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Bio 401 midterm 2
Terms in this set (126)
a unit of DNA sequence on a chromosome that codes for a specific protein.
is the specific location or position of a gene, DNA sequence, on a chromosome.
different forms of the same gene (for example the different alleles of the genes for certain blood proteins produce the different blood types found among humans.)
a particular combination of alleles that an individual possess
the morphological characteristics of an individual that result from the expression of its genotype in a particular environment
the gene is only expressed in offspring when it has been inherited from both parents
Dominant traits are those that are expressed or seen when a heterozygous genotype is present.
Relating to two alleles of a gene pair in a heterozygote that are both fully expressed.
a pair of genes where one is dominant and one is recessive — they're different.
When an individual has two of the same allele, whether dominant or recessive, they are homozygous.
containing two complete sets of chromosomes, one from each parent.
(of a cell or nucleus) having a single set of unpaired chromosomes.
Quantifying Genetic Diversity: Polymorphism
Proportion of genes that have
multiple forms (alleles) present in the population.
Quantifying Genetic Diversity: Heterozygosity
For any given gene, what proportion of individuals
Hardy-Weinburg equilibrium: 5 key assumptions
1. No natural selection
2. No random allele frequency changes ("genetic drift")
3. No gene flow into or out of your population
4. No mutation
5. Random mating
This allows the use of simple rules of probability to generate expected genotype frequencies given the allele frequencies.
H-W Link to Conservation Biology
Calculating the allele frequencies is an important step in determining whether the observed proportion of heterozygous individuals in the population is the same as what is expected by chance alone. In other words: Does Hobs = Hexpected? If not, something is going on...
Why is genetic diversity relevant to conservation, at multiple levels (individual, population, distinguishing taxa)?
If an individual has greater genetic diversity it has greater individual fitness.
If a population has greater genetic diversity they have the ability to adapt to changing conditions and a higher chance to evolve. and higher resistance to disease.
Genetic diversity can reveal the correct units of conservation. Population-specific genetic traits allow scientists to study gene flow and connectivity among populations, and to identify the appropriate units for
conservation (is it 1 species or 2 species?)
How does Genetic Diversity Relate to evolution
allows for genes to be "hidden" or unexpressed in the genome until the certain situation arises in which they need to become expressed, then keep getting replicated as a result.
What techniques are currently being used in conservation genetics
Sequencing- Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of As, Cs, Gs, and Ts that make up an organism's DNA.
SNP- single nucleotide polymorphism,
a variation in a single base pair in a DNA sequence.
Microsatellites- are di-, tri-, or tetra nucleotide tandem repeats in DNA sequences.
is the improved or increased function of any biological quality in a hybrid offspring
a disturbance causes a population size to be greatly reduced, reducing the populations genetic variation for future generations.
breed from closely related people or animals, especially over many generations.
lowered reproduction, or production of weak offspring following mating among close relatives
the specific adaptive genes are "swamped" from outside sources that arent as adapted to that specific habitat.
a cause of genetic drift, typically in smaller populations, that causes an allele to get fixed and its counterpart is lost.
reduced genetic variability that occurs when a new population is established by a small number of individuals
the relative difference between the theoretically most fit genotype within a population and the average genotype. Species with a lower genetic load have higher fitness and produce more fit offspring.
Small isolated populations lose genetic diversity by chance alone. Positive feedback loop is created.
breed from parents not closely related.
A genetically effective population size of:
50 is needed for short term
(to avoid inbreeding depression)
500 is needed for long term
(to avoid genetic drift)
This "rule" is problematic for several
reasons and is no longer accepted as a
"scientific fact", although it is still widely
invoked as a "rule of thumb" by managers. The underlying principle remains valid, but there is no "magic" to 50 or 500.
Cheetah case study
Extremely low genetic diversity
No variation in Major Histocompatability Complex (MHC): reciprocal skin grafts were not rejected.
Link to reduced fitness?
Difficulty breeding in captivity High infant mortality rates Low sperm counts, high (70%) sperm abnormalities Susceptible to disease
Tasmanian Devil case Study
population is so similar due to isolation all individuals immune systems are susceptible to face tumor. No immune system recognizes the disease as different tissues.
In Ireland all potatoes were propagated and clones of each other. because of this there was no genetic diversity and all potatoes were infected with potato blight.
Banana Case Study
Bananas all clones of each other and therefore have very low GD and resistance to disease. The Panama disease wiped a lot of them out.
Case Study Florida Panther
Florida panthers were suffering from inbreeding depression, brought in texas panthers to genetically rescue the population, since then the population has vastly increased.
Sickle cell anemia Case Study
There is a heterozygote advantage in malaria zones. Recessive individuals have horrible SCA, while heterozygotes have Milk SCA but are immune to malaria, homozygotes are immune to maliara
HLA Case Study
females prefer the scent of males who are heterozygous at all three MHC loci. The reasons proposed for these findings are speculative; however, it has been argued that heterozygosity at MHC loci results in more alleles to fight against a wider variety of diseases, possibly increasing survival rates against a wider range of infectious diseases.
How do you calculate the number of DNA products from a PCR?
two dots means heterozygote?
equation for NE?
Proportion of Genetic Diversity lost over multiple generations equation
% of original diversity
H retained after g generations: Note: % diversity lost = 1- (retained)= 1 - (Hg / Ho)Hg / Ho = [1 - (1/2Ne)]g
How does NE differ than NC? importance?
NC is the actual population size, while ne is the effective breeding population size. It is important when there is unequal sex breeders contributing to the next generation.
Increase in direct human-caused mortality of a
species to an extent that threatens its viability.
5 types of overexploitation
e) Persecution / Eradication- wolf killing
2 largest ($$$) international industries in biological products
Forestry, commercial fishing
General Pattern of Commercialization of
Renewable Natural Resource
Boom or bust. People overharvest until they are forced to create a market substitution for that product.
how can recreational hunting benefit a species?
Managed hunting can raise $10,000s for conservation programs
How are sustainable yields calculated?
A sustainable yield is when Harvest = Production.
(Therefore, any point on the Production Curve is a sustainable yield.) so you find production ΔN = Nt+1 - Nt and as long as your harvest is less than that or equal it is sustainable
how do sustainable yields relate to logistic population growth
it is the parabola that compares the growth rate of the population (the slope of logistic growth) to the population size
Maximum Sustainable Yield
you harvest here when population growth is the highest. at the inflection point where K/2
Tragedy of the commons
commons= owned collectively by the public
people cheat to get ahead of competition because their livestock is private while the land is not. "somones lost money on the ground Example"
As object becomes more and more rare, people are unwilling to pay more.
Extraction becomes more difficult and less profitable.
This leads to supply switching, for a cheaper / easier alternative.
"Commercial extinction" - depletion, but not necessarily eradication.
As object becomes more and more rare, people are willing to pay more.
This creates a tremendous market incentive to harvest the last available
units. Rarity leads to greater price and greater profits.
Can easily lead to eradication, extinction
- local harvesting (limit or prohibit)
- supply chain and transportation
- end-user demand (not just purchasing)
resource is depleted for commericial use but not actually eradicated
Meat from any wild animal
Hunt wild land animals for commercial gain
What kinds of species are targets of persecution? Similarity to other types of exploitation? Differences? Relevance to California?
Top predators are typically targets for persecution. Its similar to other types of exploitation because they are still being over harvested. California Grizzly was persecuted to extinction.
A species living outside its native range.
An exotic species that has been released to the wild.
An introduced species that maintains its local
populations. Self-perpetuating populations.
An established species with special ecological
characteristics that permit it to expand its range into
Fire ants and purple loosestrife came in thru dry ballasts of ships. Come in through cargo. Zebra muscle came in through the wet ballast
Domesticated animals and plants- Pigs
Sport animals and fish (game)-trout, nile perch
Biological control- redfox
Acclimatization societies- starling
when a domesticated animal becomes wild.
People colonize a new area and release wild animals for "biotic Improvement" because they believe it will make the Environment better, or becuase people from other areas want to make their new home like their old one. Starlings.
Main impacts of exotics on native species (direct and indirect effects). Which is most likely to cause extinction of native species?
a. Direct effects upon native species: competition,
predation, hybridization, etc. (most likely to cause extinction)
b. Indirect effects upon native species by changing
ecosystem properties: hydrology, fire regime, nutrient
c. Indirect effects that facilitate other non-native species.
What are the main characteristics of successful invaders / invasions?
"weedy" species are more likely to become invasive.
r-selected life history strategy
high reproductive output
vegetative spread, reproduction (fragments)
early-successional / disturbance / human-associated
Larger Groups more likely for establishment
Islands very vulnerable
Why are "weedy" species more likely to be invasive?
r-selected life history strategy
early-successional / disturbance / human-associated
How does group size affect likelihood of establishment?
The larger the group the less likely it is to be effected by random factors such as demographic and genetic factors.
Know several reasons why islands are particularly susceptible / vulnerable to invasive exotics.
they are ecologically naive with no native predators.
Why are island plants susceptible to exotic herbivores? What impact does this have on native herbivores? On other exotic plants?
Because they dont have any natural grazers eating them so they havent coevolved to produce thorns or other defenses to them. It facilitates the development of other exoctic plants that have these defenses. probably allows them to outcompete other native herbivores.
Why are mammalian carnivores so devastating to island wildlife?
They are ecologically Niave, no natural predators.
Management of exotic species: "black list" vs "white list" - which is most effective? which is most practical in the real world?
Black list: species absolutely cannot come into the area
White List: All nonnative species are prohibited, besides the ones that are known to be safe.
White list is probably more effective
Black is probably more practical and easier to enfore
Types of invasive removal and control
chemical, mechanical, biocontrol
How does modern biocontrol differ from that practiced 50+ years ago?
only use species that have tight physiological connection between invasive species. Usually only insects and other disease causing organisms.
American Chestnut, Avian Maliara,Chytridiomycosis, White nose syndrom in bats
Killed all Hawaiian bird besides on peaks.
Killed yellow legged frogs, introduced by afr. clawed frogs
Funugs, Irritates them and wakes up from hybridnation
What is Bd? What disease does it cause, in what kinds of species? How did it arrive?
Fungus, causes Chytridiomycosis, from afr clawed frogs
What kind of disease is primarily affecting native Hawaiian birds? How did it arrive? What other exotic species has/have been important in the transmission of this disease?
Avian maliara, From mosquitos
What is "White Nose Syndrome"? What taxa are primarily affected by WNS, and how? Where and when was it first discovered? Why is it usually fatal? How is it relevant to California?
It effects hibernating bats. it is a fungus. it causes them to wake up during hibernation and starve. first detected in 2006 in NY. California has alot of different bat species, could possibly affect.
Diminished quality for a given species. Manifests as a
reduction in fitness (survival or reproduction).
Habitat is destroyed until it is actually lost
examples of habitat degradation
loss of essential habitat elements(snags), successional stage(kirlands warbler), fire regimes, pollution / toxins (albatross chick), light and noise, etc.
What 3 things happen to a habitat as a result of habitat destruction?
a. Reduced habitat area
b. Increased edge effects
Using the Species Area curve: In general, a 50% loss of area results in __% species loss? How about a 90% loss of area?
What are "edge effects"? (know examples of abiotic and biotic factors)
B. Disturbance (wind, fire)
C. Predation from exotic or
"interior" vs "edge" species
Interior is the inner unefected by the edge part of the habitat.
interior species include: whade tolerant and late successional species. humidity sensitive animals.
edge species- cats rats raccoons
Key factors determining the intensity of edge effects on a patch (3)
contrast-Edge effects increase with greater structural contrast between adjacent communities.
Fragmentation: gaps, expansion of gaps, switching of matrix to be disturbed; remnant patches.
goes from continuous, to having gaps, to only having habitat patches. matrix goes from the natural to the disturbed community type.
What are the top 3 factors (in order) causing habitat destruction and fragmentation for species listed under the Endangered Species Act?
land development for commercial development
Why are roads particularly problematic to populations? Know several different factors.
They create edge effects and divides habitat into fragments. alot of species wont cross roads so if they are stuck in a smaller population they will go extinct.
can also cause direct mortality
facilitates exotic species spread
physical effects (pollution)
easy access to hunters
What about dams? Be able to explain how dams alter upstream and downstream habitats.
upstream is now a lake with possibility of new created island habitats associated with exoctic fish stocking.
downstream flow is greatly reduced. no migration. disturbance regime greatly altered
sediment flow is blocked
patch, matrix, connectivity, dispersal, extirpation, colonization / migration rate, rescue effect, deme
4 main types of metapopulations: know the characteristics of each, and be able to illustrate
Patchy populations- populations exist in small clumps but dispersal is high
island mainland- 1 mainland, alot of islands
Levins- interactions is high in the patches, dispersal not as common.
source sink- source population with outflow, sink with inflow
Key to metapopulation persistence: a balance between demic extinction and colonization
1. Size of demes.
2. Number of demes.
3. Connectedness between demes.
4. Independence of demes.
Given extinction rate and colonization rate, be able to calculate the equilibrium proportion of patches occupied, using this formula:
O = 1 - (E/M)
as e approaches 0 a higher proportion of patches are occupied. as e increases a lower proportion of patches are occupied. reverse goes for M
Be able to calculate the probability of extinction of the whole metapopulation, given the following formula
p(EXT) = [p(E)]^n
what does n stand for?
number of independent occupied patches
What management recommendations flow logically from each factor?
1. Keep local populations big, and
maintain the big populations.
2. Maintain the individual patches.
(even unoccupied patches)
3. Maintain connectivity.
4. Keep the populations independent.
What pair of factors seems contradictory, creating inherent tension and debate among management approaches?
maintaining connectivity and keeping the populations independent seem contradictory.
The proportion of occupied patches in a metapopulation represents a balance between Colonization (immigration) and Extinction of patch-level populations (demes). (single Species)
Equilibrium Theory of Island Biogeography
The number of species on an island represents a balance between Colonization (immigration) and Extinction (extirpation) processes.
The number of new species arriving
onto the island. The more species that occur on the island, the less likely it is that a "new species" will colonize - because it's probably already present there.
The number of existing species
going locally extinct on the island.
The more species present, the
higher the potential that some go
extinct, just due to random chance.
Simberloff's "mangrove island"
Bug bombing, proved the island biogeography model.
when is there the largest amount of species?
Highest # species will be on large
islands close to the mainland.
(many colonists and low extinction)
Fewest # species will be on small
islands far from the mainland.
(few colonists and high extinction)
Extinction rate is a function of island size.
Extinctions are more likely on small islands.
Immigration rate is a function of isolation.
Immigration will be higher for islands nearer the mainland.
main point from kakaru island example
there is a carrying capacity, but species turnover.
when a land bridge island is formed and the species numbers start to decline
In ecology, extinction debt is the future extinction of species due to events in the past. Extinction debt occurs because of time delays between impacts on a species, such as destruction of habitat, and the species' ultimate disappearance.
land bridge islands what are they?
"Land Bridge" Islands: Patches of habitat that once were connected to mainland or each other, but have become fragmented and isolated
and how do they differ from recolonization scenarios such as Simberloff's experiment and Krakatau?
they go thru relaxation. Once was connected now not, so alot of species cant live there anymore. Simberloff has always been isolated.
Biological Dynamics of Forest Fragments (Lovejoy) projects.
From 1980 - 1991, created 11 forest fragments:
1 hectare (n = 5)
10 hectare (n = 4)
100 hectare (n = 2)
Matched with control sites in contiguous rain forest.
Monitored changes in species abundance and ecosystem function.- some habitats went completely unproductive
>450 published papers to date.
Lago Guri dam (Venezuela)
Dam put up, dude monitored species change throughout years on the different size islands.
Principles of Reserve Design
1. Bigger is better than smaller.
2. 1 big is better than several small. *
3. Closer is better than spread out.
4. Clumped is better than linear.
5. Connected is better than not.
6. Circular is better than linear.
7. Buffer zones are better than not.
"Single Large or Several Small"
When fragmentation occurs,
what happens to species and communities?
A single species: Metapopulation theory
Community (multiple species): Island Biogeography theory
a population of populations.
an interconnected network of local populations, connected by occasional dispersing individuals.
4 types of metapopulations
1. Classical or "Levins"
2. Patchy Population
3. Core-Satellite (or Mainland-Island, or Source-Sink)
4. Stepping Stone
characteristics of a levins metapopulation
a) Patches are all identical. Same
size, shape, and equally-connected.
b) Are either Occupied or Empty.
characteristics of a patchy population
-Patches are not identical.
-Have varying sizes, shapes, and local population sizes. --Migration rate is very high.
-Any patch that goes extinct is almost immediately recolonized by immigration from another patch.
-As a result, virtually all patches are occupied.
-Every patch connects to every other patch
-Cattails are a good example.
mainland island metapopulation
-Core has a p(E) = 0.
-Satellites receive dispersers from Core.
-Dispersal from satellites back to core or to other satellites is very rare.
-Persistence of the Core population is what maintains the entire network.
-Patches are connected sequentially, like links in a chain.
-Local extinction is easily recolonized by adjacent patches. (Resilient)
-But loss of connection severs the network into 2 smaller isolated populations (much less resilient).