measuring biodiversity

policy definitions of biodiversity

vague, immeasurable, changes depending on who you ask, no agreed upon empirical definition

aspirational but not scientific

scientific definitions of biodiversity

variety of chromosomes/alleles/species/families/biomes/ecosites etc

generally focuses on organismal biodiversity

species richness, diversity, composition and abundance

species richness

simplest measure of species diversity

number of species

univariate - 1 number used to describe

species diversity

measure of diversity

index which combines species richness and species evenness - ex shannon, simpson’s

univariate - 1 number used to describe

species composition

measure of species diversity

list of species names and their relative abundances

multivariate - many numbers used to describe

number of individuals

not measure of species diversity but commonly used similarly

counts number of total individuals

univariate measure - one number used to describe

why is sampling important?

when taken in a standardized way, can represent an unbiased sample of the total biodiversity

ex quadrats, cameras, insect traps - can all have their biases but depends on objective

sampling bias

when one component or species of a population is over emphasized in a sample

goal is to include all elements of parent in same proportions to avoid this

is observed species richness biased?

hard to accurately measure or estimate by observation - downward biased

problems w number of individuals and number of species - standardizing by sampling effort, need rarefaction curve vs species accum curve

and sample area and number of species - standardizing by area sampled (species area curve)

(need to be exactly the same across samples)

species area curve

non-linear curve means species richness increases with area but with diminishing returns. so depends critically with amount of area sampled

control by ensuring the same area is sampled between sites

general species accumulation curve

number of species increases as numbers of individuals examined increases but with diminishing returns

depends on order sampled, which is why it changes every time you do it

individual component of rare fraction curve

control with rarefaction

rarefied species richness

the average number of species that you will find from looking at x individuals (same number of individuals in each site)

need to compare number of species encountered after encountering the same number of individuals from each site

the closer to plateaued the closer to having measured the true number of species aka more sampling is unlikely to find more species

note axes

species accumulation curve vs size-based rarefaction curve

one re-sampling of sample, an individual component of rareified richness

need to keep re-sampling in different orders to gain a reliable estimate and see plateaus

sample coverage

the proportion of the total number of individuals in a community that belong to the species represented in the sample

coverage-based rarefraction

allows comparison of species richness at equal sample coverage instead of sample size for a better comparison

only accurate if the sample is large enough, 5-20 individuals - but when used it is the best method

alternative to size based

asymptotic estimator - chao1

tool to correct the observed richness by adding a term based on the number of singletons, doubletons, or few individuals

used to estimate total species richness when the curve has not plateaued

species diversity index

used as species richness leaves out information

a function of species richness and evenness (its both not individual measure)

two common indices are Simpson’s and Shannon’s

species evenness vs species dominance

equalness of abundance among species vs

the inverse, a lack of equalness - one species is most common

simpson’s diversity index

has many variants, gives less weight to and so cant easily detect rarer species rather detects dominance

shannon’s diversity index

has many variants, gives more weight to and so can detect rarer species (but not as well as species richness does, which counts all species)

hill numbers

unified concept of diversity, the continuum of possible diversity measures are now thought of as effective number of species (unit and def)

more intuitive measure, the number of equally abundant species necessary to produce the observed value of diversity

bias in diversity indices

less extreme as species richness as it is now only one component of the measure

but should still keep sample area constant and use rarefraction to account for the richness

species evennes doesnt have same constraints with sample area or individuals sampled