Conservation Bio Midterm 1

Extinction:

loss of all individuals in the population of a given species

local extinction:

species disappears in one geographic area but persists in other areas (also called extirpation)

Global Extinction

loss of species over its entire range

Endangered Species:

A species that is presently threatened with extinction

What makes a species vulnerable to extinction?

• Valuable and easy to harvest

  • Low reproductive rate (often long-lived species)

  • Larger animals

  • “Rare” species

  • narrow habitat/niche

  • small populations

  • small geographic ranges

  • Combination of these characteristics

  • Poor dispersal ability

  • Dependent on some other species

  • Seen as a pest by humans

Local Extinction of North American buffalo (Bison bison)

Bison losses from hunting

Not in danger of extinction

Because now domesticated

For meat.

Bison have mostly been replaced with cattle

Very different ecological effects

Cattle crop grass much lower down

Cattle require less land, but reduce biodiversity,

increase erosion and cause topsoil loss

Columbicola extinctus

passenger pigeon chewing louse

Found (dead obviously) on

museum specimens in 1937

IUCN Red List

International Union for Conservation of Nature

Non-profit, non legislative

• most species have NOT been assessed, little data used in most assessments

• Many assessed species are “DD” – Data Deficient

Threats to - cause endangerment

biodiversity

IPAT equation

I = P x A x T

I = Environmental impact

P = Population

A = Affluence

T = Technology

T or F: usually only one threat is present to a species

F: usually multiple

T or F: Direct observation of recent extinctions is only really possible for well studied species

T

Why does habitat loss cause endangerment

• less area = fewer species

The -(smaller or bigger) the patch, the more species you will lose when you destroy a unit of habitat!

smaller

Why species-area relationships might Overestimate (or appear to overestimate) extinction

1) Species take time to go extinct. After loss of habitat

there may be an “extinction debt” – species

doomed but not yet extinct.

Estimates run as high as 70,000 – 2,700,000 already

doomed

“Extinction debt”

is good news because species doomed

by habitat loss might still be saved if we act!

T or F: Protected areas might be better for biodiversity than average

T

If we preserve the very best

areas for biodiversity -

we may

be able to preserve way more

biodiversity than “total area”

would have predicted

SAR does not account for species

does not account for species that can live in

the new (converted) habitat

Why species-area relationships might underestimate

extinction

They don’t account for any factors other than

habitat loss.

C

Biggest threats to plants and animals for extinction

• habitat loss

• invasive species are a big “cause”

Simple species (bivalve mollusks, plankton) have average durations

of - (years) before extinction

10 million

Mammals tend not to persist for more than -(years)

3 million

T or F: Recent extinction rates are way above background extinction rates

T

T or F: Probable speciation rates are also up, but much less than extinction rates

T

Endangered Species Act 1973

• US government law

• Managed by US Fish and Wildlife Service and National Marine Fisheries Service

• designed to protect critically imperiled species from extinction as a "consequence of

economic growth and development untampered by adequate concern and

conservation."

What does the endangered species act actually do

• Federal government must avoid adverse impacts on critical habitat.

• Prohibits all “take” of listed animals on private land. Prohibits “malicious damage” to listed plants on private land.

• The act protects “distinct populations” of animals, but not of plants and invertebrates

To be considered for listing (as Endangered or Threatened),

the species must meet one of five criteria (section 4(a)(1)):

1. There is the present or threatened destruction,

modification, or curtailment of its habitat or range.

2. An over utilization for commercial, recreational, scientific,

or educational purposes.

3. The species is declining due to disease or predation.

4. There is an inadequacy of existing regulatory mechanisms.

5. There are other natural or manmade factors affecting its

continued existence.

Endangered Species Act

- Success:

• prevention of 227 extinctions

Endangered Species Act

- Shortcomings:

• 42 species went extinct while being considered for

listing (before declared endangered)

- Average time to get listed is >10 years

- Between 40-90% of U.S. species listed on IUCN Red

List are not listed on ESA

Which group is the endangered

species act best structured to protect?

Vertebrate animals

Preservation ethic focuses on

biodiversity

Sustainable use ethic focuses on

ecosystem services

What is biodiversity good for?

Biodiversity is a source of provisioning services (e.g. new medicines)

Supporting services=>

ecosystem function

What are ecosystem functions?

• primary productivity

• soil fertility

• water quality and availability

• resistance to disturbance

• speed of recovery (resilience)

In Minnesota grassland, productivity (increases or decreases) with diversity

increases

Capacity to resist disturbance (increases on decreases) with diversity

increases

The extinction of the passenger pigeon

is hypothesized to have resulted in what change in

eastern north America?

A) Increased Lyme disease risk

B) Decline of eastern gray squirrels

C) Increase in nutrient transport

D) Lighter, more open-canopy forest habitats

A

World is warming

Arctic permafrost is melting

- Disease outbreaks, giant craters, flooding

Decomposing organic mater releasing methane

and CO2 could cause runaway climate change

Pleistocene park

Wants to use EXTINCT large herbivores to

return Siberia to grassland

What species should we revive?

1. Preferentially select de-extinction candidate species that

have low levels of functional redundancy.

2. Prioritize species for de-extinction that went extinct

recently.

3. Concentrate on the resurrection of species that can be

returned to functionally meaningful abundance levels

Reversing extinction methods

Option 1 – breed something similar from

existing DNA

Option 2 – mix existing DNA with DNA from

extinct organisms

Option 3 – insert genome of extinct

organisms into modern surrogate

Option 1 – breed something similar from

existing DNA

- Can definitely work

- New tools expands remix options

- Does not add to genetic diversity

- Does not really reverse an extinction

- BUT result could replace a lost

ecological function

“backbreeding”

-Cross breed primitive cattle breeds to create an ecological proxy for auroch

-Goal is wild grazer that maintains grasslands on land no longer farmed

-Prioritize function over genotype/phenotype match

breed something similar from

existing DNA

- Select for mammoth-

like traits from existing

elephants

- Add genes for hair, cold

tolerance from OTHER

existing species

- CRISPR opens huge

possibilities….

mix existing DNA with DNA from

extinct organisms

- Might work … but:

- Can we recover enough intact DNA

- Can we identify relevant genes?

- Revives lost genetic diversity

- Does not really reverse an extinction

splice existing DNA with DNA

from extinct organisms

Liquid blood recovered from frozen mammoth, hair

preserved from various Pleistocene mammals….

mix existing DNA with DNA from

extinct organisms

- Current plan is to start with

Asian elephant

- Add mammoth genes for more

hair, smaller ears, more body fat

- Use African elephant as

surrogate

- Will it still be an Asian elephant?

insert genome of extinct

organisms into modern surrogate

Based on

existing cloning

technology

- Can it work?

- Probably someday with good DNA

- Unclear with ancient DNA

- Can we find a modern surrogate that would work?

- Recovers genetic diversity

- Truly reverses an extinction

POPULATION

a group of actually or potentially interbreeding organisms occupying a

defined area during a specific time.

A population can be described by

the number of individuals in it

T or F: In many cases a count of females only is used

T

Why is a ‘population’ a unit of interest to us?

Human interests and management often occur at population-level scales

Census

count of all individuals

Total population

Number observed

T or F: A true census is rare.

T

Census mapping trees

• technically easy still expensive

Census can be an

aerial survey of large mammals in fixed areas

Tails of humpback whales are used to

identify each individual for a census if we stop seeing new individuals

Census is more common

in conservation and in small intensively managed populations than in ecology more broadly

Population estimate

guess at total based on observing a subset of the population:

- Extrapolate up from density in subsamples

Subsampling uses

quadrats, transect

Average density=

total observed/area sampled

total population =

Average density * (total area of interest)

Total abundance=

Number of individuals in an area, (i.e., Density, number/area)

Relative abundance =

some metric that scales with the number of individuals (but cannot be converted

to density)

proxies for abundance

• Vocalization frequencies

– # calls per unit time

• Traps

– Pitfall traps, light traps

• Fecal pellet counts

– Rodents, mammals,

caterpillars

• Artifact counts

– Nests, insect pupal cases,

bird tracks

• Fishing catch per unit

effort

Subsampling

As the number of samples goes up….

Our estimate of the total population may go up or down

Our confidence in our estimate of total population increases

Sources of uncertainty:

- Going from samples to population

- More samples => less uncertainty

Subsampling Error depends on

number of samples (more samples = lower error)

Error also depends on the species distribution

Are regular or clumped samples easier to sample well?

regular

Subsampling- For a clumped distribution, errors are often

large

Which species are especially hard to sample?

Rare species with clumped distributions

Habitat suitability models- Presence of clumped species may be predictable based on environment

- If you are sampling fish, their

distribution is clumped

- But predictable based on whether a

location is a pond or not.

- Further factors may be important (pond

depth, permanence, surrounding habitat)

- By modeling habitat suitability, can focus

your sampling only on plausible habitats

Landscape factors that might affect species abundance

– Topography

– Temperature

– Nutrients

– Substrate

– Wind exposure

But be aware that the species may not

be present everywhere it could be (example)

Mountain lion present in yellow and

black, darker grey is suitable habitat,

light grey is unsuitable habitat.

The model alone would mislead you

about population status in the east

Distance sampling main idea

you often need to account for detection probability

account for different probabilities of

detecting individuals that are

close (counted well) vs far (counted poorly)

We can correct for this – guessing how many “far”

organisms we missed.

Factors we adjust for in distance sampling

- Distance we are searching

- How we are searching

- Habitat we are searching

- Weather conditions

- Characteristics of individuals (size, lifestage,

male/female, etc.)

T or F:Different life stages may have different probabilities of being observed

T

Mark–recapture methods are commonly used for

mobile organisms

The essential idea of a mark recapture study is you are using

the history of observations to guess how many organisms you have NOT yet observed

estimated population size

and N=MC/R

m= # individuals captures

c= number of individuals captured on second visit

R= number of individuals captured and marked on the first visit that were also recaptured on the second visit

Assumptions of Mark-recapture methods

the population is closed

• no movement into the population

• no births/deaths

• sampling events should be pretty close time

• population is mixed and sampling is random

• no tags are lost

• tags/traps do not affect recapture, mortality et.

Natural Markers

• use of photo ID, sighting rate and mark-recapture methods (dorsal fin ID techniques using natural markings) and genetic sampling to monitor populations of great white sharks and bottlenose dolphins in Mossel Bay, South Africa

Two approaches to figuring out a successful management strategy

1. Do an experiment. Try different approaches, take data, see which is best.

But what if you can’t do an experiment (not ethical, not feasible)? And by the time you find out if the experiment worked it might be too late!

2. Make a model. Use math to predict what will happen.

Populations can change in size as a result of four processes:

Birth, death, immigration, emigration

T or F: In an endangered species we normally ignore immigration and emigration

T

R is

the birth rate per female minus the death rate per female

λ =

1+R

Geometric/exponential growth

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Discrete time models

If a population reproduces in synchrony at regular time intervals (discrete time

periods), and growth rate remains the same, geometric growth occurs

Discrete time models equation

If λ = 0.9 and you start in year 0 with 100 individuals, how big is your population in year 10?

(Assuming exponential growth)

N10= 0.9^10 (10)

Measuring λ from data: If you know the size of the population at two times