Final Exam Review Flashcards
What was the 1992 Rio Earth Summit?
Conference with over 100 countries participating on Environment and Development
What is Agenda 21?
The product of the Rio Earth Summit, it’s a document which outlines the international plan of action for sustainable development and key policies for environment and sustainability
- Became the blueprint for sustainability and forms the basis
for sustainable development strategies
UN Definition of “Biodiversity”
“the variability among living organisms from all sources, including, inter alia, terrestrial, marine, and other aquatic ecosystems, and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems” (UN 1992)
when did the word “Biodiversity” first appear?
First published appearance in 1988 by E.O Wilson as a contraction of “biological” and “diversity”
Is there a single definition of Biodiversity?
No, there are actually more than 25 definitions
- “the totality of genes, species, and ecosystems in a region or the world”
- “functional diversity ‐ thevariety of different responses to environmental change, especially the diverse space and time scales with which organisms react to each other and the environment”
Basic definition of Biodiversity
Biodiversity is the variety of life in all its manifestations
Examples of biodiversity
Species diversity, genetic diversity, molecular diversity, ecological diversity, etc.
How many species are there on earth?
We don’t really know, estimates are around 10-100 million
Can we make accurate predictions of the number of species?
Mora et al. (2011) showed how higher taxonomic classification of species follows a consistent and predictable pattern from which the total number of species in a taxonomic group
can be estimated
- Linear increasing line
Have most species been discovered already?
No, most species actually have not been discovered. The majority of them being insects (most) and bacteria
What is the correlation of description date with species geographic region (carnivores and primates)?
Date of description vs geographic range is correlated in that species with a very large geographic range were described earliest, and rarer/smaller geographic range species have only been described more recently.
What are the distinctive attributes of ‘newly discovered’ species?
- geographically restricted
- small body size
- live in difficult to access locations
- small population size
- high risk of extinction
- hard to distinguish morphologically
- nocturnal
- Symbiont with another organism we already know of
- probably an insect or beetle
Global species richness is difficult to measure, how could you estimate species richness?
Chao et al., 2011 - The simplest non-parametric estimator of true species richness in a community (= asymptote of species accumulation curve)
S(est) = S(obs) + a^2/2b
what is a species abundance distribution (SAD)?
A species abundance distribution graphs the number of species (y axis) by the number of individuals represented in sample (x axis)
what is a rank abundance distribution?
A rank abundance distribution graphs the abundance of individuals (y axis) by the species rank (usually from most abundant to least) on the x axis.
(usually looks like a decreasing exponential graph)
what is the advantage of modelling species richness as a log series?
species richness (S) can be estimated simply as
S = alpha*ln(1+N/alpha)
where N = number of individuals sampled
alpha = Fischer’s alpha (calculated from ur data set)
what is Fischer’s alpha?
Fixed values calculated for the number of species (S) and number of individuals minus number of species (N-S) in a sample
what is Preston’s log-normal distribution of species abundance?
- If you sampled all the species in an area, they would graph a log-normal distribution on # of species (y axis) by log abundance (x axis).
- however, it requires extensive sampling before the log‐normal distribution becomes evident or accurate
what is Preston’s Veil Line?
There are always a few rare species that are missed in sampling, so you must do extensive sampling to remove this veil on the very rare species to achieve more accurate richness
what is alpha in Preston’s log-normal distribution?
‘a’ represents the equitability of species and is typically ≈ 0.2
what are Whittaker’s spatial levels of diversity?
An hierarchical structure composed of alpha diversity, beta diversity, and gamma diversity
what is Alpha Diversity?
Local diversity within a community
what is Beta Diversity?
Diversity between communities
- When you have two communities, there may be some overlap in the species present in both. Beta diversity would be the remaining species that are NOT in both samples (species which are not overlapping)
what is Gamma Diversity?
Total diversity within a region (basically result of combining alpha and beta diversity)
what does Jaccard’s formula measure?
This formula can be used to measure beta diversity using presence-absence data
what does Sorensen’s formula measure?
Another way to measure beta diversity using presence-absence data
- Tends to give higher estimates
what is Nestedness?
a pattern of biodiversity which represents the species in a site may be a subset of a larger group of species present in another site
what is Turnover?
Turnover is a pattern of biodiversity which indicates replacement and occurs when the loss of species is counterbalanced by the gain of new others in a site
How does Nestedness and Turnover relate to Beta Diversity?
These two are additive components of biodiversity which together reflect the two basic mechanisms underlying the overall change in species identities across the landscape (the replacement of species or their loss) and how much overlap there is between sites.
What does Sorensen Dissimilarity Index (Bsor) measure?
Bsor incorporates both spatial turnover and differences in richness to measure beta diversity
What does Simpson Dissimilarity Index (Bsim) measure?
Bsim measures the species turnover without the influence of richness gradients
How can you calculate Nestedness?
you can combine Bsor and Bsim to get the formula
Bnes = Bsor - Bsim
What are the variables a, b and c in terms of sites and overlap?
a = overlap between sites b and c
b = # of species in site b
c = # of species in site c
what does Bray-Curtis Dissimilarity measure?
This accounts for abundances of species in measuring beta diversity between two sites
Cij = the sum of the lesser values for the species common to both sites
Si and Sj = total number of individuals counted at both sites respectively (all individuals of all species summed)
what are the primary determinants of species richness?
- Theory of island biogeography
- Emigration and immigration rates
- Climate and environmental pressures
What is MacArther & Wilson’s (1967) equilibrium theory of island biogeography?
Theory that there is a dynamic equilibrium between the immigration of new species to an island and the extinction of species previously established on that island
- Graph shows number of species present (x axis) and rate of change in number of species (y axis) where immigration and extinction lines intersect at the equilibrium point
Theory of Island Biogeography - How does distance of the island from mainland impact equilibrium?
Islands closer to the mainland may have higher rates of immigration
Those farther away have much lower rates of immigration
Theory of Island Biogeography - How does size of the island impact equilibrium?
Larger islands tend to have lower rates of extinction because they can support more species
Small islands have less space and higher rates of extinction
Theory of Island Biogeography - How do environmental/climatic factors impact equilibrium?
Wind/sea currents, dispersal abilities of species, island climates, etc. can all impact the rates of immigration and extinction
Theory of Island Biogeography - Species-Area Relationship formula?
S = CA^z
S = number of species present
C = constant which varies with the taxonomic group under study
A = area of the island
z = constant (island situations usually around 0.3)
Theory of Island Biogeography - What does the Species-Area Relationship demonstrate?
This formula shows the relationship between area of the island and the number of species it supports
what is the SLOSS debate?
SLOSS = Single Large Or Several Small (areas)
- Since species richness increases with area, a larger block of habitat would support more species than any of the smaller blocks and would therefore be preferable to conserve
what is Z in species-area curves?
Z is the slope on a graph of number of species by area, giving the percentage of species expected to go extinct
- Values of Z seem to lower for mainland systems compared to islands (or small geographic areas)
What happens to species richness if you increase area?
Species richness increases fairly linearly with habitat area (log scale)
define Evenness (of species)
Evenness is a description of the distribution of abundance across the species in a community. Species evenness is highest when all species in a sample have the same abundance
why is evenness an important component of biodiversity?
more even species abundance distribution means a more diverse community
what is Shannon’s Diversity Index (H) ?
a measure of diversity which takes into account the number of species present, as well as the relative abundance of each species.
- it is particularly useful when comparing ecosystems or habitats
what is the usual range of Shannon’s Diversity Index?
Typically in the range of 1.5 (low richness and evenness) to 3.5 (high evenness and richness)
what is Simpson’s concentration index (λ) ?
A weighted arithmetic mean of proportional abundance and measures the probability that two individuals randomly selected from a sample will belong to the same species
- given by λ (lambda)
what do small versus large values of λ mean for Simpson’s concentration index?
small values of λ = dataset with high diversity
large values of λ = dataset with low diversity
What is 1-λ (Simpson’s concentration index)?
1-λ = the probability that two individuals taken at random are from different species
What is Berger and Parker’s dominance index?
Measures inverse dominance, so that the more dominant the most abundant species, the lower the index.
d = P1
P1 value equals the relative abundance of the most abundant species
what is in common between all the diversity measures (Species richness, Shannon, Simpson, Berger & Parker)?
- They all combine species relative abundances to yield a sum
- They give different weights to relative abundances by raising them to different powers
What is entropy? In relation to diversity?
Entropy is the quantitative measure of disorder in a system
- Entropy/diversity is maximized (for a fixed n) when all the species occur in equal abundance
What is Renyi Entropy?
Renyi entropy is a generalized entropy measure of order a which, when calculated, gives the “effective” number of species
How does ‘a’ influence the Renyi Entropy value?
The higher the order a, the stronger the relative influence of the commonest species and the smaller the sample size necessary to obtain a reliable estimate
What does Renyi entropy return when at order a=1?
at a=1, Renyi entropy returns Shannon (H)
What is Multiplicative partitioning of diversity?
gamma = alpha x beta (diversity)
What is Additive partitioning of diversity?
gamma = mean alpha + beta (diversity)
- mean alpha and beta diversity adds up to gamma diversity
what is Hill’s Diversity Number?
Hill’s diversity mumber = Sa
is the geometric mean of alpha diversity
what is Pij in additive partitioning of diversity?
relative abundance of species i in community j
sum of all Pij values = 1
what is Daj in additive partitioning of diversity?
Daj = alpha diversity of community j
What are the advantages of addititive partitioning of diversity?
- alpha, beta, and gamma are measured in the same units
- analogous to an analysis of variance
- can be applied to multiple nested spatial scales
- can be used to measure overall similarity between communities
How do you measure diversity with sampling? What impacts results?
- Quadrats, more gets a greater picture of what the diversity is
- Amount of time spent sampling/observing those areas will result in more species being observed.
- Time of day, go back at different times to see different species
- Number of people present
what is the Platonic Ideal?
in Plato’s philosophy everything has a true form, a perfect representation of an idea. Earthly versions of this perfect form are imperfect reflections of the idea.
- The objects that we see around us are imperfect representations of the ideal form
What did Aristotle believe?
Aristotle thought that creatures were arranged in a graded scale of
perfection rising from plants on up to man: the scala naturae
- Specific differences distinguish one species from another.
What did Carl Linneas come up with?
The Linnean Taxonomy: Systema Naturae
- species of organisms were real entities, which could be grouped into higher categories (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species)
What did Carl Linneas believe about species?
- Initially, Linnaeus believed that species were not only real, but unchangeable.
-He abandoned this concept that species were fixed and suggested that some species might be able to go through hybridization
What is Anagenesis?
- Pattern of speciation discovered from fossil records
- Phyletic speciation which is the accumulation of heritable changes in a population associated with speciation
What is Cladogenesis?
- Pattern of speciation discovered from fossil records
- Branching speciation which is when new species arise from a population that buds from a parent species (basis for biological diversity)
What are Species Concepts?
Species concepts are various definitions that people have come up with to explain what characterizes a species
- there are many and none of them quite fully explain what a species is
What is the Typological Species Concept (TSC)?
- A group of individuals that differ from other groups by possessing constant diagnostic characters
- Based on collecting and describing a “type” specimen for a given species.
Problems with the Typological Species Concept?
- Polymorphism within populations (species)
- Geographic variation among populations
- Sibling or cryptic species: species that are morphologically indistinguishable
What is the Ecological Species Concept (ESC)?
- A set of organisms adapted to a particular set of resources (its niche) in the environment
- Concept supposes that ecological niches in nature occupy discrete “zones”
- Adaptive zones - abstract space set by resources and competitors in nature within which a type of “body plan” is adaptive. Hybrids fall between zones and are maladaptive – selection maintains species in their niches
Problems with Ecological Species Concept?
- Some species occupy the same niches
- Phenotype vs fitness adaptive landscape (3D model) - assumes a 3D adaptive landscape in which species are trying to get to the peaks of each hill where they would have the highest fitness. This is done by selection.
- Ecological niches in nature do not always occupy discrete “zones”
What is the Biological Species Concept (BSC)?
- Species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups
- Species who do not interbreed are classified as separate species.
- Hybrid offspring are often sterile or not viable/unfit.
Problems with the Biological Species Concept?
- Not applicable to asexual species
- Reproductive isolation is often incomplete. Hybridization is common among many groups
- Ring species don’t work
What is a Ring Species?
A ring species is a situation in which two populations which do not interbreed are living in the same region and connected by a geographic ring of populations that can interbreed.
- Can hybridize with their neighbouring species, but not the ones across the world in a different part of the ring (ex. Herring gulls)
What is the Evolutionary Species Concept (EvSC)?
- An evolutionary species is a lineage evolving separately from others with its own evolutionary role and tendencies.
- ‘Independent evolutionary trajectory’
- Species share descent from common ancestry
Problems with the Evolutionary Species Concept?
- Evolutionary role and tendencies can
themselves change through time and
space - Species whose traits change over time – are they changing into new species or just evolving their traits?
- How do we assess “historical fate” of a population?
What is the Phylogenetic Species Concept (PSC)?
- The smallest diagnosable monophyletic group of populations within which there is a parental pattern of ancestry and descent
- Species arise from a distinct monophyletic group – there should be no gene flow between the species
Problems with Phylogenetic Species Concept?
- Under this definition, a ring species may be a single species that encompasses a lot of phenotypic variation
- In principle, any character, ranging from a single nucleotide change in a DNA sequence to a parameter determining the organisms’ interaction with the environment, can potentially be
diagnosable - How do we define the level of divergence?
What is the Recognition Species Concept (RSC)?
- The most inclusive population of biparental organisms that share a common fertilization system
- The concept focuses on mate-recognition systems
- Courtship displays
- Timing of reproductive events (a.k.a. Isolation by timing)
- Neuroendocrine signals (pheromones)
Problems with Recognition Species Concept?
- Not applicable to asexual species
- Recognition systems often go awry (i.e. hybridization occurs)
- Difficult to apply to dead organisms
Four Categories of Ecosystem Services
- Provisioning Services
- Regulating Services
- Cultural Services
- Supporting Services
What are provisioning services?
The supply of goods of direct benefit to people, and often with a clear monetary value (ex. timber from forests, agriculture, medicinal plants, etc.)
What are regulating services?
The range of functions carried out by ecosystems which are often of great value but generally not given a monetary value in conventional markets (ex. CO2 fixation, air/water filtration, temperature regulation, protection from landslides/disasters, etc.)
What are cultural services?
Not providing direct material benefits, but contributing to wider needs and desires of society, and therefore to people’s willingness to pay for conservation (ex. spiritual value attributed to ecosystems/nature)
What are supporting services?
Not of direct benefit to people but are essential to the functioning of ecosystems and therefore indirectly responsible for all other ecosystem services (ex. formation of soils, nutrient cycling, disease spread prevention, etc.)
Why is diversity important in terms of ecosystem services?
Diversity provides a broad amount of investment into many different things, and doesn’t put all our bets on one thing. Investing in a lot of different things covers your bases.
What is the Complementarity Effect?
When species on average increase their functioning and productivity compared to when in monoculture
- Community will be more productive than the best monoculture
- Due to better resource exploitation
What is the Selection Effect?
When a single species with higher than average monoculture yields dominate the community
- Productivity is only as good as the best monoculture
- Focuses on competitive exlcusion
What is the Tree of Life?
The Tree of Life, created by Ernst Haekel, captures similarity by descent. It plots more closely related species are more functionally and morphologically similar to each other
how is a clade defined?
A clade encompasses a group of organisms which all share a single common ancestor
What are the nodes of a tree represent?
Nodes of a tree represent speciation events
What is an unrooted tree?
An unrooted phylogenetic tree has no single root representing a common ancestor
- This allows for many different orientations of the tree to be formed
How do you measure branches of a phylogenetic tree?
Branches are measured in OTUs = Operational Taxonomic Units
- OTUs are essentially the number of branches on the tree
How does the number of OTUs determine number of trees which could be formed?
As you increase the number of OTUs of a tree, the complexity and options of tree structures scales exponentially
define Polytamy
when 3 branches on a tree come from one node because you don’t know which came first
What is a Cladogram?
A cladogram is a type of tree which contains the structure of clades but branch lengths contain no information
What is a Phylogram?
A phylogram is a type of tree in which branch lengths contain some amount of information (like amount of difference in DNA sequences, or time between speciation events)
What is an Ultrametric tree?
A type of phylogram in which branch lengths are proportional to time
How would you calculate phylogenetic diversity?
summing the branch lengths of the phylogenetic tree = greater ecological diversity
What does species extinction mean in terms of evolution?
Loss of species leads to loss of evolutionary history
Extinction of any one species leads to the loss of the unique history it
represents.
What is Brownian Motion?
Under Brownian motion, trait variance increases in proportion to square root of the sum of phylogenetic branch lengths between taxa on a dated phylogenetic tree.
- The expected variance among species is linearly related to the amount of time passed
What does Brownian Motion predict?
Brownian motion has no predicted trend except for that as time goes on, species will fill up trait space/species attributes axis due to random variance in trait evolution
What is a Gradual Model of tree?
In a gradual model, change is
correlated with time as shown on branch lengths. This represents how species diverge gradually over time in small steps.
What is a Genetic Distance Model of a tree?
Genetic distance model, in which each branch is proportional to the amount of genetic change that has occurred along it in the gene(s) used to make the tree.
What is a Speciational Change model of a tree?
Speciational change model, in which
change is correlated with speciation
events i.e. branch length has no indication to time passed
What is a Non-Historical model of a tree?
Non-historical model, in which there is no phylogenetic component to trait
evolution, each tip is equally divergent from all others
What is Phylogenetic Diversity?
A measure of evolutionary
history calculated by summing the branches (edge lengths) on the
phylogeny
- More phylogenetic diversity means more occupied niche space
What is a Punctuated Model of a tree?
Punctuated equilibrium is the idea that evolution occurs in spurts, and if evolution occurs in rapid bursts, following a punctuated model, the
correlation between PD and feature diversity might be lost
When Quantifying Phylogenetic Distinctiveness, what would Column P give you?
Column P gives the percentage
contribution for each terminal taxon
What is the rough way to quantify phylogenetic diversity?
Weights of each species are inversely proportional to number of nodes from root to tip. So, if there’s 4 nodes between that tip and the root, the weight of that species is 1/4.
How do you measure Evolutionary Distinctiveness (ED)?
By calculating Equal Splits = Split up branch lengths so each tip gets a portion of each branch length, depending on how many species it splits (descends) into, then sum the branch length associated with each tip
- this gives you the ED for each species
If you sum all values for ED, what do you get?
If you sum the ED (evolutionary diversity) value of each tip, this gives you the PD (phylogenetic diversity) of the whole tree
What is H’ED?
H’ED is an entropy measure which represents the evolutionary information content of a randomly sampled species from the
community
- Basically gives us the phylogenetic diversity (PD) of that sample
What is the “paradox of the plankton”?’
The problem that is presented by phytoplankton is essentially how it is possible for a number of species to coexist in the same environment all competing for the same resources
- Many more plankton species co-exist in a supposedly homogeneous habitat than permitted under the competitive exclusion principle
What is the competitive exclusion principle?
Competitive exclusion principle states that two species cannot coexist indefinitely on the same limiting resource
- This is predicted mathematically by Lotka-Volterra models of competition
What is the Grinellian niche?
Grinellian niche - the sum of the habitat requirements that allow a species to persist.
What is the Eltonian niche?
Eltonian niche - species niche defined by their interactions with each other.
What is the Hutchinson niche?
Combines Grinellian and Eltonian niches to be a multidimensional measure for species to compete in. Results in coexistence where species exist in their optimum niche space
What are Diamond’s (1975) rules for community assembly?
- If one considers all the combinations that can be formed from a group of related species, only certain ones of these combinations exist in nature
- Some pairs of species never coexist either by themselves or as part of a larger combination due to instability, or may exist stably in a larger combination
What was Diamond’s research on birds in New Guinea?
Found that birds of new guinea and its islands formed a “checkerboard pattern” of species co-occurrence with “permissible” and “forbidden” species combinations based on life history traits and competition, demonstrating competitive exclusion
What are Hutchinsonion ratios?
- Common in the literature in the 1960s-70s provided quantitative expectations about what morphological shifts character displacement should generate
- A ratio of 1:1.3 approximated the differences in body size necessary to allow for coexistence
How does body size impact niche occupation/competition? (hypothesized)
We may imagine the niche axis as a gradient that is related to the body size of organisms, assuming that individuals of the same size compete strongest with each other
What is functional overlap?
The functional overlap is the overlap between niches which is allowable for species to still coexist with each other
What is phylogenetic under-dispersion?
Under dispersion is essentially environmental filtering (phylogenetic clustering)
- a concept focusing on the relationship between an organism and the environment, recognizing that not all organisms will be able to successfully establish and persist in all abiotic conditions
What is phylogenetic overdispersion?
Overdispersion is essentially competition between species
- may occur when competitive interactions are linked to ecologically relevant traits that are highly evolutionarily conserved.
What is phylogenetic clustering?
When environmental conditions filter/select for similar traits in all organisms, resulting in convergent evolution in that community
How does phylogenetic clustering change with spatial scale in plant communities?
Phylogenetic clustering has been shown to increase with spatial scale in plant communities
What is the ‘Darwin-Hutchinson Zone’?
On a graph of taxonomic breadth vs. plot area, marks a region for which we might be particularly interested in community phylogenetic structure
- Where competition is expected and a plausible expectation for interacting individuals to fill niche spaces
What is the Mean Phylogenetic Distance (MPD)?
- Creates a phylogenetic tree as a matrix
- Captures the structure of the community at all depths of the tree. Includes the long distances and the short close distances, capturing more information overall of the community structure
What is the Mean Nearest Taxonomic Distance (MNTD)?
- Mean phylogenetic distance from each species to its closest relative in the focal species set
- Only looks at the tips of the tree, and is more sensitive to things happening close to present day
What is the Z value in measuring MTD or MNTD?
Allows us to calculate the Standard Effect Size (SES)
- The Z value is a dimensionless metric that indicates the number of standard deviations an observation is from the mean of the null distribution
+Z = greater than null expectation
-Z = less than null expectation
What is NRI?
Net Relatedness Index
- Standardized measure of the MPD of the taxa in a sample, relative to the phylogeny of an appropriate species pool, and quantifies overall clustering of taxa on the tree with this formula
NRI = -1 x Z
What is NTI?
Nearest Taxon Index
- Mean phylogenetic distance from each species to its closest relative in the focal species set (uses MNTD)
- NTI quantifies the extent of terminal clustering, independent of deep level
clustering
What is Functional Diversity?
Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems.
How do you measure functional diversity?
This is the most important axis of diversity but the most difficult to measure
- Species are distributed in 2-dimensional trait space, you can do pairwise distances between traits or phenogram (like a tree) to see how traits have split off and see their branch lengths
What are the four Biodiversity Ecosystem Service Relationships?
- species diversity increases forage yield in grasslands
- species diversity acts as insurance against environmental change
- species diversity as a reservoir of adaptation to environmental changes
- biodiversity reduces risk of human exposure to disease (the Dilution Effect)
What is the Dilution Effect?
Dilution effect is that some hosts are more competent than others, and if there is greater biodiversity, it dilutes the number of competent hosts in the community, preventing a disease (for example) from spreading
3 Requirements of the Dilution Effect
- Vector must be a generalist
- Hosts parasitized by the vector vary strongly in their reservoir competence, such that some are highly infective and other are dilution hosts
- The most competent reservoir host(s) must be dominant members of the host community
Limitations of the ecosystem service framework?
- Value of ecosystem services is strongly dependent on the social and economic context
- The ecosystem service framework is anthropocentric, it assumes that nature is at humans’ service
- Intrinsic and cultural values of biodiversity cannot be reduced to a utilitarian perspective
- Stated-preference methods used to estimate values ASSUME that individuals behave as rational economic agents (we don’t)
Economic Valuation of Biodiversity: direct use value
Assigns value from consumptive use, productive use, and non-consumptive use.
Economic Valuation of Biodiversity: indirect use value
Essentially the ecological value, arises from ecosystem services
Economic Valuation of Biodiversity: existence value
The intrinsic value – measures people’s willingness to pay or forgo benefits to ensure the continued existence of biodiversity irrespective of any present or future use
Economic Valuation of Biodiversity: option value
Arises from uncertainty about the future demand or supply for goods and services
Economic Valuation of Biodiversity: bequest value
Arises from the desire of individuals to preserve biodiversity for the use of future generations
Economic value pollinators annually
4-6 billion dollars per year in the US alone
Estimate of economic value of global ecosystem services?
~$125 trillion dollars/yr in 2011
