conservation bio exam 1 Flashcards
How do we predict how populations change?
can use Demography
Incorporating Demography
- Most populations do not grow constantly
- Most models treat the entire population as one unit when in it
might be better divided into different cohorts - for most species, reproduction and mortality vary by cohort (ex: age, size, or stage)
- survivorship curves, reproductive value
demography definition
the study of statistics such as births, deaths, income, or the incidence of disease, which illustrate the changing structure of human populations.
The contributions of different age/stages/ sizes to the next generation are heavily dependent on:
The survivorship of individuals of a particular cohort
* The fecundity of members of the cohort
* The number of individuals in that cohor
fecundity
the ability to produce an abundance of offspring or new growth; fertility.
cohort- structured information
(birth, death, growth rate, etc.)
Demographic Matrix Models
demographic technique for understanding population dynamics based on cohort- structured information (birth, death, growth rate, etc.)
cohort definition
a group of people banded together or treated as a group.
cohort definition
a group of people banded together or treated as a group.
What proportion of immature individuals survive? (take a look at the graph and come back!)
0.5 (stay immature) + 0.2 (develop to maturity) = 0.7 or 70%
50% of the immature (I) population survives from one year to the next as immature.
20% of the immature (I) population survives and moves on to the next, mature (M) stage.
None of the immature (I) population moves on to the final, post-fertile (P) stage.
What proportion of mature individuals survive?
0.6 (stay mature) + 0.2 (develop to post-fertility) = 0.8 or 80%
- For each mature fertile adult, 0.8 new offspring are born each year
- 60% of the mature (M) population survives from one year to the next as mature.
- 20% of the mature (M) population survives and moves on to the next, post-fertile (P) stage.
What proportion of post-fertile individuals survive?
- 0.7 (survive as post-fertile) = 0.7 or 70%
- Post-fertile adults (P) produce no offspring
- None of the post-fertile adults get younger.
- 70% of the post-fertile (P) population survives.
do you understand how to read a demographic matrix model?
yes
How can we calculate population growth within each demographic over time?
- multiply the proportion alive by how much you started with– both for many survive and how many are born or mature
- then add to each other
Why Bother with Demographic Matrix Models?
-To summarize per capita survival and reproduction rates
-the rate at which the population size changes per individual in the population
- determined by birth, death, emigration, and migration rates
- To calculate finite population growth rate (λ) and generation
time
- gives the proportional change in population size from one time period to the next
- Can be used to determine the status of threatened and endangered species
how to find allele frequency
divide the amount of the allele of interest by the total amount of alleles
percent polymorphism
-add the loci that are polymorphic to together
remember that
-polymorphic means that it has two different alleles
What would genotype frequencies be at locus 2 in this population if it were in Hardy-Weinberg equilibrium?
- If individuals 1-3 were males and individuals 4-6 were females, what would be the effective population size of this population (all are breeders)?
Effective population size (NE)
- the size of an ideal population (i.e., one that meets all the Hardy-Weinberg assumptions) that would lose heterozygosity at a rate equal to that of the observed population
- a number that, in some simplified scenarios, corresponds to the number of breeding individuals in the population
Ne =
(4Nm Nf) / Nm + Nf
If 50 females & 50 males, what is Ne?
If 20 females & 80 males, what is Ne?
100
64
Models of Population Dynamics
- In models, parameters are values that are crucial to describing the behavior of a particular system – for instance a particular population’s growth.
-They are typically constant for a given situation (e.g., a particular population) as compared to variables (such as time and population size).
Models of Population Dynamics
- In models, parameters are values that are crucial to describing the behavior of a particular system – for instance a particular population’s growth.
-They are typically constant for a given situation (e.g., a particular population) as compared to variables (such as time and population size).
Exponential Growth
Continuous increase or decrease in a population in which the rate of change is proportional to the number of individuals at any given time
Population Growth at High Density
Density dependence
- when an effect is proportional to the population density
-Example: death by starvation, disease
*the proportion that die increase as the density itself facilitates the problem
Density independence
- not related to population density
Example: increased death rate due to extreme weather conditions
*the proportion that die increase as the density itself facilitates the problem.
equilibrium density
is termed the carrying capacity, K
carrying capacity
an equilibrium between the availability of habitat and the number of animals of a given species the habitat can support over time
carrying capacity also
represents a population density
The impacts of density-dependent factors become more severe as population size increases
– at equilibrium density, the population size (N) will be at carrying capacity (K)
– We can approximate the impacts of density on the growth rate by using the carrying capacity (K):
Logistic Growth
– a population’s per capita growth rate gets smaller and smaller as population size approaches a maximum imposed by limited resources in the environment, known as the carrying capacity (K)
*Carrying capacity represents a pop. density
not a constant and can fluctuate
Growth in Natural Populations
–Not all population growth will naturally fit a perfect exponential or logistic growth model
– rate of change can fluctuate
–Population booms and busts
–Stochastic variation in K
Time Lags in Logistic Growth
–Time lags are due to synchrony of various life history events
–organisms are buffered from changes and make life history
–for example, events that lead to poor condition of population members (high competition) in one season may not show up as higher d and lower b until much later
*organisms are buffered from hangs and Make life history
“decisions.”
biodiversity and evolution
the core things we care about in Conservation Bio.
can’t look at one pop. level
change in genetics and demographics
Current population size may depend on the population size at some previous time when something happened to influence future growth
–as time lag increases, the growth rate of the population depends more and more on far-past population sizes
–important implications for the ability to predict population size
How do we predict how populations change?
-Life History
-Population Growth Dynamics
-Demography
-Reproductive Value
life history
R-strategist species
K-strategist species
R-Strategist Species
-Emphasize high growth rates
-Produce many offspring (ie.e high r, low K)
-High fecundity, small body size, early maturity, ability to disperse offspring, short generation time
-Semelparous
K-Strategist Species
-typically living at high densities close to carrying capacity (K)
-invest more heavily in fewer offspring, which have high probability of surviving to adulthood
-Large body size, long life expectancy, fewer offspring, extensive parental care
-Iteroparous
Demography
the study of statistics such as births, deaths, income, or the incidence of disease, which illustrate the changing structure of human populations.
Demographic Characteristics
-Life history traits
include factors such as:
* the number of offspring produced (or some stand-in such as the number of eggs produced
* the timing of these offspring – when are they produced over a female’s life
* the survival of individuals from one time period to the next (and therefore, longevity).
what could increase life history:
-technology in medicine and agriculture
Biodiversity refers to the many types and levels of biological variation
- Species
- Systems
-Ecozones & Biomes
-Communities & Ecosystems - Genetic
- Population
Polymorphism
: the proportion or percentage of a sample of genetic loci from a population that are polymorphic
-Two or more possibilities of a trait on a gene
phenotype google
two or more clearly different morphs or forms, also referred to as alternative phenotypes, in the population of a species.
there are 10 people and we look at 4 loci of those 10 people
Locus 1 has all AA genes
Locus 2 has BB, Bb and bb genes
Locus 3 has CC, Cc and cc genes
Locus 4 has DD, Dd and dd genes
what is the percent polymorphic of the locus?
if the locus is polymorphic that is it given a 1, if it is not polymorphic then it is given a 0 all divided by the amount of loci that we looked at
P = (0 + 1 + 1 + 1) / 4
P = 3/4 = 75% or 0.75
locus
The physical site or location of a specific gene on a chromosome.
Average Observed Heterozygosity
a measure of the genetic diversity at the population scale and indicates the average proportion of individuals that are heterozygous for a given trait.
N is the number of individuals
n is the number of loci
Hi is the amount of polymorphic genes
how to find the Average Observed Heterozygosity for the 4 loci from the 10 people
count the amount of heterozygote genes there at in each loci and add them together
then divide by the amount of genes that we looked at
so we looked at 4 loci from 10 people so
10 x 4 = 40
so we can do
(0 + 7 + 3 + 1)/ 40
Restriction Fragment Length Polymorphism
are often used to quickly and simply examine differences in allele frequencies
-able to sequence and visually assess RFLPs of known regions (loci) -Less intensive analysis than DNA sequencing
for restriction fragment length polymorphism
what are Enzymes are used
Enzymes are obtained from bacteria (and other organisms) and used to recognize specific nucleotide sequences in DNA and cut the DNA molecule where these sequences are found.
- different restriction enzymes cut at different sequences.
For each locus under study (and each individual), the restriction fragments are separated using agarose gel electrophoresis.
-Restriction fragments will move through the gel based on size
-Individuals can be either homozygous (2 bands for AA, 1 band for a) or heterozygous
(3 bands for Aa)
Why do conservation scientists care about genetic diversity within species?
- Long-term: evolutionary potential
-populations may diverge into new subspecies or even full species - Long-term: evolutionary flexibility
-ability to respond to epidemics, climate change - Short-term: individual and population health -genetic diversity improves an individual’s fitness
Genetic Stochasticity
These processes may lead to lower H and P causing:
Variation in allele frequencies and loss of alleles as a result of:
- inbreeding
- genetic drift
- bottlenecks
- short-term problems with inbreeding depression
- loss of variation to handle a significant environmental change
Demographic stochasticity
efers to the random fluctuations in population size that occur because the birth and death of each individual is a discrete and probabilistic event.
Random fluctuations in environmental conditions that affect survival, reproduction, etc.
-less related to the number of individuals and more to the geographic concentration of the remaining individuals
-small numbers often means that the geographic extent of the population has declined
Genetic drift
involves the loss of alleles from a population by chance. Random fluctuations in allele frequencies in small populations reduce genetic variation, leading to increased homozygosity and loss of evolutionary adaptability to change
Inbreeding
refers to the mating of organisms closely related by ancestry.
-increases as a population decreases Causes a decrease in heterozygosity
-More highly related individuals are more likely to share the same allele at any given locus
Inbreeding depression
-is a reduction in fitness in offspring due to inbreeding among parents
-is not always the result of inbreeding
ex: rare, deleterious, recessive alleles (Tay-Sachs, sickle cell anemia, etc.)
Genotype
the genetic constitution of an organism
Phenotype
set of observable characteristics of an individual resulting from the interaction of its genotype with the environment
Gene
distinct sequence of nucleotides forming part of a chromosome, the order of which determines the order of monomers in a polypeptide (protein) or nucleic acid which a cell may synthesize
fixed position on a chromosome where a particular gene or genetic marker is located
Allele
one of two or more alternative forms of a gene that arise by mutation and are found at the same locus on a chromosome
Mutation
- changes in the genetic sequence; the main cause of diversity among organisms
Allele frequency
- relative frequency of an allele at a particular locus in a population
- Diploid organism -
organism that has paired chromosomes, one from each parent
- Homozygous -
having two identical alleles of a particular gene or genes
- Heterozygous -
having two different alleles of a particular gene or genes
- Recombination -
the rearrangement of genetic material, especially by crossing over in chromosome (meiosis)
Genetic linkage -
tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction
Sexual reproduction -
the production of new living organisms by combining genetic material from two individuals of different types (sexes)
phenotype is constructed from
information from both genes and the environment.
Heritability:
a measure of the proportion of phenotypic variance in a population that is ascribable to genotypic variance
Factors Affecting Genetic Diversity
-Directed Agents
-Chance Agents
-Others
Directed Agents
-Selection (+ / - / 0)
-Migration (including outbreeding) (+ / - / 0) -Inbreeding ( - )
- Chance Agents
-Mutation ( + )
-Genetic Drift ( - ) - Others
-History (+ / - / 0)
–Founder events: population is descended from a small number of colonizing ancestors ( - )
-Bottleneck events: famine, earthquake, fire, other disasters ( -)
-Wahlund effect: subdivision into genetically distinct subpopulations (- heterozygosity)
Aggregate Measures of Genetic Variation: Polymorphism (P) and Heterozygosity (H)
Measures of population, not individual genetic diversity
-Genetic health of a population
-Indirect conservation of genetic resources
-Power: compress/combine allele frequency data from different genetic loci into overall useful measures that communicate and
overall level of genetic diversity
-Limitations: inference from a sample
-Using a limited number of measurements to characterize overall genetic variability in a population
Methods for Measuring Genetic Diversity
- Protein Morphology
- Broad-scale DNA Morphology
- Fine Scale DNA Morphology
- Protein Morphology
-Protein electrophoresis
-Looks for allozymes (versions of enzymes produced by different alleles) and isozymes (proteins that are functionally similar) - Broad-scale DNA Morphology
-Restriction fragment length polymorphisms (RFLP)
-Uses specific features of DNA molecules independent of specific genes to estimate differences in genotypes in a population - Fine Scale DNA Morphology
-DNA sequencing
-Uncovers all variation that exists within a given locus in a population.
-Cost continues to decline rapidly making this more and more the choice.
-There are many techniques currently used; they can be targeted at specific genes by the use of specific primers.
Polymorphism
the proportion or percentage of a sample of genetic loci from a population that are polymorphic
-Two or more possibilities of a trait on a gene
- Investigators select a sample of different genetic loci
-Independence
-Ease of measurement -Different selective pressures
- Ideally, samples are drawn from a number of animals
Thresholds
–a particular locus is considered to be polymorphic if the most common allele’s frequency is < 0.95
–Making up less than 95% of the total alleles in the population
However, new techniques in DNA sequencing can uncover finer details in genetic difference have led conservationists to use thresholds of 99% (< 0.99)
-As long as the less common alleles total to more than 1%, the locus is considered polymorphic
Case Study: American Bison
-A total of 24 loci were sampled for 5 bison in a wild population using protein electrophoresis
At each given locus, an individual animal could be homozygous or heterozygous
Of the 24 loci sampled, only the MDH-1 locus was found to be polymorphic based on our threshold. In fact, many of the other loci had more than one allele, but it was rare.
What is the Proportion of Polymorphism (P)?
P = 1/24 = 0.042 or 4.2%
Case Study: American Bison
-A total of 24 loci were sampled for 5 bison in a wild population using protein electrophoresis
At each given locus, an individual animal could be homozygous or heterozygous
Of the 24 loci sampled, only the MDH-1 locus was found to be polymorphic based on our threshold. In fact, many of the other loci had more than one allele, but it was rare.
What is the Proportion of Polymorphism (P)?
P = 1/24 = 0.042 or 4.2%
Only a small number of bison (5) were sampled
-A common issue for endangered species populations
Limits of Sampling
Heterozygosity:
the chance that two alleles from any locus from any individual in a population will be different
We will deal with two types of H (heterozygosity)
-Observed - estimated from data
-Theoretical - estimated using the Hardy-Weinberg principle
Systems Diversity
Ecozone
-
based on the distributional patterns of terrestrial organisms
An area isolated by large regions of strikingly different environment (e.g., isolation by water (or by land)) where evolution has been independent enough of other regions that a distinctive assemblage of species exists.
Biome
-Climatically (temperature and precipitation) similar geographic area, often defined by dominant plant species analogs and a characteristic ecological succession pattern.
- Can be similar on different continents and biorealms using organisms with ecologically equivalent roles.
Community Diversity:
he populations of different species that naturally occur and interact with a particular environments
