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Tufts OpenCourseware
Author: J. Michael Reed
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OCW Zoological Medicine 2008
Ecology and Conservation Biology Review (2009)
M. Reed, PhD
Cummings School of Veterinary Medicine at Tufts University

1. An Illustration - Large Blue Butterflies - Ants - Sheep Story

  • U.K. - populations of large blue butterflies declined due to habitat loss - e.g., urbanization, afforestation

  • Extinction forecast starting in 1880s

  • Causes considered : habitat loss, over-collecting, pesticides, weather

  • Real reason more complicated

  • Depends on sheep and ants



  • Grazing

    • kept open ground, where the ants nested

      • if turf increased by 2cm = another species of ants colonize!

    • promoted growth of thyme – colonized bare ground

      • food plant of young caterpillars

  • Obligate parasite

  • Caterpillars wander around waiting for ants to adopt them

    • trick the ants – give them sugar (they produce it and exude it)

    • ants bring them back to nest

    • there ants acquire smell of ants, provide sugar, BUT eat ant larvae

  • Figured out too late >>>> went extinct in Britain in 1979

  • Reintroduction efforts have been ongoing since 1980s

  • Bottom lines:

    • Species within an ecosystem interact

    • Interactions are often unpredictable based on current knowledge

    • Humans are part of many ecosystems – they affect & are affected

    • Humans can make things worse accidentally, even when trying to help >>> Fallacy of Benign Interference

  • When interacting with the environment, proceed cautiously

1.1. This class will provide an Introduction to:

  • Biodiversity – definitions, patterns

  • Risks to biodiversity

  • Distribution, abundance, and extinction of species

  • Sources of problems, potential solutions

2. Biodiversity

  • Species

  • Genetic variability

  • Population structure

  • Communities

  • Ecological processes

  • Abiotic processes

  • “Biological phenomena”

2.1. Species and diversity of species

  • α diversity

  • Genetic makeup of species is raw material for:

    • evolution

    • new crops

    • modifying crops

    • transgenics

2.2. Evolution – central to:

  • Adaptation to a changing environment

  • Local adaptations

  • Disease re-emergence – development of antibiotic resistance

  • Emergence of pesticide resistance

  • Diseases affecting host behavior to increase disease spread

  • Creating and maintaining crops

  • Creating transgenic species

2.3. Population structure – sub-populations differ

  • Genetics

  • Morphology (function of genetics + environment)

  • Behavior

  • Interactions with other species

Goal (often) is protection throughout a species’ historic range.

When might this be an unreasonable goal?

2.4. Species composition – communities, assemblages; and how they change across space

  • Gamma (γ) diversity

  • Species composition across landscapes

  • γ = α * β

  • β diversity is a measure of species turnover

  • β = γ /α = total diversity divided by mean local diversity

2.5. Interactions among species

  • Predator-prey

  • Competition

  • Symbioses

2.5.1. Symbiosis – tight relationship between 2 species

  • Parasitism – 1 species benefits, 1 harmed

  • Commensalism – 1 species benefits, the other not affected

  • Mutualism – both species benefit

Examples of mutualisms – often important in conservation biology:

  • yucca plants and moths

  • lichens

  • ants-swollen-thorn acacia

2.6. Abiotic environment & processes that support the biotic community

  • Nutrients, water

  • Elevation, slope, aspect, temperature

  • Humidity, salinity

  • Competition, predation

2.7. Biological “phenomena”

  • Migrations

  • Large aggregations

  • Fall colors

“Save Biodiversity” = not very useful command – what do you mean? How?

2.8. Species extinctions

  • Natural/geologic - 5 mass extinctions, & extinctions in between

    • e.g., Cretaceous (65 ybp) – 85% of species went extinct, including dinosaurs

    • account for 10% of pre-historic extinctions

  • Current – on pace with previous mass extinctions

    • As a society, we have decided that human caused extinction are something we need to prevent (or minimize)

  • Differences compared to pre-historic extinctions?

    • pattern - currently = mostly endemic species and subspecies worldwide

    • vs. genera at subcontinental scale

    • cause - currently = humans

  • Current problems:

    • 20% of all bird spp extinct in past 2000 yrs

    • 50% of fungi spp in Europe may have become extinct in past 60 yrs

    • in jeopardy – IUCN 2004 report:

      • 1/8 of all bird species

      • 1/4 of all mammals

      • 1/3 of amphibians

      • almost 1/2 of turtles and tortoises

    • 15,589 species are known to be in a perilous position

2.9. Species richness

  • 1.5 million species described

  • 30-100 million thought to exist

  • New species described each year

    • 2003

      • a new species of whale!

      • a new order of insect described = 1st since 1914

    • 2001-2004 – 100s of new marine species (including fish)

    • 2006 – Indonesia – dozens of new animal and plant species found

2.10. Estimating what we do not know (#species, extinction rate) is hard

  • Access to new habitat typically yields new species

  • Also, access to new parts of traditional places

  • Need experts to ID species

Canopy fogging in tropical forests

  • ~55,000 species of trees & vines

  • ~9 unique specialized beetles each

  • only ~44% of beetles are in the canopy

  • ~1/5 insects is a beetle

So, 55,000 x 9 x 2 x 5 = ~5 million insects in tropical forests

2.11. Why are species where they are? Why do we care? (Aside from extinction estimates)

  • Knowing where to reintroduce species

  • Understanding what limits distributions of endangered species

  • Allows us to understand and perhaps anticipate consequences of environmental changes

  • Identifying hotspots

  • Reserve design

  • Identifying exotic species that are or might become a problem

  • Need to know for successful recovery & restoration

2.12. Does species diversity matter?

  • Intrinsically, yes, to some people

  • How about practically? (for the other people)

  • Primary productivity in grassland plants increase diversity a little, and productivity increases

    • determines energy available in an ecosystem

    • affects: # of species, # of individuals, # of trophic levels in an ecosystem

  • Biodiversity might reduce disease impact

    • many infectious diseases of humans reside in nonhuman reservoirs

    • vectors often feed from many hosts

    • spp differ in their “competence” = their probability of transmitting the infection from host to vector

    • presence of hosts with poor competence might act to “dilute” the effect of competent reservoirs = reduce persistence in environ and spread to humans

3. Biogeography = study of the distributions of species and processes that cause them

3.1. Large scale: geologic factors & time frame

  • Plate tectonics

  • Mountain, river formation

  • Speciation and extinction patterns









    habitat distribution

    mineral limitation

    prey distribution


    breeding requirements (e.g., distribution of pollinator; presence of trees; etc.)

    soil type



    presence of symbiont


    physical complexity - more places to be, more species (e.g., rocky intertidal vs. sandy beach)

  • Recent/proximate forces – abiotic

  • Biomes = largest spatial scale ecologically recognized

    • Climate is responsible for major distribution of biomes

  • Climate affected by

    • ocean currents (redistribute heat - currents, upwellings)

    • chemical makeup of atmosphere (greenhouse gases)

    • topography (mountains - rain shadow)

    • land type (trees vs. desert vs. water - e.g., affects amount of moisture entering the atmosphere)

So you can see that anything that disrupts weather patterns (temperature, rainfall) would have a dramatic effect on species distributions

3.2. Humans impacting the world:

  • Food production

  • Water use

  • Energy

  • Urbanization

3.3. Climate change

Global Warming = the rise in temperature of the Earth’s atmosphere due to increased presence of greenhouse gases from human-related activities.

Better to refer to global “ climate change ”, since more than just temperature is affected.

  • Greenhouse effect

  • Greenhouse gases

    • ex., carbon dioxide, water vapor, methane

    • GHGs related to atmospheric temperature

    • ↑ GHGs = ↑ temperature

    • humans messing with GHG content of atmosphere

    • 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

  • Evidence of global warming and/or greenhouse gas (GHG) increases

    • mean surface temperature has increased - rainfall pattern also has changed

    • melting glaciers and permafrost

    • mountain peak air temperature records

    • freezing elevations in the tropics have risen

    • atolls are disappearing under water (Carteret atolls evacuated – part of Papua New Guinea)

  • Link to greenhouse gases

    • increased CO2 in atmosphere - Greenland and Antarctic ice core records - 2 paths of evidence

      • CO2 concentrations were steady for over 1700 years, then skyrocketed

      • radioactive 14C ratios - fossil fuel are millions of years old, so radioactive form is gone

    • burning fossil fuel should increase CO2, but dilute 14C

    • this is observed = most CO2 increase in atmosphere has been due to burning fossil fuels

Scary stuff:

  • Increases of other greenhouse gases

  • Some arguments against global warming, GHGs as cause, human’s role, what to do

    • even if temperatures increase a few degrees, this is less than nightly fluctuations and yearly fluctuations - what’s the big deal?

    • maybe it will be beneficial

3.3.1. Lots of Evidence of Global Warming

  • Research; images from space

  • IPCC = Intergovernmental Panel on Climate Change

  • Ice caps melting, glaciers receding

  • Effects on wildlife

    • extinctions

    • disrupting ecological processes

    • range & phenology (timing) shifts

    • sea level rise

3.3.2. Human sources of GHGs

  • CO2 - burning fossil fuels & forests

  • Methane

    • rice paddies, cattle and sheep (fermentation, animal waste), coal mining, natural gas, biomass burning, Landfills

  • Nitrous Oxide

    • burning coal, forests, breakdown of N fertilizers, nylon production, rice paddies

  • CFCs

    • leaking refrigerators and air conditioners, evaporation of industrial solvents, plastic foam production, aerosol propellants

Given observed global warming, if human-caused emissions are not the primary cause of the problem, should our response be different than if human-caused emissions are the primary cause?


3.4. Island biogeography is the study of the distribution of species on islands

  • Tried to approach the problem differently than tradition

  • Instead of looking at phylogenetic patterns of speciation and dispersal, it used a dynamic approach that ignored taxonomic affiliation

  • Focused on :

    • colonization rates

    • extinction rates

  • A basic concept, first proposed in 1963 by Robert MacArthur and E. O. Wilson, to explain what determined the number of species on an island.

    • inspired by patterns observed on islands, especially those being colonized after volcano cleared the islands

    • observed:

      • numbers go up rapidly

      • species turnover

      • close on an equilibrium number of species

  • Has become an important principle in conservation biology

  • Applied to reserve design and placement

Island Biogeography
Island Biogeography

4 Island Biogeography model
4 Island Biogeography model

  • Provides insight to species’ extinctions

    • # 1 cause of extinction globally = habitat loss & fragmentation

      • decreased area = smaller populations

      • increased isolation = decreased colonization and rescue

    • both increase extinction risk

    • both decrease species richness

3.4.1. Species – area relationships

  • Bigger area = more species

  • Steeper on islands >> species lost faster on islands, colonization slower

Species Area Ratio
Species Area Ratio

3.4.2. Edges:

  • Where habitat types meet ( ecotone )

  • Species that live in one habitat type can encroach on the other habitat type

  • Increased predation and competition

  • Abiotic effects

  • Important to species whose distributions depend on abiotic effects

  • Some species live only in the interior of habitat types = most affected

  • Interior gets smaller as you create edge

  • Edge effects:


    Distance (m)


    Desiccation, temperature, humidity, wind, sunlight

    100 -1000


    Predators, competitors, symbionts

    50 - 1000

3.4.3. Application = Reserve Design

“Rules” based on island biogeography theory, edge effects, protecting habitat-interior specialists, studies of diversity patterns

4. Community = a group of interacting organisms; subset of ecosystem

4.1. 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.

Food Webs = a more detailed model of species interactions

Disrupted by climate change

4.2. “Ecosystems are fragile”, “Endangered species are fragile” = semi-MYTHs

  • Many of the impacts we have on the environment are as subtle as paving

  • Do not make the mistake of thinking that each component of the ecosystem is necessary for the functioning of the ecosystem

  • The “semi” part: there are components of some ecosystems that truly are fragile

    • e.g., cryptobiotic soils in deserts => walk on it = 100 years to recover

      • (blue green algae = cyanobacteria)

      • fix N ( often limits growth of plants and some animals

  • There are numerous examples of ecosystems losing species and the ecosystem goes on functioning in an apparently fine fashion

  • Not all species are created equal -> some species are more important to maintaining ecosystems than are other species -> loss of some spp has smaller impact

All species are NOT created equal (from a biological function point of view)

4.3. Keystone species :

A species whose effect on the ecosystem is large, and disproportionately large relative to its abundance. Ways to be a keystone species:

  • 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

  • Model:

    • Keystone species = high community influence = change in a community or ecosystem trait per unit change in the abundance of the species

Community Influence
Community Influence

  • Examples:

    • keystones: sea otters, predatory whelk, freshwater bass

    • dominants: trees, kelp, prairie grass reef-building coral

  • How to determine whether or not a species is a keystone?

    • experimental removal is best, but often not possible

    • comparative studies less good - sites with and without the species

    • descriptive least good, but necessary (need to know your species)

5. Exotic, invasive species

#2 on extinction cause list

5.1. Definitions

  • Native – evolved there

  • Exotic = alien – in range outside that where it evolved

  • Introduced – brought in by people

  • Colonizer – made it to the new place itself

  • Invasive – expands its range, usually rapidly

  • => native spp can become invasive

  • Naturalized – adapted to its new geography

  • Feral – domestic animal that escapes and persists

5.2. Why do people move animals to another area?

  • Hunting or lonely

    • Nile perch

    • European rabbits

    • European boar

  • Aesthetics

    • European starling

    • mute swan

    • gray squirrel

  • Horticulture, Agriculture & Ornament

    • kudzu

    • tamarisk (salt cedar)

  • Accidental transport

    • rats

    • brown tree snake

  • Incidental Invasion due to Human Activities

    • brown-headed cowbird

    • rats

      • Laysan rail ( Nesoclopeus immaculatus )

      • endemic to Laysan Island, Hawaiian Islands

      • flightless

      • omnivore

      • population size estimates pre-WWII 2000-5000

      • rabbits introduced to Laysan – as food for local guano harvesters

      • harvest eventually stopped, rabbits stayed

      • no predators = rabbits soon ate the entire vegetation cover on the island, turning it into a barren dust bowl

      • rail extinct on Laysan in the 1920s

  • Biological control = deliberate

    • rats in Jamaica

    • rats in Micronesia (diagram below)

      • good / bad refers to human interests

      • solid line who at what (eaten is what is pointed to)

      • dashed line = should have eaten, did not

Rats in Micronesia
Rats in Micronesia

5.3. 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

5.3.1. Success stories?

  • Lady beetle vs. cottony cushiony scales

  • Weevil vs. spotted knapweed

  • Cactoblastis moth vs. prickly pear cactus

5.4. If a species’ introduction hurts an ecosystem, is this a clear mandate to remove it?

  • NO – it all depends on the public

  • Species often are desired by the public regardless of the impact on the ecosystem:

  • Example, rainbow trout

    • hybridized with local trout, such as cutthroat trout, and wipes out the species

    • BUT, public wants to fish for rainbow trout

5.4.1. Cats as environmental disasters?

  • Urban and suburban settings

  • Pets that are allowed to wander free & feral cats

  • Study done in Britain on impact of cats on wild animals

    • average 1 cat / 4 houses

    • study done in a small town (173 homes)

      • 70 pet cats studied for a year (pet = being fed at home)

      • killed and brought home 1090 wild animals; 37 species

      • known = minimum

    • another study - brought home 50% of kills

      • = double kill estimates

    • recreational - not for food

    • Estimated that 30% of sparrow deaths in that village was due to cats

    • Britain has ~6 million domestic cats

    • if this predation rate is typical, 200 million birds & small mammals killed per year in Britain

  • no process of feedback to decrease domestic cat populations when bird populations impacted

  • Why so little public concern?

6. Threats to Endangered Species (U.S.)

6.1. General Patterns – Extinction Risk

  • Within species

    • smaller populations = higher risk than larger populations

    • larger population fluctuations = higher risk

  • Stochastic events = those with variability / unpredictability

    • demographic

    • genetic

    • environmental

      • catastrophe

  • Heath Hen example

    • subspecies of greater prairie chicken

    • Eastern grasslands, heathlands

    • Moderately large range

    • harvested

    • threats:

      • hunting

      • habitat loss

      • fire & grazing suppression

      • introduced predators

    • last population wiped out by multiple stochastic events

      • fire (destroyed cover)

      • a gale

      • a cold winter

      • late frosts

      • sudden upsurge in the number of predators

  • General patterns among species of extinction risk

    • narrow geographic range

    • 1 or a few populations

    • habitat specialists at higher risk

    • species in symbiotic relationships

    • declining population size

    • harvested by people

    • use multiple habitats during lifetime

    • behaviorally vulnerable

    • rare species are at risk

    • species on islands

  • Why are island species so vulnerable?

Humans are a problem:

Factors affecting vertebrate extinction following human colonization on oceanic islands

Promotes extinction

Delays extinction

Abiotic factors

Island size




Flat, low

Steep, rugged


Sandy, non-calcaneous, sedimentary

Limestone, steep, volcanics


Nutrient rich

Nutrient poor


No near islands

Many near islands


Seasonably dry

Reliably wet

Biotic factors

Plant diversity



Animal diversity



Marine diversity



Terrestrial mammals



Species specific traits

Ground-dwelling, flightless, large, tame, palatable, colorful feathers, long and straight bones for tools

Canopy-dwelling, Volant, small, wary, bad-tasting, drab feathers, short and curved bones

adapted from Steadman and Martin, 2003

7. Identifying problems and evaluating solutions

In general, How do we ID problems? How do we evaluate solutions? --Using the Scientific Method!

  • Make observations

    • Amphibians: disappearing from sites all over the globe

  • Make hypotheses

    • Habitat loss

    • Climate change

    • Increasing UV-B radiation exposure

    • Environmental contamination

    • Introduction of non-native species

    • Disease

  • Select one to test; make predictions – observational, experimental

    • Hypothesis: UV-B radiation exposure

    • Prediction: exposing amphibian eggs to UV-B radiation will increase egg mortality

  • Do experiments, collect data

Scientific method
Scientific method

  • Reminder: hypotheses, theories, & laws can be rejected by new data.

    • If you can’t reject an idea based on data you can gather, it is NOT science

    • understood, accepted, & required by scientists

7.1. Management as experiment

  • All management actions are an experiment, but some experiments are better designed than others - Example: Long-billed curlews

    • hypothesis: grazing negatively affects long-billed curlew reproduction

    • experiment: effect of grazing on breeding success

    • control?

    • data?

  • Treat management & its goals as hypotheses to be tested

  • Need controls

  • Alternative solutions should be directly compared

  • Avoid confounding factors

  • Need to do follow-up (monitoring) to evaluate effectiveness

  • Example: wood ducks

    • harvested species

    • problem: populations limited by number of cavities

    • solution: nest boxes

  • If possible, design management with these experimental ideals in mind

  • Often this is not possible – why?

  • Modify management based on what has happened previously = “Adaptive management”

  • Management should be adaptive

  • Changes in management should be based on experimental comparisons

7.2. Dealing with too much success: elephants

  • Options:

    • do nothing (= let them destroy the habitat then starve)

    • culling (= killing)

    • contraception

    • translocation

    • other alternatives?

7.3. Models: How do you resolve basic questions about the best way to solve environmental problems?

Life Cycle Assessment

Life Cycle Stages
Life Cycle Stages

  • People are making money doing this!

  • Consultants, NGOs, governments – evaluating organizations for ISO compliance (can be part of “green” certification)

  • Field of Industrial Ecology emerged as academic field – does some LCA

  • E.g. Paper vs. Plastic

    • bottom line?

    • it depends:

      • amount of recycling

      • thickness/strength of plastic

      • what you measure

      • what else?

  • To further demonstrate the difficulties of LCA, consider the consequences of using carbon output as your dependent variable when evaluating energy use

    • nuclear power would be the clear winner

8. References and Resources

8.1. Organizations and websites

Endangered species

Encyclopedia of Earth

National Library for the Environment

The Society for Conservation Biology

Bibliography of Genetic Variation in Natural Populations

IPCC = Intergovernmental Panel on Climate Change

Journal: Emerging Infectious Disease

United National Environment Programme

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

Primack, Richard B. Essentials of Conservation Biology . 4th ed. Sinauer Associates, 2006.

Wilson EO. The diversity of life . Harvard University Press, 1992.

8.3. Important journals (not exhaustive)

Biological Conservation

Canadian Journal of Zoology

Conservation Biology

Conservation Ecology


Ecological Applications

Ecological Letters

Emerging Infectious Diseases

International Zoo Yearbook

Journal of Applied Ecology

Journal of Ecology Journal of Wildlife Management

Landscape Ecology Landscape and Urban Planning



Trends in Ecology and Evolution

Zoo Biology

8.4. Articles

Strasburg, Jared L. Conservation biology: Roads and genetic connectivity. Nature 440, 875-876 (13 April 2006)