Introduction to community ecology: How does HMSC relate to

Lecture 2Introduction to community ecology

& Typical data collected in community ecology

Nerea Abrego

University of Jyväskylä & University of Helsinki

[email protected]

Lecture 2

Part 1. Introduction to community ecology: How does HMSC relateto theory in community ecology?

1.1. What is community ecology?1.2. What is an ecological community?1.3. What are the prevailing theories in community ecology?

Part 2. Typical data collected in community ecology: What kind of data does HMSC take as input?

Lecture 2




A multidisciplinary field that aims to describe and understand the spatio-temporal structure and dynamics of ecological communities.

It has relatively recently rooted in ecologyas a field, as its entity as field has beenstrongly questioned.

1.1. What is community ecology?

http://www.enviropedia.org.uk

Lawton 1999: ”community ecology is a mess with so muchcontingency that useful generalizations are hard to find”


Lawton 1999: ”community ecology is a mess with so muchcontingency that useful generalizations are hard to find”


The last two decades have experienced a proliferation of unifyingtheory and general conceptual frameworks in community ecology

1.2. What is an ecological community?

Although the term ecological communityhas acquired disparate meanings throughhistory…

The assemblage of at least two potentiallyinteracting species at a given time and location

http://www.enviropedia.org.uk

1.2. What is an ecological community?

Plant community Fungal community Bird community

In typical HMSC analyses we usually work on data on specific taxonomical groups(taxocenes), and often it is unclear how thespecies are ecologically related (speciesassemblage data)

https://www.dreamstime.com/ https://www.dreamstime.com/ https://depositphotos.com/

1.2. What is an ecological community?Can we use the term ”ecological community”?In HMSC we follow the consensual definition by Fauth et al (2016):

A collection of species occurring in the same place and at the same time, thespecies not being necessarily restricted by phylogeny or resource use, and allowing the spatial boundaries to be either natural (e.g. islands) or arbitrary (e.g. study plots).

1.3. What are the prevailing theories in community ecology?

1.3.1. The assembly rules framework

1.3.2. Metacommunity Theory

1.3.3. Vellends theory of ecological communities

1.3. What are the prevailing theories in community ecology?




HMSC


What is an assembly rule?

Diamond (1975) introduced the term ‘assembly rule’ to refer to the restricted species combinations to which competitive interactions can lead.

Fruit doves

Distribution of two fruit dovespecies in New Guinean islands. Split circles are co-occurrencesand dots are co-absences

https://www.naturepl.com/



After Diamond’s work, the meaning of assembly rule was broadened, from competition to any ecological process favouring or disfavouringthe occurrence of a species (Keddy 1992).



After Diamond’s work, the meaning of assembly rule was broadened, from competition to any ecological process favouring or disfavouringthe occurrence of a species (Keddy 1992).

More generally than in Diamonds definition, co-occurrence of species is a product of stochasticity, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive.


Rather than assembly rules, nowadays we talk about assembly processes

species

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environmentalfiltering

biotic filtering

dispersal

The assembly processes can be conceptually viewed as ‘filters’ acting at the scales ranging from the regional species pool to increasingly finer scales until the local community composition isdetermined (Zobel 1997)

phylogeographicassembly rules

ecologicalassembly rules

stochasticity


Phylogeographic assembly rules refer to the historical patterns of

speciation and large-scale migration

species

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biotic filtering

dispersal



stochasticity


Ecological assembly rules refer to smaller-scale dispersal (dispersal assembly rules), the effects of the abiotic environment (environmental filtering), biotic

interactions (biotic filtering) and stochastic processes

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biotic filtering

dispersal



stochasticity


Response traits influence ecological assembly processes (competitive ability, dispersal capability,

resource specialization…)

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stochasticity

1.3.1. How HMSC relates to the assembly rules framework

Species

traits

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filtering𝜷

Biotic filtering(𝜴)

Dispersal(𝜶)

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Stochasticity𝑹𝟐

Metacommunity Theory explains how networks of local communities result from the interplay of stochastic (e.g. demographic stochasticity) and deterministic (e.g. niche differentiation, competition & dispersal rate) processes at differentspatial scales


Leibold and Chase 2017


Metacommunity Theory synthesizes fourperspectives (also called archetypes orparadigms), each arising from different –but not mutually exclusive – conceptualperspectives:

Metacommunity paradigms

a. Neutral paradigm b. Patch dynamics

c. Species sorting d. Mass effects

Habitat patch type 1


Species ASpecies B

Assessing the empirical communities from the metacommunityperspectives is challenging

Habitats are often more continuous than conceptualized in MetacommunityTheory. Local communities lack of discrete boundaries

Sampling units


Leibold and Chase 2017

Variation in species

composition

C. Statistical analysisA. Metacommunity scenarios B. Data collection

D. Linking patterns to processes

a. Neutral paradigm b. Patch dynamics

c. Species sorting d. Mass effects



Species ASpecies B

R2

Variation in habitat quality

INDEX-BASED RESULTS

MODEL-BASED RESULTS

VHAB 𝛽SøR𝛽SIM𝛽NES

RDD

Distancedecay

NEG, POS

Species-to-speciesassociations

VRAND, RUS

Variancepartitioning

Predictivepower


What kind of signature do the metacommunity paradigms leave?

SPECIES SORTING

MASS EFFECTS

NEUTRAL

PATCH DYNAMICS

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HMSC:

Predictive powerthrough cross validation(𝑹𝟐)

The match betweenenvironmentalconditions and speciesoccurrences 𝜷


Vellend proposed that all processes can be synthesized into four “high-level” processes

speciation dispersal drift selection



Creation of new species through

evolutionary processes

Movement of organisms in

space

Stochastic changes in the occurrence and abundance of

species

Processes creating deterministic fitness differences among

individuals of different species



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Lecture 2




Manipulativeobservational

studies

Non-Manipulativeobservational

studies

2. Typical data collected in community ecology

• Lab experiments

• Field experiments

• Field observations

Data collection

Non-manipulative observational are the mostcommon type of data in community ecology.

These data are shaped by the full complexityof assembly processes.

However, because the processes cannot beobserved directly it is difficult to causally linkthe observed patterns to the underlyingprocesses.


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Xcovariates

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Community Environment

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TraitsPhylogeny

Spatio-temporalcontext


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species

By community data we refer to data aboutspecies occurrence or abundance in a set of temporal and/or spatial replicates (samplingunits).

Depending on the objectives of the study and subject organisms, community ecologistsrecord community data in various ways

2. Typical data collected in community ecology –The community data


Direct species observations:

When species are recorded through direct observations

Indirect species observations

When species are recorded through indirect cues

Direct species observations:

For example vascular plants, insects, lichens… are usuallyrecorded by direct observations

Sound recordings for birds and frogs or camera trapping for mammals are also a type of direct observation

Plant surveyInsect survey


Mammal survey

https://en.wikipedia.org

http://www.countrysideinfo.co.uk/hpr_survey_00/methods.htm

Indirect species observations:

Mammals are often recordedusing indirect cues such as tracksand droppings

DNA-based molecularidentification of environmentalsamples is also an indirect wayof recording species

Soil sampling for lattereDNA analysestargetting soil biota(fungi, bacteria, microarthropods)


http://www.naturetracking.com/mammal-tracks/

Mammal tracks

https://www.winfieldunited.com/


Metabarcoding approaches applied to environmental samples (eDNAapproaches) are becoming increasingly used in community ecology.

This is done by amplifying and sequencing barcode gene regions (ITS region for fungi, COI region for animals…).

Species 1Species 2Species 3Species 4

Environmentalsample

DNA extraction PCR amplification Sequencing Taxonomicassignment

Data originating from databases compiling many sources are alsobecoming increasingly used

Global BiodiversityInformation Facility (GBIF)

iNaturalist


Species can be measured in many ways:

- Presence/absence- Abundance (percentage cover, counts

of individuals, biomass)

In plant communities, abundance is oftenmeasured usingpercentage cover orbiomass

In bird communities, abundance is oftenmeasured by counting thenumber of individuals

In fungal communities, it is challenging to quantify theabundance of the speciesbased on fruit bodies and thus presence-absence data is usually recorded


https://en.wikipedia.org/

http://www.countrysideinfo.co.uk/hpr_survey_00/methods.htm

False negatives: When due to toolittle sampling effort not allspecies and individuals arerecorded in the sampling units

False positives: When errors suchas misidentifications introducedata on species/individuals thatare not present

Imperfect detection

Typical in DNA-basedsurveys

Typical in directsurveys


Data originating from databases compiling manysources are spatially biased toward wherepeople live or most accessible places and taxonomically biased toward charismatic species

Biased samplingeffort

By environmental data we refer to data aboutthe environmental conditions in the set of temporal and/or spatial replicates (samplingunits) where the community data has beenrecorded.

The environmental data that are recorded arethose that the ecologists hypothesizes to beimportant for the species/community understudy

Xcovariates

Environment

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2. Typical data collected in community ecology –The environmental data

Environmentalconditions

Experimentaltreatment

Environmental data can be measureddirectly or indirectly.

Small-scale environmental conditions(e.g. microclimate, soil nutrientcontent) are usually measureddirectly

Large-scale environmental conditions(e.g. macroclimate) are oftenmeasured from projected data

Temperature data logger

WorldClim Global Climate projections

2. Typical data collected in community ecology –The environmental data

https://fi.vwr.com/

The spatial and temporal scales are recordedalong with the community data:

Temporal studies:Day/month/year of sampling

Spatial studies:Plot/site identityLatitude and longitude coordinates

19802000

2020

S, Π


2. Typical data collected in community ecology –The spatio-temporal context

When the aim is to understand how species’ traits influence assembly processes, one caninclude species-level traits

The traits that are measured are those thatthe ecologist hypothesizes to influence speciesresponses (called response traits)

Ttraits

spec

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Traits

2. Typical data collected in community ecology –The trait data

Traits can be measured directly in thefield, or indirectly from existing data sources such as databases or publishedliterature.

Bird body-size measurement

Open Traits Network

Leaf area measurement

2. Typical data collected in community ecology –The trait data

https://opentraits.org/https://www.tactivity.in/

https://news.cgtn.com/

When the aim of the study is to understandhow phylogenetic relationships affect species’ responses to the environment, one caninclude phylogenetic data C

species

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Phylogeny

2. Typical data collected in community ecology –The phylogeny data

The phylogeny is not usually measured directly, but compiled from existing data.

When quantitative phylogenetic data is not available for the subject community, taxonomic trees may used as a proxy of phylogeny.

BirdTree: Phylogeny of birds

2. Typical data collected in community ecology –The phylogeny data

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TraitsPhylogeny



HMSC basic input data

HMSC optionalinput data

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TraitsPhylogeny


Lecture 2

Species

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Dispersal(𝜶)

Phylo

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THEORY DATA

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Introduction to community ecology: How does HMSC relate to