Lectures Biodiversity & Global Change
Lecture 1: Sampling biodiversity
What is biodiversity?
= the degree of variation of life and composition from the level of genes to ecosystems
Diversity = number of different species and their relative frequency, which can be at the level of
different ecosystems, genes, and molecules
Levels of biodiversity
- Taxonomic diversity/species diversity: species richness (number of species) and
relative abundances of individuals
o Alpha
o Beta
o Gamma
- (Phylo)genetic diversity: heritable variation within and between populations
- Functional diversity (similar traits such as WD, seed dispersal mechanisms)
- Interaction diversity
- Ecosystem diversity: such as vegetation heterogeneity or soil types
Species richness and evenness
Species evenness = level of equality of the relative abundances between the different species
per site (how equally the species are distributed)
Diversity indices:
- Shannon index:
- Simpson index:
Which is basically the same as D = sum(n / N)2 with n being the number of individuals in a specific
species and N being the total number of individuals from all the different species present in the
community
Thus, higher index = lower diversity (i.e. higher similarity)
- Take both species richness and species evenness into account
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Index increases when species richness and evenness increases (max. value = when all
types are equally abundant)
- Gini-Simpson index: 1-D: so a high Gini-Simpson index means higher diversity
Vegetation sampling
- Visual estimation of vegetation samples: however, not so accurate since one tends to
overestimate the coverage
- Species-area relationship: thus plot size choice is very important
Sampling animals
- Transect counts: measure along a transects e.g. along a road
- The further you go away the harder the detectability of animals
- Point counts: from one specific point e.g. monitoring bird populations
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Camera trapping: to generate occupancy data
Phylogenetic diversity
- Left one is more diverse because it has more distantly related and more phylogenetically
diverse species (but the same amount of species, so species richness wouldn’t give a
difference)
Functional diversity
- Built on traits
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From species pool, traits are of individuals are measured, functional matrix is generated
where the trait values are demonstrated in a table per species, then a graph with on xaxis trait 1 and on y-axis trait 2 are represented and species as values, then functional
richness and functional evenness are visualized
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Can be measured using functional diversity indices
Interaction diversity
- Amount of species interaction within a community
- Interaction networks: e.g. with 2 trophic levels (plants and dispersals) with different
indices (indices such as connectance, total number of interactions, ratio between animal
and plant species, size of interaction matrix, modularity)
- Connectance = proportion of possible links between species that are realized
(links/species2)
- You can count number of links and number of species and then put it in the formula:
Interaction richness/connectance (first one is 6/100 = 0.06; 12/100 = 0.12, 100 is
deduced from 10^2 for squared number of species)
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Interaction diversity = interaction richness (=number of links)/connectance (species2)
There is a difference between a food web and bipartide network. In a food web, all
species can potentially interact:
- Connectance = the proportion of possible links between species that are realized
(links/species^2)
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In a bipartide network, plants (P) can only interact with animals (A) and vice
versa, and hence not with species at the same level. Thus:
C = I/(A × P)
So, on slide 28 I should have used C = I/(A × P) because it is a bipartide network
and not a food web.
Lecture 2: Species distribution
Current estimates of species richness
>1.9 million living species are described, experts estimate that global species richness equals 3
to 100 million species
Why hard to sample and find new species?
- It is often difficult to go these areas (such as deep sea) or it is very expensive
- Estimates are uncertain due to controversial approaches
How is species richness distributed?
Vertebrates
- 5000 mammal species
- 9900 bird species
- Of which 9000 (so around 90%) are terrestrial species
- Of which 7500 are forest birds
- Of which 7000 in tropical forests, 900 outside tropics, 500 both tropical
and extra-tropical
- 6000 amphibian species
- 7500 reptile species
- In total around 30000 vertebrate species (0.1-1% of total species diversity)
Much more species in the tropics, due to latitudinal gradient of species richness = most species
between -10 and 10°
Plants
Around 300,000 - 400,000 vascular plant species
Insects
Around 2-30 million insect species (is not yet known)
Most species rich when compared to all the other major groups of organisms (followed by fungi
and bacteria)
Methods for estimating global species richness
ESTIMATION METHOD
TAXONOMIC EXPERT KNOWLEDGE
DESCRIPTION
an expert on 1 species (more qualitative)
LIMITATION(S)
No robust extrapolation possible and hard
to verify
Difficult to verify
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TIME-SPECIES ACCUMULATION
CURVES
DIVERSITY RATIOS (HOST
SPECIFICITY RATIOS)
Predicting unknown species numbers using
discovery curves, x-axis is time, y-axis is
cumulative species described, is only useful
when asymptote is approached
Only useful when the inventory of a group
is nearly complete
Uses host-specific ratios, for example, to
estimate species number
Locally estimated ratios may not be
representative globally
Needs to be almost complete
Local ratios = not global ratios
SPECIES-AREA RELATIONSHIPS
Looks at the number of species in specific
plots → extrapolates for total number of
species in larger areas
You can’t extrapolate too far because you
can reach a different habitat which affects
species richness as well as habitat
heterogeneity
No simple scaling across taxa
HIGHER TAXONOMIC DATA
Higher taxonomic levels are more well-known,
resulting in pretty accurate curves. With these
data lower taxonomic level curves can be
estimated via extrapolation (e.g. using
asymptote from higher taxonomic curve) (best
method, but still has limitations)
Approach depends on e.g. species
definitions, changes in higher taxonomy,
changes
in taxonomic effort over time, and
completeness of taxonomic inventories
Depends on taxonomic status
For exam: Name and briefly describe methods + limitations
Mora et al. for further explanation of these methods
Lecture 3: Species Distribution data
Species distribution = geographical locations of all its individuals during a specified period of
time
Methods to measure species distribution:
- GPS/tracking
- Camera traps
- Based on species occurrence data
- Occurrence records from specimen collections of museums
- Occurrence records in GBIF
- Occurrence records from citizen science projects (e.g. eBird)
Types of species distribution data
- Dot maps: present-only records (limitation = no absence data, this has consequences
for significance tests etc.)
- Range maps: expert-based information on distributional limits of where species occur
(limitation = do not have a specific resolution, therefore, at a coarse level it is ok, but at a
finer level it lacks dots where species are common)
Extent of Occurrence (EOO) = outer range of polygon around the inner dots
where distribution occurs, but you don’t know if the area inside the polygon is
densely or sparsely populated
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Area of Occupancy (AOO) = occupancy within the area, area within its 'extent
of occurrence'. The measure reflects the fact that a taxon will not usually occur
throughout the area of its extent of occurrence, which may, for example, contain
unsuitable habitats. In some cases (e.g. irreplaceable colonial nesting sites,
crucial feeding sites for migratory taxa) the area of occupancy is the smallest
area essential at any stage to the survival of existing populations of a taxon
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Atlas data: provide presence and absence data (limitation = fixed resolution, often
specific)
How is species absence measured?
Spatial scale dependence: importance of grain size (= size of individual sampling units =
resolution)
- Presence data à using grid cells to look in which the species was present and in which
it wasn’t (depends on grain size)
Coarser resolution leads to higher occupancy than finer resolution (so coarser resolution is often
better, because finer resolution often overestimates species distribution)
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Abundance maps: show geographic variation in abundance (limitation = abundance
data are, however, scarce at large scale and must be interpolated/modelled)
Thus, data differs in spatial variation, temporal variation, spatial resolution etc.
Summary
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Lecture 4: Ecological niches and range dynamics
Hutchinson’s multidimensional niche concept
- Ecological niche = set of environmental conditions under which a species can ‘exist
indefinitely’
- Persistence of a species in a given location depends on its population growth rate in
relation to limiting factors (e.g. salinity, temperature etc.). This means that population
growth rate should be positive according to Hutchinson’s model when:
- Growth rate r = b + i - d - e
- Multiple factors cause the niche space to be a multidimensional volume
Other examples of ecological niche models:
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Which factors determine species distributions and geographic range limits across space and
time?
Examples:
- Physical barriers
- Light gradient
- Predator-prey interactions
- Mutualism
BAM diagram (Biotic Abiotic Movement) (Soberon and Peterson’s BAM framework)
Abiotic factors:
- Temperatures
- E.g. low temperatures can kill frost-intolerant individuals directly or hash climates
can reduce resource (such as food) availability and thus kill or impair individuals
indirectly
- Water availability
- Soil chemistry
Biotic factors
- Competition:
- E.g little range overlap is caused by competition among similar species leading to
just little overlap in ranges (competition = limiting factor in this case) or invasive
species displaces native species (competition = major cause)
- Resource-consumer interactions (e.g. interaction between birds and plants they feed off)
- Pathogens
- Herbivory
- Predation
Movement & dispersal
- Dispersal mode
- E.g. Post-glacial recolonization (recolonizations of trees after the last Pleistocene
glaciation)
- E.g. Winter range of Arctic birds (the fluctuating food availability in arctic
environments can lead to migration and movement of consuming birds)
- Accessibility
How to measure a niche
- Experimental approach: experimentally and observationally measure an individual and
quantifying what makes the upper and lower limits of the range
- Species distribution models (measuring ecological niches from geographical
distributions) and ecological niche modelling
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2 aspects of the niche modelling
- Fundamental niche: all the environmental conditions and resources an organism can
possibly occupy and use (with absence of limiting factors)
- Realized niche: subset of fundamental niche that an organism occupies as a result of
limiting factors
The real geographic distribution may not reflect fundamental niche and thus not the areas with
positive growth rate
3 mismatches that could occur between the Hutchinson’s niche-concept and environmental
niche derived from geographic distribution data
- Source-sink dynamics: sinks have a population growth of <0 (so no positive growth
rate which is a condition for Hutchinson’s model) while source have a population growth
of >0
- Migration limitation: many areas are qualitatively suitable but there are no occurrences
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Time-delayed extinction: many areas have already negative environmental conditions
for some species, but the species are still present (think of old trees in an area that was
suitable but not anymore)
The actual geographic distribution is at the intersection of BAM diagram of all the factors
Potential distribution is at the intersection between biotic interactions and abiotic niche in the
BAM diagram
Summary
The ecological niche can be defined in various
ways, most commonly as the environment in
which species can persist based on abiotic and
biotic factors.
Key factors influencing species distributions and
range limits are abiotic (e.g. harsh climates),
biotic (e.g. competitors, host plants), and
movement (e.g. dispersal limitation).
Actual geographic distributions do not reflect the
fundamental niche and may not necessarily
reflect areas of positive population growth (e.g.
non-equilibrium with environmental conditions,
source-sink dynamics, migration limitation etc.)
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Lecture 5: Global patterns and determinants of species richness
There is a latitudinal gradient in species richness, what are its key determinants?
Global
determinants of vertebrate SR in mountains:
- Precipitation (obtained from weather stations)
- Temperature (weather stations)
- Topography (obtained from remote sensing)
- Soil
(obtained from soil profiles and remote sensing-bases soil covariates)
Data sources for studying global plant diversity:
- Inventory data: to obtain number of native species from books
- Geographical units: either natural units (e.g. mountain ranges,
deserts) or political units (e.g. countries, national parks)
- Global coverage (e.g. all biomes and floristic kingdoms)
Modeled plant SR
Spatially explicit models
Inventory data
environmental data (on climate, elevation, etc.)
Statistical modelling
& hypothesis testing
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Global determinants of plant diversity
- Modern climate, especially energy availability:
- High-energy regions have higher potential
evapotranspiration than low-energy regions,
but low-energy regions have higher
correlation between SR and potential
evapotranspiration
- High-energy regions higher correlation
between wet days and SR than low-energy regions
- High-energy regions have higher correlation between topography and SR
- High-energy regions have higher correlation between habitat diversity and SR
- Past climate change: quaternary climate change has a negative effect on continental
SR, but no effect on islands (maybe due to climatic buffering)
Summary
- Factors influencing the broad-scale distribution of species richness are manifold, but can
be grouped in course classes such as climate, geodiversity and history
- Modern climate is a strong determinant of large-scale biodiversity patterns: energy &
water availability are particularly important
- Topographic heterogeneity, erosion and soil types heterogeneity are important
geodiversity variables to explain species richness (e.g. in mountains)
- Historical factors are at least equally important: e.g. glaciations in the Northern
hemisphere and climate oscillations during the Quaternary, and historical immigration
routes etc. (corridors explain mainly the historical dispersal of African lizards)
Lecture 6: Biogeographic regions
Compositional dissimilarity:
According to Sclater (1858) “an important problem in natural history is that of ascertaining the
most natural primary divisions of the Earth’s surface, taking the amount of similarity or
dissimilarity of organized life solely as our guide”
So other factors that should be considered:
- Plate tectonics → barriers or isolation → evolution of life
Most of biodiversity that we see today has evolved over millions of years
Very large influence of meteorite strike so mammals and other species could flourish
Wallace’s zoogeographic regions
- Neactic
- Palearctic
- Neotropical
- Ethiopian/afrotropical
- Oriental
- Australian
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Holarctic = Nearctic + Palaearctic
Wallace’s zoogeographic regions
It is hard to draw boundaries between different realms, so there are transition zones
Floristic kingdoms
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Differences in Holarctic, Cape, Palaeotropical and the position of New Guinea
Modern biogeographic regionalization
How to quantitatively determine biogeographic regions?
To determine similarity of regions you should use beta diversity calculations → species turnover
Start with distribution data such as range maps → based on grids you can see which species
occurs where → distribution data → selection of distance metric → distance matrix: visualize
turnover in map.
Distance matrix
- From distance matrix to visualizing turnover
- Bétasim = (dis)similarity measure: the higher the more dissimilar grid cells are
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You can calculate this per grid cell with a = number of shared species
between 2 grid cells, b = number of species that are unique to grid
cell 1, and c = number of species unique to grid cell 2
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Visualizing the distance matrix to map of results
- Nonmetric multidimensional scaling (NMDS) = ordination method used to visualize map
of results: close points in the plots (with similar colors) have more similar species
assemblages
Cluster analysis
- Allows you to come up with discrete regions on Earth (makes it easier for conservation
and politicians)
- Either non-hierarchical or hierarchical
- Non-hierarchical: optimized unique solution for a specific number of cluster
- Hierarchical: hierarchy of clusters of species, looks like phylogenetic tree, in this
case each tip (of the ‘tree’) is a grid cell, the distance indicated how closely
related the grid cells are
With the distribution data that we have now, a more defined map of species is generated. When
adding phylogenies biogeographic regions are generated that are derived from phylogenetic
turnover and clustering using all amphibians, birds and mammals:
Beta sim formula can also be used for phylogenetic beta diversity, to calculate how similar
certain species are regarding phylogeny and therefore, evolutionary history
a = number of branches shared between the two grid cells
b = number of branches unique to grid cell 1
c = number of branches unique to grid cell 2
Summary
- Distribution of taxa can be described in terms of geography, biogeography and politics
- Major biogeographic regions differ in their species composition (compositional similarity)
mainly due to long-term isolation and plate tectonics
- Modern statistical methods are used to quantify biogeographical regionalization: they
use species distribution data, dissimilarity indices and ordination and cluster analyses.
Phylogenetic info can be added to quantify phylogenetic dissimilarity (apart from
taxonomic dissimilarity)
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Lecture 7: Island biogeography: biological perspective
Eilanden zijn uniek op soortenniveau (evolutionair) en op gemeenschapsniveau
(biogeografisch)
Species-level
Island adaptations
- Dwarfism/gigantism (= the island rule): species that are big at the continent become
smaller on islands due to predation (even humans shrink on islands!), while small
species on the continent become big on the island e.g. due to interspecific competition
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Woodiness increases: islands often have trees or bushes while the same orders
elsewhere only include herbaceous species. Explanation = competitional advantage to
grow taller (e.g. more light available):
- Trees are not very likely to reach distant oceanic islands; however, herbaceous
plants are more likely to establish on islands à competition with other
herbaceous plants for resources such as light à advantage = growing tall and
overtopping other plants à convert into woody bushes à convert into trees
Relicts: islands can provide a better (isolated) environment so that species can survive,
even if their species is extinct on the continent (mammoeten waren uitgestorven op
continent en pas 6000 jaar later op geïsoleerd eilandje)
Loss of disperseability: veel insecten en vogels die niet kunnen vliegen op eilanden,
vanwege minder aantal predatoren op de grond en insecten die heel goed kunnen
vliegen geven niet hun genen door en verre dispersie is minder belangrijk omdat het
gebied relatief klein is
Ecological naivety/tameness: veel ongevleugelde soorten zijn heel tam (denk aan
Galapagos) want ze zijn niet gewend aan mensen → veel grotere kans op uit te sterven
Archipelagic speciation: oriëntatie van eilanden binnen archipel zorgt voor unieke
soortvorming (adaptieve radiatie)
- If islands are too close to each other there will be constant exchange, so no
genetic divergence
- Evolutie + omgeving en oriëntatie van eilanden
Adaptive radiation: snelle soortvorming vanuit 1 voorouder (Darwin vinken)
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Community level
- Eilanden zijn relatief soortenarm, door de barrière en dat ze redelijk jong zijn
- MAAR heel uniek in soorten, komen nergens ter wereld voor = endemisch
- En higher species abundances
- Island disharmony: op eilanden ontbreken vaak bepaalde groepen geheel (bijv.
kikkers), terwijl vogels meer in harmonie zijn met continent want oceaan vormt voor hen
een minder grote barrière (vooral amfibieën en reptielen een beetje zijn in disharmonie)
- Interactions and behaviors: island disharmony → soorten passen hun gedrag en rol in
ecosysteem aan omdat andere soorten dus niet vertegenwoordigd worden op het
specifieke eiland (bijv. reptielen die aan bestuiving doen of vleermuizen die overdag
leven)
Theory of Island Biogeography
Meerdere modellen van eiland biogeografie
Island Equilibrium model:
Focus op immigratie en extinctiesnelheid
Immigratiesnelheid is hoger op grote eilanden, en lager op kleine eilanden
Extinctiesnelheid is hoger op verre eilanden, en lager of dichtstbijzijnde eilanden
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Hoe meer soorten op eiland, dan schuift evenwicht naar rechts: meer kans op uitsterven (er zijn
immers meer soorten om uit te sterven + meer concurrentie) en kans op een immigrant van een
nieuwe soort is lager (want de meeste soorten zijn al vertegenwoordigd op het eiland)
Evenwicht wordt bereikt als immigratiesnelheid = extinctiesnelheid
Volgorde van snelst evenwicht bereikt/eiland dat de minst aantal soorten kan ondersteunen:
1. Ver van vasteland + klein eiland (A)
2. Dichtbij vasteland + klein eiland (B)
3. Ver van vasteland + groot eiland (C)
4. Dichtbij vasteland + groot eiland (D)
2 belangrijke aannames:
- Extinctie(snelheid) wordt beïnvloed door ruimte/gebied (effect of island size)
- Hoger op kleine eilanden
- Lager op grote eilanden: want grote eilanden kunnen een hoger aantal soorten
supporten
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Immigratie(snelheid) wordt beïnvloed door isolatie (effect of distance)
- Hoger op dichtstbijzijnde eilanden: soorten kunnen deze eilanden makkelijker
bereiken
- Lager op verre eilanden
Dynamisch evenwicht wordt bereikt
Species-area relationships
- Power law (Arrhenius): S = cA2 → log S = log(cA2) = hoe snel soortenrijkdom toeneemt
= lineair met logaritmische assen
- The decline of species richness is often a negative exponential or sigmoidal function of
isolation
Islands vs habitat patches on continent
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Habitat patches on continent kunnen wel matrix ‘gebruiken’ terwijl eiland dat natuurlijk niet
kunnen (matrix = oceaan) dus nog wel verschillen tussen deze 2 (check nog ff slides)
For exam:
- Biotische eigenschappen van eilanden
- Belangrijke kenmerken van het evenwichtsmodel
Summary
Lecture 8: Island biogeography: geological perspective
Eilanden zijn niet statisch maar in evenwicht.
Waarom zou eiland altijd in evenwicht moeten zijn?
- Eilanden zijn niet statisch met betrekking tot evolutionaire tijdschaal
- Dynamic Equilibrium Theory (DET) kan alleen een perfect model van de natuur zijn
als processen zoals immigratie, soortvorming en extinctie relatief snel gaan vergeleken
met de snelheid waarop eilanden veranderen over tijd
Verschillende soorten eilanden:
- Continentale eilanden: relatief oud
- Ontstaan uit continentale plaat, ofwel afgebroken van plaatfragmenten of
afgebroken en afgedreven van continentale plaat (bijv. Madagascar)
- Ontstaan door isolatie door zeespiegelveranderingen (bijv. Groot-Brittannië)
- Oceanische eilanden: relatief jong
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Ontstaan door hotspot vulkanisme (bijv. Hawaï)
Ontstaan door subductive arcs (bijv. Solomon eilanden)
Levenscyclus van eilanden: vorming à groei à bewegen à zinken/krimpen
Hoe groeien eilanden:
Oceanische eilanden: op bepaalde plekken in oceaan breekt korst door → lava gaat stromen en
na heel veel jaar ontstaat een bult (= eiland) → korst beweegt boven hotspot heen → rij met
vulkanische eilanden ontstaat (de hotspots blijven op dezelfde plek voor hele lange tijd)
Eilanden veranderen ook fysisch:
- Bodemvorming: over algemeen 500 jaar om 2.5 cm bodem te vormen
- Hierdoor ook vestiging van planten/bomen
- Kans op dat dit allemaal goed gaat is hoogst op grote en dichtstbijzijnde eilanden
Kolonisatie
Eerste kolonisatie door: vogels, insecten, varens, andere planten door verspreiding door vogels,
spinnen, schimmels, bacteriën, vissen, schildpadden
Eilanden vormen hun eigen habitat en microhabitat:
Wolkvorming door wind en botsen tegen beginnend eiland → mistbossen ontstaan → hele
bijzondere habitats (en dus meer soorten kunnen ontstaan) → eilanden vormen hun eigen
geodiversiteit à successie
- Geodiversiteit (zoals bodemsoorten) is hoger bij oudere eilanden dan bij jongere →
invertebraten reageren hierop
Time + Isolation = Speciation
- Anagenese vs cladogenese (soort komt op 1 eiland terecht en verspreidt zich over
andere eilanden → 2 of meer nieuwe soorten ontstaan)
- Gedurende bepaalde tijd worden eilanden groter en geodiverser: meer habitats voor
meer soorten
Op eilanden dichtbij continent minder soortvorming dan op meer geïsoleerde eilanden vanwege
de continue genenstroom van de originele populaties
Eilanden bewegen:
- Vulkanische eilanden bewegen door tektoniek over hotspot
(hotspoteilanden)
- Eilanden verst van hotspot zijn het oudst à keten
van eilanden ontstaat
- Dispersie treedt op tussen de hotspoteilanden
- Continentale eilanden bewegen door tektoniek (bijv.
Madagaskar)
- Vicariantie = ontstaan van gebieden door splitsing
van 1 gebied
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In evenwichtsmodel wordt geen rekening gehouden met deze bewegingen van de eilanden,
terwijl dit wel echt invloed heeft op soortvorming en dispersie
- Dit is gebeurd op Hawaï: op jongere eilanden zijn door dispersie allemaal nieuwe
spinnensoorten ontstaan
Eilanden zinken ook ( → worden kleiner)
- Omdat eiland over zachte aardkorst beweegt die warm is waardoor eiland daalt in korst
totdat nieuwe geostatisch evenwicht is bereikt → gezonken eilanden met nieuwe
geodiversiteit en habitats (en mariene ecosystemen)
- Als korst stolt zakt eiland minder snel naar beneden
- Welke gevolgen hebben kleiner worden van eilanden als gevolg van zinken op
evenwichtsmodel?
- Minder soorten: immigratie neemt af (door target effect: als doel kleiner wordt,
neemt de kans af dat je het doel/eiland treft, en natuurlijk hoe kleiner het eiland
hoe minder soorten er op passen want het eiland is al vol), sterfte neemt toe
(door bijv. afnemende hulpbronnen doordat het eiland relatief voller wordt omdat
het kleiner wordt) → evenwicht verschuift naar minder soorten
Een nieuw biogeografische theorie houdt rekening met dynamische eilanden (dus groei en
zinken van eilanden) = General Dynamic Theory
- Jonge oceanische eilanden worden groter, totdat ze losgetrokken worden van hotspot
en in grootte afnemen en uiteindelijk zinken
- General Dynamic model heeft vorm van parabool: hoogste soortenaantal in midden
omdat hoogste topografische complexiteit bereikt wordt tijdens intermediate ages
- Bij stage 1: hoge immigratiesnelheid en soortvorming
- Bij stage 2: hoge extinctiesnelheid
- Bij stage 3: extinctiesnelheid vlakt af, want minder soorten in totaal
- Hoe ruwer het eiland, hoe meer scheiding, hoe meer soortvorming
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Zeespiegelstijging heeft ook invloed op eilanden en biodiversiteit (en dispersie van soorten)
- Bijvoorbeeld soorten die leefden in een peninsula en door zeespiegelstijging afgesloten
werden van vasteland à die soorten raakten genetisch geïsoleerd van hun
zustersoorten aan land à soortvorming
- Zeespiegelstijging heeft sowieso effect op dispersie maar ook op vicariantie?
- Eilanden die met elkaar verbonden raken worden groter → netto hoeveelheid
soorten is hoger, extinctiesnelheid neemt af en immigratie neemt toe (omgekeerd
ook waar: als eilanden van elkaar gesplitst worden heb je dus een kleiner eiland,
hogere extinctie, en minder immigratie)
- Species richness is hoogst wanneer immigratie > extinctie
Glacial Sensitive Model of Island biogeography houdt ook rekening met interglacialen en
glacialen en het effect hiervan op soortenrijkdom
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Summary
- Eilanden veranderen over geologische tijdschalen: groei, beweging en verdwijnen à
heeft invloed op verspreiding en vorming van soorten
- Het Dynamic Equilibrium Theory = SR theorie gebaseerd op de aanname dat eilanden
geologisch statisch zijn en SR de functie is van huidige geografie
- De General Dynamic Theory = SR theorie voor oceanische vulkanische eilanden dat
SR uitlegt als resultaat van dynamische geologische evolutie van eilanden gedurende
miljoenen jaren
- De Glacial Senstitive Theory = SR theorie die zegt dat SR resultaat is van
veranderende evenwichten door geografische veranderingen op eilanden als gevolg van
klimaat veranderingen (klimaatveranderingen à geografische verandering op eiland à
veranderend evenwicht op eiland)
Lecture 9: Monitoring global biodiversity change
Biodiversity policy:
- Aichi biodiversity targets
- Sustainable Development Goals
- National Biodiversity Plans
- Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services
(IPBES)
Convention on Biological Diversity
Convention on Biological Diversity (CBD) = international convention supported by 195 countries
that aims at implementing conservation measures in policy
3 main objectives:
- Conservation of biological diversity
- Sustainable use of the components of biological diversity
- The fair and equitable sharing of the benefits arising out of the utilization of genetic
resources
Aichi biodiversity targets (due 2020)
- Its vision includes that by 2050 biodiversity is values, conserved, restored and wisely
used, maintaining ecosystem services, sustaining a healthy planet and delivering
benefits essential for all people
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20 targets (see pp):
- Strategic Goal A: address the underlying causes of biodiversity loss by
mainstreaming biodiversity across government and society (first 4 targets)
- Strategic Goal B: reduce direct pressures on biodiversity and promote
sustainable use (target 5-11)
- Strategic Goal C: improve status of biodiversity by safeguarding ecosystems,
species and genetic diversity (target 11 -14)
- Strategic Goal D: enhance benefits to all from biodiversity and ES (targets 14-17)
- Strategic Goal E: enhance implementation through participatory planning,
knowledge management and capacity building (targets 17 tm 20)
Example of Aichi target:
- “By 2020, the rate of loss of all natural habitats, including forests, is at least halved and
where feasible brought close to zero, and degradation and fragmentation is significantly
reduced”
ipbes = Science and Policy for People and Nature
Indicators: Biodiversity Indicators Partnership (BIP) for each Aichi goal (such as Wildlife
Picture Index based on camera trapping, or number of extinctions prevented, or protected Area
Management Effectiveness, or Living Plant Index, LPI)
LPI = an indicator that measures population trends (= relative abundance) of vertebrate species
- It takes time-series of population abundance
- Includes more than 16000 populations of 4000 vertebrate species
- Latest result: 60% decline in population abundance since 1970
Limitations of indicators:
- Bias in taxonomic coverage: bias towards bigger animals (decades ago bigger animals
were often better monitored)
- Limited temporal coverage: and temporal coverage differs between indicators
- Bias in spatial coverage (more geographic locations concentrated in Europe)
- Bias in dimensions of biodiversity: structure, functional component and composition of
ecosystems lack a lot of data, mainly focused on species data
Improving data coverage
- Operationalizing new methods for monitoring biodiversity change
- Citizen science (extensive sampling, collection of occurrence records even in
data-poor regions)
- Sensor networks (sampling at remote areas, detection of rare species, less
costly)
- DNA-based techniques such as eDNA usage (automatic identification allows
identification of incomplete or immature individuals, timesaving)
- Satellite remote sensing (facilitates coordination and sharing, less dependent of
politics, globally consistent data collection)
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Focusing on the essential: use other Essential Biodiversity Variables (EBVs) =
minimal set of biological variables, complementary to one another, that can be obtained
for large parts of the Earth with the aim to study, report and manage biodiversity change
at national to global scales
- 6 EBV classes such as ecosystem-level (e.g. community compositions,
Ecosystem structure, Ecosystem function) and species-level (genetic
composition, species population, species traits) classes
Much data is collected, but a lot is still unavailable/inaccessible: so to improve data
coverage it is essential to make data Findable, Accessible, Interoperable, Reusable
(FAIR), such as:
- Open access to data: data needs human- and machine-readable licenses
- Machine-readable data and metadata: applying standards such as Darwin Core
and Ecological Metadata Language
GEO BON (Group on Earth Observations Biodiversity Observation Network)
Global coordination of monitoring
Governance structure of GEO BON (see pp)
Focus on EBVs and developing additional new biodiversity change indicators
EXAM: to be able to explain what the CBD, Aichi Target, BIP, Biodiversity Indicators, EBVs,
GEO Bon and Darwin Core (incl. Event Core) are and which biases exist, and how biodiversity
data coverage can be improved.
Lecture 10: Remote Sensing and biodiversity research
Remote Sensing = science of collecting and interpreting info about an object without actually
being in contact with it
- Example = satellite imagery
Uses electromagnetic energy: its optimal range is from x-rays to infrared
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Remote sensing types:
- Active
- LiDAR
- RADAR
- Passive (really dependent on the presence of sun)
- Optical
Passive Remote Sensing: spectral reflectance
- Reflected colors represent different vegetation and land use (green —> plants due to
photosynthesis)
- Blue, green, red, infrared and medium infrared do not work at night (cause they need
sunlight)
- Sensor could, however, be designed to catch other wavelengths such as temperature
that can be monitored during the night
Active Remote Sensing: backscattering
- Does not show the reflectance
- Airborne Laser Scanning (ALS) is most often used as radar and has a small footprint
- Spaceborne LiDAR has a large footprint
Platforms types used for RS (based on height)
- Spaceborne: satellites (ESA and NASA)
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-
Airborne
- Manned Aerial Vehicle
- UAV
Ground (such as drones)
Usage and indices of remote sensing
Usage
Vegetation growth and productivity
Indices
Normalized Difference Vegetation Index,
Enhanced vegetation Index, etc.
Biophysical vegetation parameters
Structure Intensive Pigment index, etc.
Indicate water content
Soil Water Index, etc.
Burnt area
Normalized Burn ratio, etc.
Normalized Difference Vegetation Index (NDVI)
- Red and near infrared
- Used to assess whether the observed target contains live green
vegetation or not.
- Radiation of near infrared (NIR) minus radiation of red, the
answer must be divided by radiation of near infrared + radiation
of red wavelengts.
- A high NDVI indicates green vegetation, whereas a low NDVI
means dying or dry vegetation and soil
A global map with NDVI shows water, barren land, grasslands and
forests:
- Negative values (approaching -1) = water
- Values close to zero = barren rock/sand/snow
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Low positive values = shrub and grasslands
High positive values = temperate and tropical rainforests
Normalized Burn Ratio to detect wildfires
- Mid infrared
Resolutions
- Spatial = size of field of view (e.g. 10x10m): the lower (e.g. 0.5x0.5m) the more detailed
the image is
- Spectral = number and size of spectral regions the sensor records data in (e.g. blue,
green, red, near infrared, thermal infrared, microwave) (very important!)
- Temporal = frequency of data acquisition by the sensor (e.g. every 30 days, 5 per day)
- Radiometric = sensitivity of detectors to small differences in electromagnetic energy (e.g.
8 bit, 16 bit)
What can RS contribute to biodiversity monitoring?
- It’s independent of method of measurement (in contrast
with in-situ monitoring)
- It allows increased harmonization
From field data to ecosystem variables:
Predictions + response —> algorithm —> model --> spatial
prediction
Thus it can help monitoring land cover (change), fire, biophysical vegetation parameters,
vegetation productivity, vegetation cover/density, biomass
Read appendix of the article mentioned in pp for clear summary
+
Active Remote Sensing
Passive Remote Sensing
Able to examine wavelengts with insufficient energy provided by
the sun (e.g. microwaves)
Passive RS does not disturb the area of interest
Able to better control the way a target is sensed
Ability to obtain measurements anytime, regardless of the time of
day or season
Independent of cloud coverage and bad weather conditions
-
Require the generation of a fairly large amount of energy to
adequately sense targets
Can only take place during daytime (except for thermal infrared)
Cloud coverage can hamper detailed imagery
Emit radiation and thus disturb the area of interest
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RS has some advantages compared
to in-situ observations:
Disadvantages of in-situ
observations:
- Huge effort of sampling
- Inaccessibility of some
habitats
- Need a priori knowledge of
terrain
- Results cannot be
extrapolated to the
surrounding landscape
Remote sensing cannot replace traditional in situ methods for compiling initial inventories of
species, except in case of very large species identi able on airborne images, and very high
resolution imagery collected by UAVs. However, remote sensing is a valuable large scale
biodiversity monitoring tool at the level above species if coupled with quality ground data and
likely to grow in value if embedded in a global, harmonized observation network
Lecture 11: LiDAR used for characterizing habitat structure
LiDAR = Light Detection And Ranging = active RS
2 types of platforms:
- ALS (= Airborne Laser Scanning, kind of plane), TLS, ULS, MLS
- Small footprint
- Spaceborne LiDAR
- Large footprint
ALS sends radiation, and then measures the wavelengths that come back:
you know the position and orientation of the plane, and with the time of oneway flight and the speed of light the
distance can be determined:
𝒕
d= 𝒄
𝟐
TLS = Terrestrial Laser Scanning
Spaceborne LiDAR: Global Ecosystem Dynamics Investigation
(GEDI)
- GEDI sees to and through the trees à can discriminate
dense upper canopy from open understory for example
à data on canopy height can be obtained à 3D
vegetation reconstruction with maps
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LiDAR can thus be used to look at ecosystem structure (= EBV class) to map extent of forest
and which type of forest it is, map the biomass or carbon storage
Thus LiDAR linked to EBV:
- LiDAR can show the vegetation height (ranging from low to high)
- LiDAR can show vegetation density (ranging from sparse to dense)
- LiDAR can show vertical vegetation structure/complexity (ranging from simple to
complex)
Lecture 12: Global change
Global change = planetary scale changes to atmospheric circulation, ocean circulation, climate,
carbon cycle, nitrogen cycle, water cycle and other cycles, sea-ice changes, sea-level changes,
food webs, biological diversity, pollution, health, fish stocks, and more
- Large driver = civilization: population, economy, resource use, development, energy,
transport, communication, land use and cover, urbanization, globalization
- Human Influence Index (HII) quantifies the global human presence (per 1 km2 grid cell)
- HII includes urban extent, population density, roads, navigable rivers, and
agricultural land
In dark green the major threats to biodiversity:
- Habitat loss/alteration/fragmentation: land degradation impacts 75% of terrestrial
ecosystems
- Overexploitation and agricultural activity (driven by overconsumption) = dominant causes
- Invasive species
- Pollution: catastrophic decline in freshwater biodiversity
- Climate change
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Key threats per taxonomic groups
- Birds: most important threat = habitat degradation/loss
- Mammals: most important threats = habitat degradation/loss and exploitation
- Fishes: most important threat = exploitation
- Reptiles and amphibians: most important threat = habitat loss/degradation
Habitat degradation and loss
Forest loss à
- Reduced forest area
- Increased forest fragmentation à increased isolation of forest patches
- Increased edge effects
-
Last of the wild = areas that are least influenced by man, defined as 10% wildest areas
based on HII (especially deserts, inner tropical forests, boreal zones)
Overexploitation
- Hunting and fishing à defaunation = human impacts on animal biodiversity including
global extinction as well as the decline in abundance of individuals within populations:
humans especially harvest largest individuals (e.g. biggest elephants) leading to trophic
downgrading à downsized communities
- Consequences of defaunation: Large wildlife removal à cascades to other
consumers à plant-animal interactions are affected à functions and services of
the ecosystem are affected
- Wildlife trade: especially vertebrates
Invasive species
- Hotspots and coldspots of alien species richness
- Definitions
- Alien (exotic): non-native species introduced by humans
- Naturalized: alien species forming self-replacing populations
- Invasive: naturalized species with strong ability to spread
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Weeds: plants (not necessarily alien) that grow in sites where they are not
wanted
Climate change
- Biodiversity redistribution
- Species move upwards and species move toward poles
- Range reductions
- Phenological changes in the arctic: advance in spring and delay in fall
- Phenology = timing of life history events (e.g. flowering, breeding, migration)
- Mostly triggered by temperature changes
Lecture 13: The Anthropocene
Anthropocene is global
- Stratigraphic definition emphasizes the global effects rather than causes
- The causes and effects can be heterogeneous, inequal, and diachronous; this is the
same for effects
- E.g. causes are diachronous = start at different times
- E.g. effects are heterogeneous = some people and ecosystems are more
affected by humans than others
Anthropocene at local scale
- Human impacts on islands are large: HII is much higher on islands than on mainland,
while protection status of mainland is slightly higher than islands
- Islands are less than 8% of the global land mass but 61% of extinct species and 37% of
critically endangered species occurred on islands
- Number of extinctions higher for birds than mammals
Causes of extinctions (not islands specific)
- Habitat destruction: islands are better protected against tropical cyclones/storms when
there are more trees (so when habitat destruction occurs à more vulnerable)
- Invasive species: mammals are the most common invasive animals (found on 97% of
islands with threatened species). Shipping and plane routes and roads decrease
geographical distance (à change in isolation in the Anthropocene à formation of a
theoretical Pangaea again)
- Pollution
- Population (and consumption: difference between NYC and Ethiopia for example)
- Sometimes changed to ‘climate change’
- Overharvesting
= HIPPO
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In the island biogeography model, the I-lines become closer to
each other (since due to human transport systems effective
distance decreases and there is just a slight difference
between near and far islands)
Adding speciation would not matter significantly, because
speciation would balance extinction in millions of years (= too
long)
Disharmony: specific transportation methods might facilitate
different species
Introduction pathways: either intentional (e.g. livestock) or
accidental (e.g. under shoes)
Species introduction = not necessarily the same as invasive species
The introduced species become invasive when (Tens Rule):
- The geographical barrier is overcome
- Species are introduced into the wild (and thus left the ship/plane)
- Are able to survive and reproduce in the wild
- Are able to cross dispersal and environmental barriers to spread à invasive
The impact of invasions on islands:
- Ecological naïveté (competition, predation)
- Societal/economic (diseases, pests)
Impact of invasives on island biodiversity
- Particularly the native vegetation is affected by introduced herbivores
- Extinctions are most common for plants, then for birds, then for mammals and finally for
ampibians
- 86% of recorded extinctions related to invasive species are on islands
Human impact on species turnover
The number of species (species richness) may stay the same, but the composition changes:
turnover of species is very important:
Human impact on species turnover: due to human influence many species go extinct, but also
many species are introduced, what does this mean when you think about species turnover?
Species richness increases regionally, especially on islands.
- On local scale land use, habitat fragmentation, climate warming, N deposition influences
temporal biodiversity change
- Intense land use decreases biodiversity, while climate warming and lands use
without conversion positively affect biodiversity change
- Local positive biodiversity change (increase)
- On regional scale: more colonization (usually nonnative) than extinction (usually native)
à increase in SR
- On global scale: less speciation than extinction (we lose specialists to the advantage of
the generalists) à decrease in SR
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Lecture 14: The future of biodiversity
What are the consequences of biodiversity loss for us humans? Why does it matter?
- Ecosystem services:
- Provisioning services e.g. food, medicine, timber, bioenergy
- Regulating services e.g. water regulation, air quality, pollination
- Supporting services e.g. nutrient cycling, photosynthesis
- Cultural services e.g. aesthetic values, spiritual values, recreation, ecotourism,
mental health
- Intrinsic values of nature (biodiversity): captured in the Nature Futures Framework
- Nature for Society: ecosystem services, natural capital, sustainable management
nature contributions to people, nature-based solutions,
- Nature as Culture: living in harmony, people one with nature, cultural landscapes,
relational values, cosmovision
- Nature for Nature: intrinsic value of nature: ‘is not fair to drive species to
extinction just for our consumption’ (this dimension is often not captured in
capita), land sparing, wilderness and rewilding
Future changes in climate, land use (especially decadal in Eastern Africa, Turkey and Thailand,
Vietnam and Cambodia), and infrastructure (China’s new road development to increase
accessibility to Europe and Africa) and increases in urbanization (especially in Africa)
How can we gain insights into the future of biodiversity when looking at these changes that are
coming?
- Scenarios = descriptions of plausible future conditions (which could be about specific
drivers of change like climate change or policy options or socioeconomic development)
- Models = translation scenarios into consequences for nature, nature’s benefits and
quality of life (from the side of environmental conditions and biodiversity data)
Difference between biodiversity indicators (that can inform policy about how biodiversity is
changing until now) but if you want to look at the future you will need scenarios and models
2 broad classes for essential biodiversity variables (EBVs) in models:
- Species-focused EBV classes: variables measuring an attribute of a collection of
organisms mainly grouped by species identity
- Genetic composition: variables measuring genetic diversity within species
- Species populations: variables measuring species distribution and abundance
- Species traits: variables measuring traits of species
-
These species-focused variables = species-based models:
Species Distribution Models (SDMs) using occurrence records (species data) +
environmental data à look at model response functions à replace current
environmental data with future environmental data
-
Ecosystem-focused EBV classes
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Community composition: variables measuring the collective diversity of
organisms within ecosystems
- Ecosystem structure: variables measuring structural attributes of ecosystems
- Ecosystem function: variables measuring functional attributes of ecosystems
These community-based models include:
- GLOBIO modeling framework: processes as climate change, N deposition, land
use, roads, hunting are used as pressures, and then the mean species
abundance (MSA) is generated to project changes in the future
- Shared Socioeconomic Pathways (SSP): are scenarios of projected
socioeconomic global changes (e.g. human population, economic growth,
urbanization) up to 2100. Used to derive greenhouse gas emission scenarios
with different climate policies. Include developed narratives that explain the 5
different scenarios (à can be translated into more specific changes e.g. climate
change, these scenarios can be implemented by IPCC which uses these
scenarios to generate emission scenarios, and these are then used in a range of
climate models)
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Harmonizing data, scenarios, and models on land use, biodiversity and climate change
In each step there are uncertainties, which can be quantified, uncertainties lie in:
-
Initial conditions (biological distribution etc. might not be fully known)
Model classes: different statistical or process-based models
Model parameters: e.g. regression coefficients or values of parameters in process-based
models
Boundary conditions: uncertainty in future environmental changes e.g. emission
scenarios or climate models: the uncertainty can be quantified by using an array of
different scenarios
For the Exam:
-
Be able to define what biodiversity is, to give examples of sampling abundance data,
and to calculate a diversity index as well as connectance for an interaction network
-
Be able to name and briefly describe methods for estimating global species richness,
and what problems are related to each method
-
Be able to explain the differences between species distribution data (in terms of presence/
absence, abundance, EOO/AOO, spatial/temporal extent and resolution)
-
Be able to provide a definition of the ecological niche, to explain the BAM diagram, and
to provide examples of which factors are limiting the distribution of species
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Be able to name and explain different key determinants of global species richness
patterns and which kind of distribution data can be used to perform broad-scale species
richness analyses
-
Be able to explain: 1. typical biotic characteristics of islands 2. key features of the
equilibrium model
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Be able to understand how islands geological change and how their geospatial change
did affect the distribution of species. Understand the three species richness theories.
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Be able to (1) describe species distributions with biogeographic terms, (2) name major
biogeographic regions, (3) describe the main factors causing regions to be different, and
(4) identify the main methodological steps for a modern biogeographical regionalization
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Be able to explain (incl. examples) what the CBD, Aichi Targets, BIP, Biodiversity
Indicators, EBVs, GEO BON and the Darwin Core (incl. Event Core) are, what biases
exist in indicators, and how biodiversity data coverage can be improved
-
Be able to define what Remote Sensing is, explain different types and resolutions of
Remote Sensing, and name 3 applications.
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Be able to define LiDAR, name the LiDAR platforms, give some examples how to use
LiDAR in characterizing vegetation structure
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Be able to define global change and invasive species, and to explain how global change
(habitat loss, overexploitation, biological invasions, pollution, climate change) affects
biodiversity (with examples)
-
Be able to explain: 1. The difference between the Anthropocene and human impacts
2. How biogeographical processes differ as a result of human activities
-
Be able to give examples of why biodiversity matters, to explain what kind of scenarios
and projections are needed to forecast biodiversity change, and which kind of
uncertainties can be quantified
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