) - 85% spp.
- Devonian (395 ybp) - 85% spp.
- Permian (253 ybp) - 50% all animal families - >90% all spp. (all trilobites)
- Triassic (213 ybp) - 76% spp.
- Cretaceous (65 ybp) - 85% spp. (all dinos)
- human driven
- different types of spp
Current - on par with previous mass extinctions
Differences compared to pre-historic extinctions?
- Pattern
- Then: genera, at sub-continental scale
- Now: worldwide, at speecies or subspecies level, selective, mostly endemic species - e.g. habitat specialists
- Cause
- Then: nature
- Now: humans
Rates of extinction are estimates - the majority of species on earth have not been identified
- Fossil record incomplete
- Use species-area relationships
- Patterns of species richness across world and within regions
How do we know the extinction rate is so high? - extrapolation from data on species-area relationships, & distributions and endemism vs. amount of habitat cleared
3. Key 1: Understanding Species' Distribution Patterns
Biogeography = study of the distributions of species and the processes that cause the distributions
Geologic time - long term processes
- Plate tectonics
- Speciation and extinction patterns
- Mountain and river formations
- Glaciation
- Volcanoes
Proximal Effects
| Abiotic | Biotic |
| temperature | competition |
| rainfall | predation |
| humidity | habitat distribution |
| mineral limitation | prey distribution |
| elevation | breeding requirements |
| soil type | disease |
| salinity | presence of symboint |
| fire | |
| physical complexity - more places to be, more species (e.g. rocky intertidal vs. sandy beach) |
Examples of Diversity Patterns
| >> | |
| Tropics | Temperate |
| Structural complexity | Simple habitats |
| High productivity | Low |
| Temperate deciduous forest | Temperate coniferous forest |
| Mainland | Island |
| Ecotones | Interior |
Large scale distributions = biomes (= habitat types)

Climate responsible for major distribution of biomes >>> anything that disrupts climate weather patterns would affect species distributions
Hotspots = parts of
earth with very high species richness; important focus of conservation efforts
25 areas identified - Comprising only 1.4 per cent
of the Earth's land surface, the hotspots contain as many as 35 per cent of all
terrestrial vertebrates and 44 per cent of all higher plant species.

Climate affected by
- ocean currents (redistribute heat)
- topography (mountains - rain shadow)
- land type (trees vs. desert vs. water
- chemical makeup of atmosphere (greenhouse gases)
>>>anything that disrupts climate would have dramatic effects on species distributions
3.1. Global warming
Global Warming = the rise in temperature of the Earth's atmosphere due to increased presence of greenhouse gases from human-related activities.
Global patterns
- Earth's temperature vary annually
- long-term cycles depending on tilt, distance from sun
- results in ice ages, warming trends
How the "greenhouse" system works:
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3.1.1. Greenhouse gases (GHGs)
- Examples: carbon dioxide, water vapor, methane
- GHGs related to atmospheric temperature
- Increase GHGs = increase temperature
- Humans messing with GHG content of atmosphere
3.1.2. Evidence of global warming and greenhouse gas (GHG) increasing
- measured increase in
Earth's mean
surface temperatures
- data exist from 1870s on
- show increase of 0.3-0.6oC in last 100 yrs
- 11 of the hottest years in the last 100 have occurred since 1980
- 2001 = 5th hottest ever in U.S.
- 1995 hottest year in last 100
- Problems with data?
- increased CO2 in atmosphere = best documented global
change
- atmosphere temp related to CO2
- CO2 measured accurately from 1957
- increased ~25%
- Greenland and Antarctic ice core records - 2 paths of
evidence
- Air bubbles trapped in the ice caps record
concentrations of stable gasses
- gas record for last 2000+ years
- CO2 concentrations were steady for over 1700 years, then skyrocketed
- supports recent atmosphere records
- radioactive 14C, with a half life of
5730 years, has a background level in atmosphere
- fossil fuels are millions of years old, so radioactive form is gone
- if increase is due o burning fossil fuel should see increase CO2, but dilute 14C
- this is observed = most CO2 increase in atmosphere has been due to burning fossil fuels
- Air bubbles trapped in the ice caps record
concentrations of stable gasses
- measured increases in other greenhouse gases since 1976
- methane
- chlorofluorocarbons
- nitrous oxide
- retreat of alpine glaciers
- extensive sruvace melting during the last 2 decades
- high-elevation air temperature records
- several isolated mountain peaks temp's increased >1oC during past century
- tropical freezing heights
- increased freezing-level heights over last 20 years - 4.5 m per year
- long-term changes in sea surface temperature in the tropics
All say increase in temperature or GHG
3.1.3. Arguments against causes and effects of global warming
- Little argument over the effect greenhouse gases could have on global warming
- Disagreement over: Causes, Amount of warming, Timing (rate of change), implications for life, what to do about it.
- Some criticisms = legitimate distrust of variable results
- Some = misunderstanding methods or interpretation, or desire to have the results be different
- Model predictions of global warming have not been validated by observed increases in temperature, or by smaller than expected increases.
- Models are wrong
- Even if temperatures increase a few degrees, this is less than nightly fluctuations and yearly fluctuations - what's the big deal?
- Even though the temperature is increasing, there is no demonstrated direct link between temperature changes and variation in greenhouse gases concentrations.
- Some people (including some scientists) have argued that warming will be beneficial as long as it is slow enough for crops to adapt.
- Most of the results are from computer models. Models are simplifications of the real world and will give you whatever result you want.
- Without greenhouse gases the Earth would be too cold to inhabit. Therefore, more greenhouse gases probably will make things even better.
- Even if global warming were true, and it is caused by greenhouse gases, there is nothing reasonable that we can do about it.
- Low credibility of scientists.
- Warming due to sunspots!
However, most scientists agree that
- there is a warming trend
- GHGs are a cause
- humans are increasing GHGs
3.1.4. Human-related sources of GHGs
- CO2
- burning fossil fuels and forests
- Methane
- rice paddies, cattle and sheep (fermentation, animal waste), coal mining, natural gas, biomass burning, landfills
- Nitrous oxide (N20)
- burning coal, forests, breakdown of N fertilizers, nylon production, rice paddies
- CFCs - chlorofluorocarbons
- up to 5000X the radiating force of CO2
- leaking refrigerators and air conditioners, evaporation of industrial solvents, plastic foam production, aerosol propellants
3.1.5. Consequences of global warming and greenhouse gas emissions
Some PREDICTED and some OBSERVED:
- Observed warming and rainfall pattern alteration -
predicted
- global precipitation should increase by 10-15%
- become more uneven spatially and temporally - floods and drought
- projections of 3-5oC warming in temperate regions, up to 18oC in polar regions
- Increased soil erosion due to more concentrated rainfall and expanded irrigation - predicted
- Sea level rise - observed
- global sea levels have been rising for the past 100 years (1-2 mm annually)
- Melting polar ice caps
- Coral reef bleaching - observed = expelling algal
symbiont
- due to increased water temperature
- leads to reduced photosynthesis, biochemical dysfunction, and failure to grow
- Other observed consequences (1999-2001)
- 20/50 species of frogs and toads disappeared from a 30 km2 tropical mountain-tops in Costa Rica
- crop growing season extended 11 days in Europe, 1959-1993
- poleward shifts in butterfly and bird species' geographical ranges
- earlier egg laying in wild birds in temperate zone
- fresh water lakes appearing in Arctic
Parmesan & Yohe - 2003. Parmesan C, Yohe G. A globally coherent fingerprint of climate change impacts across natural systems. Nature. 2003 Jan 2;421:37-42.
- Reviewed literature on effects of climate change on biodiversity
- >1700 species
- Looked for:
- range shifts
- advancement of spring events
- Found
- Significant range shifts averaging 6.1 km / decade towards the poles
- Significant mean spring advancement by 2.3 days per decade
- 279 species exhibit changes with 'very high confidence' due to climate change (IPCC criteria)
- IPCC = Intergovernmental Panel on Climate Change http://www.ipcc.ch/
4. Key 2: Understanding Species' Distribution Patterns
Island biogeography is the study of the distributions of species on islands and the processes that cause the cistributions >>> focuses on, colonization rates , extinction rates . A basic concept, first proposed in 1963 by Robert MacArthur and E. O. Wilson, to explain what determines the number of species on an island.
Colonization Component
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Colonization = successful immigration from mainland & establishment |
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Extinction Component
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Equilibrium Species Richness
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So, according to Island Biogeography Theory, reserves should be large & connected
5. Key 3: Understanding Species' Distribution Patterns
Species - area relationships
S = # species (species richness), A = area; c and z are constants
- Bigger area = more species
- S = cA2
- Take log of both sides, z = slope of the line: ln(S) = z*ln(A) + c
- z steeper on islands => species lost faster on islands as area decreases, colonization slower

6. Why are species going extinct?
Causes of species' Extinctions
- Habitat loss/degredation and fragmentation
- Exotic invasive species
- Loss of genetic variability
6.1. #1 Habitat loss and fragmentation
- Decreased area = smaller populations
- Increased islation = decreased colnization and rescue
- both increase extinction risk
- both decrease species richness
6.1.1. Edge Effects
affect species persistence
Edge occurs at ecotones = where 2 habitat types abut
General edge factors:
- where habitat types meet, more species are present = increase in predation and competition
- where habitat types meet, there are abiotic intrusions into the interior habitat
=> the result of habitat fragmentation is interior habitat gets smaller; species that require interior habitat types are most affected
| Effect | Distance (m) | |
| ABIOTIC | Windthrow of trees, desiccation, temperature, humidity, wind, sunlight | 100S-1000S |
| BIOTIC | Predators, competitors, brood parasites | 50-1000 |
Sao Paulo, Brazil: Atlantic Coastal Rainforest
- in 1500 - 82% forest coverage
- in 1973 - 8% forest coverage
6.1.2. Solutions for Preserving Species?
- Reserves, with buffers
- Where? Depends on what the reserve is for
e.g., save maximum diversity = on hotspots, save particular species? - Bigger = better
- bigger populations
- more species
- Connectivity
- rescue populations
- colonization after local extinction
Reserve Design "rules" based on
- Island Biogeography Theory
- Edge effects
- Protecting habitat-interior specialists

What configuration? Shape? Corridors?
Depends on goal - e.g., if interior species, round; if edge species, linear


Potential problem with corridors / connectivity of populations?
- Spread of emerging and re-emerging diseases
- Corridors as 'ecological traps'
- Disrupting local adaptations
- Spread of exotic, invasive species
6.1.3. Ecosystems
Group of interacting organisms (community) within physical environment at given point in time; includes species, processes (abiotic and biotic), and structure.
- no fixed boundaries - no matter where you draw the border to an ecosystem, there is an 'outside' that influences it e.g., many animals move, water comes from outside sources
- spatial area differs depending on what species are being considered e.g., pitcher plant vs. vernal pool vs. watershed
- disagreement over conservation focus - processes? hot spots? endangered species?
Are communities balanced? Kind of - it depends on:
- Definition of balance
- Time frame
- Degree of disturbance
Concern = assuming communities will recover
Communities tend to persist
Despite deaths of individuals within a community, a tropical forest tends to remain a tropical forest, and grasslands tend to remain grasslands.
- resilience = ability to recover from alteration
- persistence = ability to resist being altered
- constancy = keeping population numbers within bounds
Does species diversity per se matter? YES - work from Tilman et al.
- grassland plants - increase diversity a little, and primary productivity increases
- above-ground biomass after 2-yr drought = higher for more species-rich communities
In theory - work from Ostfeld et al.
- increased species diversity of disease hosts
- = increased # species with low disease competence ( = their probability of transmitting the infection from host to vector)
- = "dilute" the effect of competent reservoirs = reduce persistence in environ and spread to humans
Ecological 'services' are associated with processes e.g., Maintaining atmospheric quality & regulating climate , regulating supplies of fresh water and controlling flooding, detoxifying and disposing of wastes
1 part = Food Webs / Pyramids = The way people have schematically represented who eats whom in an ecosystem is a food web, which is a bunch of food chains. It is a model - the real world is much more complicated.
Community Structure/Trophic Levels:

Actually much more complicated.
Along with food webs, there are other interactions important to conservation biology: predation competition, symbiosis - tight relationship between 2 species:
-
parasitism - 1 species benefits, 1
harmed
- large blue butterfly
- cattle tick (Boophilus microplus)
-
commensalism - 1 species benefits,
the other not affected
- oxpecker
- remora
-
mutualism - both species benefit
- yucca - moth
- Clark's nutcracker
Complications?
- Understanding colonization patterns
- Must save both parts
- Different physiological tolerances – climate change
- Consequences of management actions
Semi-Myth: Ecosystems are Fragile
All species are NOT created equal. Keystone species: a species whose effect on the ecosystem is disproportionately large relative to its abundance or biomass.
Being a keystone
- alter structure of the environment e.g., woodpeckers, beaver, gophers, termites, leaf cutter ants ecosystem engineers
- drive energy flow of environment e.g., exotic species, provides food for many species during critical time of year, predators that drive prey diversity

Identifying keystone species:
- experimental removal is best, but often not possible
- comparative studies less powerful - sites with and without the species
- descriptive least powerful, but necessary (need to know your species)
6.2. Exotic, Invasive Species
# 2 on extinction cause list: outcompete native species, eat native species, alter community processes.
Terminology
- Native - evolved there
- Exotic - in range outside that where it evolved
- Alien - out of natural range
- Introduced - brought in by people
- Colonizer - made it to the new place itself
- Iinvasive - spread widely, push out native species (not always exotic)
- Naturalized - adapted to its new geography
- Feral - domestic animal that escapes and persists in the wild
How do species get to places they have not been in the past?
Why would people move animals to another area?
- Hunting/fishing
- Nile Perch introduced to Lake Victoria - 300 species of Cichlids before, <100 species of Cichlids now
- European rabbit in Australia - started with 12 rabbits, now ~200 million
- Aesthetics or lonely
- European Starling - eats fruits and grains, displaces native birds ; all due to Shakespeare!
- Mute Swan - displaces native birds, destroys wetland vegetation and wetland function
- Grey squirrel, introduced to Britain - eats bark from trees, eggs, chicks, brought squirrel pox
- Horticulture and agriculture - acclimatization societies
- Kudzu in the South - grows over everything
- Accidental transport
- Rats
- Brown Tree snake (Guam) - eat native animals, carry diseases, devastated ground-nesting birds (Guam Rail extinct) also lizards, power outages, no known control
- Transport through the mail, airplanes, cirt or mud under vehicle or on boots, shipped products (wood, shingles, hay, etc.) - Asian long-horned beetle
- Incidental invasion due to human effects - in particular,
habitat change
- Brown-headed cowbird
- Coyote
- Rats
- Biological control = deliberate
- Jamaica - rats, ants, bullfrog, ferret, mongoose - complete failure
- Micronesia (below)
6.2.1. Biological control - Trying to control rats in Micronesia
- good / bad refers to human interests; solid line who at what (eaten is what is pointed to)
- dashed line = should have eaten, did not

Bottom Line for Biological Control
- We do not understand ecosystem ecology well enough to predict what will happen when we introduce species
- Especially to control vertebrates
- Fallacy of Benign Interference
Success Stories?
Mostly controlling crop pests with invertebrates, control does not mean elimination
- Lady beetle - cottony cushion scales = eats citrus trees
Why are some species successful and some not? hypotheses based on ecology:
| Successful invaders should be/have: | |
| abundant in original range | fertilized female able to colonize alone |
| polyphagous (foraging generalist) | larger than most relatives |
| short generation times | associated with H. sapiens |
| much genetic variability | habitat / environmental (abiotic) generalist |
| Disturbed habitat users |
=>none of the ecological predictions yet tested work across all examples
Are all species introductions always a problem? NO
- most fail
- some gamebirds
- transplanting rare species
- Kalish Pheasant on Hawaii
- Black Robin on an island in the Indian Ocean
Can you mandate to remove exotic species from places they cause problems?
Not that simple - must reconcile societies needs/desires.
| Species | Problem | Public wants |
| rainbow trout | hybridize wih local trout | to fish for rainbow trout |
| chukar | displace mountain quail | to hunt easier species |
| honey bees | out compete native bees | honey |
| wild pigs | destroys habitat, eats natives | to hunt boar |
| cattle | can destroy habitat | cheap beef |
| cattle egret | eat endangered species (HI) | to see the species |
6.3. Loss of genetic variability
General l RULE of THUMB = genetic variability is good - * exceptions are common
Corollary = loss of genetic variability is bad
Observation: all closed populations lose genetic variability over time

Why is variability lost?
- selection - loss of genetic variability through selective disadvantage
- genetic drift - random loss due to chance as gametes are sampled from generation to generation
Inbreeding depression = decreased individual fitness due to the expression of deleterious alleles
Effective population size (NE) = the size of an ideal population that has the same rate of loss of genetic variability as the real population in question.
Ideal population: monoecious, fixed size, equal sex ration, random mating, no selection, closed, equal chance of producing young, non-overlapping generations, Hardy Weinberg equilibrium
How fast is genetic variability lost from a closed population?
Fraction of heterozygosity lost per generation from drift (neutral alleles)
1/2Ne=> 1-1/2Ne retained per generation from drift
=> a population reduced to size Ne will retain how much variability?
Proportion of original heterozygosity (H0) left after multiple generations
Ht = (1-1/2Ne)tH0
- t = time in generation, H0 = amount of genetic variability you start with
- Ne = effective population size, Ht = amount of genetic variability left after t generations
| Population size
(Ne) |
Amount of
genetic variability retained |
Amount present after 10 generations at that size |
| 50 | 99% | 90% |
| 10 | 95% | 60% |
| 4 | 87.5% | 26% |
| 2 | 75% | 5.5% |
Results of loss
- Loss of evolutionary potential
- Increased homozygosity
- Inbreeding depression = decreased individual fitness due to the expression of deleterious alleles
Inbreeding does not equal consanguineous mating
- Population can have increased inbreeding homozygosity without any mating of relatives.
- Mating with relatives increases the rate at which homozygous alleles are expressed.
Lethal equivalents = number of loci in heterozygous state that if homozygous would be lethal.
Scenario:
- Diploid organism, requires 2 individuals to produce young
- Focus is on one locus; first generation, all individuals unrelated. This means they share no genes in common (f=0). Each individual (numbers) starts with unique, neutral alleles (letters).
- Discrete generations (not overlapping)
- Mating with your sibling does not occur - referred to as "inbreeding avoidance"
- Imagine starting a new population in captivity, and you control who mates with whom

Genetic load = think of as # of "bad" alleles
Lethal equivalents = number of loci in heterozygous state that if homozygous would be lethal
Affecting Loss Rate:
- population size
- sex ratio / mating system
- variance among individuals in reproductive success
- fluctuating population size
Conservation goals for Ne:
- 50/500 rule - conceptually interesting, actually bunk
- Ne = 50 large enough to alleviate problems due to inbreeding
- Ne = 500 large enough to alleviate problems due to drift
- "acceptable inbreeding rate" varies by species, and within species depending on lethal equivalents
- level at which genetic variability is being retained: morphological trait vs. amino acid, answer varies by 8 orders of magnitude
- No simple rules
Things affecting Ne
- sex ratio of breeders matters; affected by mating system:
- variance among individuals in RS matters:
- Ne = 4N-2/Vk+2
- Vk = variance in gamete production, or variance in family size
- => as Vk increases, Ne decreases
- Change in population size over time matters:
- Fluctuations over time require averaging - not standard average - why? harmonic mean across years or generations

main point here is that average Ne is driven by smallest population size
Outbreeding depression
- a result of breaking up coadapted gene complexes
- through natural selection, populations become adapted to local conditions; drift also causes divergence
- Example: plants growing on soils that differ in their amount of heavy metal contamination are genetically different than those growing on clean soil
7. Emerging and Re-emerging Diseases
Developed more in the next lecture.
- Emerging disease = diseases whose incidence in humans has increased within the past two decades or threatens to increase in the near future
- Reemerging = disease that used to be a problem, but had become minor => becoming a problem again
Factors contributing to disease emergence or re-emergence:
- Evolution of existing organisms
- Kknown diseases may spread to new geographic areas or new human populations
- New contamination source
- Breakdowns in public health measures for previously controlled infections
- Population increase of hosts
- Living or working in areas undergoing ecological changes
- Global transportation, globalization of food supplies
- Human behavior
- Bushmeat trade
8. References and Resources
8.1. Organizations and websites
Endangered species http://eelink.net/EndSpp/
National Library for the Environment http://www.cnie.org/nle/#indepth
The Society for Conservation Biology http://conbio.net/
Bibliography of Genetic Variation in Natural Populations http://www.lib.umt.edu/guide/allendorf.htm
IPCC = Intergovernmental Panel on Climate Change http://www.ipcc.ch/
ProMED-mail web site at http://www.promedmail.org
Journal: Emerging Infectious Disease http://www.cdc.gov/ncidod
WHO Rabies Network http://www.who.int/GlobalAtlas/home.asp
AHEAD Emerging Animal Disease (Federation of American Scientists) http://www.fas.org/ahead/
National Wildlife Health Center http://www.nwhc.usgs.gov/
United National Environment Programme http://www.unep.org/
8.2. Books
Baron, David. 2004. The Beast in the Garden : a modern parable of man and nature.New York : W.W. Norton & Co.
Colburn, T. et al. 1996. Our stolen future. Dutton Pub.NY
Costanza, R (ed). 1992. Ecosystem Health: New Goals for Environmental Management. Island Press, Washington, DC.
DeSalle, R. (ed). 1999. Epidemic! The world of infectious disease. The New Press, NY.
Garrett, L. 1994. The coming plagues. Farrar, Strauss and Giroux. New York.
McCormick, JB and S Fisher-Hoch. 1996. Level 4: Virus hunters of the CDC. Turner Pub. Atlanta
Meffe & Carroll. 1997. Principals of Conservation Biology. Sinauer
Rapport, D, et al.. 1998. Ecosystem Health: Principles and Practice. Blackwell Science.
Rickelfs, R. Ecology. Chiron Press.
Wilson EO.1992. The diversity of life. Press, Cambridge, MA.
8.3. Important Journals (not exhaustive)
Biological Conservation
Canadian Journal of Zoology
Conservation Biology
Conservation Ecology
Ecology
Ecological Applications
Ecological Letters
Emerging Infectious Disease
International Zoo Yearbook
Journal of Applied Ecology
Journal of Ecology Journal of Wildlife Management
Landscape Ecology Landscape and Urban Planning
Nature
Oikos
Trends in Ecology and Evolution
Zoo Biology






