Effects of Biological Extinctions across Scales and Trophic Levels

PhD WorkFlow

Motivation

Throughout my PhD project, I aim to understand and predict the consequences of differential extinctions across trophic levels on a global scale. In doing so, I am focusing on drivers of differential extinctions, species-associations, extinction debt, biodiversity changes, shifts in functional communities, as well as ecosystem processes. These are my initial plans which have been set aside in favor of a revised PhD research project with a new set of work packages. My PhD project is a part of the greater BIORATES project.

Description

  1. Co-Occurrences & Species-Interactions. Firstly, I collect(ed) species range estimates from a variety of data sources and aggregate(d) these to global and local co-occurrence matrices at the species-level. Subsequently, I use additional data such as phylogenies and trait expressions of all species included in my analysis to delineate species-interactions and build global as well as local species-dependce networks.
  2. Climate Data & Extinction Risks. My PhD project leverage(s/d) state-of-the art climate reanalysis data which vastly improves on previously utilised legacy data sets of macroecology (see my KrigR project for more information). I use(d) these spatio-temporal data sets to assess local and global risk of extinction for each species contained within my analysis by virtue of safety margins, range shifts/contractions, or IUCN red list status.
  3. Extinction Debt Effects. Using the estimates of species extinctions, I perturb(ed) local and global species-dependence networks by removing vertices of species estimated to go extinct. This generates an extinction cascade (also known as extinction debt) which I analyse(d) on three different levels:
    • Biodiversity – This step look(s/ed) at changes in local species richness and species-dependence network architecture.
    • Functional Spaces – These are/were assessed by quantifying the changes in local functional trait hyperspaces.
    • Ecosystem Function – I am currently unsure how to link these up, but am hoping for a viable link to be establishable with my recent vegetation memory work.

Work Packages

Updated Plans

Work Package 1 - KrigR

  • Products:
    • R Package KrigR + KrigR paper
    • SDM comparison paper
  • Resources:
    • Global and local data bases of species presence
    • ERA5 climate data
    • HWSD DEM product
  • Deadline: 31/08/21

Within this work package, I am identifying the best practices of downscaling state-of-the-art climate data to biologically relevant spatial resolutions.

Work Package 2 - Cross-Scale

  • Products:
    • A set of species-networks based on different input data
    • “Cross-Scale Changes in Association Network Topology” paper
  • Resources:
    • Global and local data bases of species presence:
      • PFTC data
      • sPlot, GFBI
      • GBIF
      • SDM outputs (e.g. IUCN, BirdLife, and BIEN)
    • Global and local data bases of trait expressions:
      • BirdLife
      • Phylacine
      • TRY
      • BIEN
    • Species phylogenies
  • Deadline: 30/07/22

Within this work package, I am investigating the ups and downs of leveraging different data sources of varying quality and coverage for the purpose of establishing species-networks .

Work Package 3 - Biodiversity Simplification

  • Products:
    • Species-vulnerability proxies
    • “Cross-Scale Effects of Biodiversity Simplification/Reduction on Network Topology” paper
  • Resources:
    • Outputs of Work Package 1 & 2
  • Deadline: 30/07/22

Throughout this work package, I am building the synthesis of work packages 1 & 2 by analysing the consequences of simulated extinctions on species-dependence networks given species vulnerability and fine-scale climate projections. This work is carried out within trophic levels (e.g. plants and herbivores separately).

Work Package 4 - Cross-Trophic Effects

  • Products:
    • “Cross-Trophic Effects of Extinction Debt on Network Topology” paper
  • Resources:
    • Outputs of Work Package 1, 2 & 3
  • Deadline: 31/12/22

In this work package, I am investigating the consequences of differential extinctions and extinction debt across trophic levels (e.g. plants and herbivores in one network of species-dependence).

Work Package 5 - Science Dissemination

  • Products: PhD Diary, Presentations, Posters
  • Resources: Outputs of all other Work Packages, This website
  • Deadline: 15/01/23

I have elected to set aside some serious time for science communication throughout my PhD studies. This work package is the catalyst.


Initial Plans

WP 1 - Co-Occurrences

  • Products: Global co-occurence matrix, local species-dependency networks
  • Resources: Global and local data bases of species presence
  • Deadline: 13/11/20

Within this work package, I am establishing a global understanding of species-dependence on one-another from a data-driven standpoint.

WP 2 - Prerequisites

  • Products: Downscaling Method for climate data, measures of species vulnerability (i.e. extinction risk)
  • Resources: Global and local data bases of species presence, ERA5 climate data, HWSD DEM product
  • Deadline: 26/02/21

Within this work package, I am identifying the abiotic drivers of species vulnerability and best practices of downscaling those to biologically relevant spatial resolutions.

WP 3 - Biodiversity

  • Products: Estimate of global change of biodiversity patterns following simulated extinctions
  • Resources: Outputs of Work Package 1 & 2
  • Deadline: 15/05/21

Throughout this work package, I am building the synthesis of work packages 1 & 2 by analysing the consequences of simulated extinctions on species-dependence networks given species vulnerability and fine-scale climate projections.

WP 4 - Function & Demography

  • Products: Estimate of global changes of functional trait space patterns following simulated extinctions as well as changes in demographies of communities.
  • Resources: Outputs of Work Package 1 & 2, Functional trait data and COM(P)ADRE data
  • Deadline: 28/01/22 In this work package, I am investigating the consequences of differential extinctions and extinction debt to local expressions within functional trait spaces and along axes of life history variation.

WP 5 - Ecosystem Functions & Processes

  • Products: Estimate of global changes of ecosystem functioning and processes following simulated extinctions
  • Resources: Outputs of Work Package 1 & 2, Measures of Ecosystem processes/functions
  • Deadline: 14/10/22

This work package is aimed at understanding how extinctions and extinction debt may affect ecosystem services and processes of future biological landscapes.

WP 6 - Science Dissemination

  • Products: PhD Diary, Presentations, Posters
  • Resources: Outputs of all other Work Packages, This website
  • Deadline: 15/01/23

I have elected to set aside some serious time for science communication throughout my PhD studies. This work package is the catalyst.

Erik Kusch
Erik Kusch
PhD Student

In my research, I focus on statistical approaches to understanding complex processes and patterns in biology using a variety of data banks.

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