NERC-MOST Biodiversity change: integrating taxonomic, phylogenetic and functional diversity
Lead Research Organisation:
University of St Andrews
Department Name: Biology
Abstract
Global warming, environmental change/degradation and human activities have led to an unprecedented threat to the world's biodiversity. How to quantify and estimate biodiversity change - how biodiversity is changing over time - has become one of the most pressing issues in biology, ecology, evolution, environmental science, bioinformatics, and related research fields. Robust and meaningful diversity measures that possess good mathematical/statistical properties and support biological reasoning about diversity are required. To date, most of the effort has been directed towards quantifying taxonomic diversity - i.e. species relative abundance and composition. However, it is now recognized that biodiversity has multiple dimensions and that it is essential to consider phylogenetic and functional diversity as well. Fortunately, remarkable progress in our understanding of phylogenies and the extensive collection of species traits opens the door to innovative approaches to the measurement and assessment of biodiversity change. At the same time, this is a complex challenge; collaboration among ecologists and mathematicians/statisticians is essential to tackle it.
This project will bring together world experts in the assessment of biodiversity, in a new collaboration. Its goal is to develop an integrated mathematical and statistical framework to quantify and estimate changes in taxonomic, phylogenetic and functional diversity, focusing on the BioTIME database. The focus of the work will be ecological assemblages, and how they change through time. Project partners are Sandra Diaz (Argentina), a world leader in quantifying functional diversity, and Anne Chao (leading the MOST component of the work) who is globally renowned for her statistical contributions to the quantification of biodiversity. They will collaborate with the UK (St Andrews) team (Anne Magurran and Maria Dornelas) who have pioneered the quantification of biodiversity change in taxonomic diversity. The new methodology will permit rigorous analysis of diversity changes for alpha, beta and gamma diversities based on all three dimensions of biodiversity (taxonomic, functional, phylogenetic). Access to the BioTIME database (biotime.st-andrews.ac.uk), currently the world's largest repository of assemblage time series, will provide a proof of concept of the methodology. We will also develop appropriate user-friendly, self-interpreting software, complete with online versions, and maintain a website featuring all software and statistical tools developed in this project. By offering a number of short visiting fellowships to postdocs, who will have an opportunity to work on key components of the analyses, we will increase the global reach of the collaboration. A workshop will provide a further opportunity to disseminate findings and secure the future of the collaboration. The project will thus forge a strong partnership between researchers who have not had the opportunity to work together in the past, while providing innovative solutions to an urgent ecological challenge.
This project will bring together world experts in the assessment of biodiversity, in a new collaboration. Its goal is to develop an integrated mathematical and statistical framework to quantify and estimate changes in taxonomic, phylogenetic and functional diversity, focusing on the BioTIME database. The focus of the work will be ecological assemblages, and how they change through time. Project partners are Sandra Diaz (Argentina), a world leader in quantifying functional diversity, and Anne Chao (leading the MOST component of the work) who is globally renowned for her statistical contributions to the quantification of biodiversity. They will collaborate with the UK (St Andrews) team (Anne Magurran and Maria Dornelas) who have pioneered the quantification of biodiversity change in taxonomic diversity. The new methodology will permit rigorous analysis of diversity changes for alpha, beta and gamma diversities based on all three dimensions of biodiversity (taxonomic, functional, phylogenetic). Access to the BioTIME database (biotime.st-andrews.ac.uk), currently the world's largest repository of assemblage time series, will provide a proof of concept of the methodology. We will also develop appropriate user-friendly, self-interpreting software, complete with online versions, and maintain a website featuring all software and statistical tools developed in this project. By offering a number of short visiting fellowships to postdocs, who will have an opportunity to work on key components of the analyses, we will increase the global reach of the collaboration. A workshop will provide a further opportunity to disseminate findings and secure the future of the collaboration. The project will thus forge a strong partnership between researchers who have not had the opportunity to work together in the past, while providing innovative solutions to an urgent ecological challenge.
Planned Impact
Our project sets out to contribute to the important goal of evaluating biodiversity change, by developing new approaches of quantifying how ecological assemblages are changing through time, taking account of the taxonomic, functional and phylogenetic dimensions of diversity. Its potential beneficiaries include scientists and policy makers, conservation managers, senior school students, and interested members of the general public. The IPBES Global Assessment, published 6 May 2019, underlines the timeliness of this challenge.
Anne Chao and her team will develop appropriate user-friendly, self-interpreting software, complete with online versions, and maintain a website featuring all software and statistical tools developed in this project. The BioTIME database, developed by Maria Dornelas and Anne Magurran, and hosted at the University of St Andrews; it is already open access. By linking the database and the software we will increase the potential impact of the work. Social media and University Press Offices will help disseminate these outputs to wider audiences. We can measure the uptake of these resources through download statistics. The project will conclude with a working group that maps out the extended collaboration. This group will be tasked with maximizing the societal impact of the work, as well as establishing future scientific goals. Sandra Diaz is a world leader in sharing information about biodiversity and biodiversity change with policy makers and wider society, and co-chair of the IPBES Global Assessment. We will be able to draw on her skills in developing strategies to disseminate the work to beneficiaries.
Anne Chao and her team will develop appropriate user-friendly, self-interpreting software, complete with online versions, and maintain a website featuring all software and statistical tools developed in this project. The BioTIME database, developed by Maria Dornelas and Anne Magurran, and hosted at the University of St Andrews; it is already open access. By linking the database and the software we will increase the potential impact of the work. Social media and University Press Offices will help disseminate these outputs to wider audiences. We can measure the uptake of these resources through download statistics. The project will conclude with a working group that maps out the extended collaboration. This group will be tasked with maximizing the societal impact of the work, as well as establishing future scientific goals. Sandra Diaz is a world leader in sharing information about biodiversity and biodiversity change with policy makers and wider society, and co-chair of the IPBES Global Assessment. We will be able to draw on her skills in developing strategies to disseminate the work to beneficiaries.
Organisations
- University of St Andrews (Lead Research Organisation)
- National University of Cordoba (Collaboration)
- University of Maine (Collaboration)
- University of Vermont (Collaboration)
- Arthur Rylah Institute for Environmental Research (Collaboration)
- Hessian Agency for Nature Conservation, Environment and Geology (Collaboration)
- National Tsing Hua University (Taiwan) (Collaboration)
- Indian Institute of Science Bangalore (Collaboration)
- National University of Córdoba (Project Partner)
- National Tsing Hua University (Project Partner)
Publications
Chao A
(2023)
Rarefaction and extrapolation with beta diversity under a framework of H ill numbers: The iNEXT . beta3D standardization
in Ecological Monographs
Chao A
(2021)
Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization
in Methods in Ecology and Evolution
| Description | A new method of measuring how biodiversity changes over time has been developed. This approach has substantial statistical advances over prvious methods, and provides results that support insightful ecological interpretations of change. The paper is currently in review in a specialist journal Chao, A., Henderson, P.A., Chiu, C-H, Moyes, F. , Hu, K.-H., Dornelas, M., Magurran, A.E.. Measuring temporal change in alpha diversity: a framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT-3D standardization. Submitted to Methods in Ecology and Evolution |
| Exploitation Route | We believe these methods will have considerable application in environmental management and conservation. The project will continue to develop this proof of concept |
| Sectors | Environment |
| Title | Data supporting - Measuring temporal change in alpha diversity: a framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT-3D standardization |
| Description | Supporting files for the proposed paper - Measuring temporal change in alpha diversity: a framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT-3D standardization |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | http://140.114.36.3/wordpress/software_download/inext-3d/ provides code to allow users to replicate the analyses using these data |
| URL | https://risweb.st-andrews.ac.uk/portal/en/datasets/data-supporting--measuring-temporal-change-in-alp... |
| Title | Measuring temporal change in alpha diversity: a framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT-3D standardization |
| Description | Biodiversity is a multifaceted concept covering different levels of organisation from genes to ecosystems. Biodiversity has at least three dimensions: (i) Taxonomic diversity (TD): a measure that is sensitive to the number and abundances of species. (ii) Phylogenetic diversity (PD): a measure that incorporates not only species abundances but also species evolutionary histories. (iii) Functional diversity (FD): a measure that considers not only species abundances but also species' traits that influence ecosystem functioning among coexisting species. We integrate the three dimensions of diversity under a unified framework of Hill numbers and their generalizations. Our analysis informs a mechanistic interpretation of biodiversity change in the three dimensions of diversity. Accompanying free ware, iNEXT-3D, is also being developed. This work is currently in review |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | N/A - too early, will report next year |
| Title | R code for running new methods of biodiversity assessment generated during this project |
| Description | The code can be found at https://github.com/AnneChao/MS_iNEXT.beta3D . It supports a paper describing these new advances in biodiversity assessment - the paper is in review at Ecological Monographs |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | only just available |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | Arthur Rylah Institute for Environmental Research |
| Country | Australia |
| Sector | Public |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | Hessian Agency for Nature Conservation, Environment and Geology |
| Country | Germany |
| Sector | Public |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | Indian Institute of Science Bangalore |
| Country | India |
| Sector | Academic/University |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | National Tsing Hua University (Taiwan) |
| Country | Taiwan, Province of China |
| Sector | Academic/University |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | National University of Cordoba |
| Country | Argentina |
| Sector | Academic/University |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | University of Maine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |
| Description | Ongoing collaboration with Drs Anne Chao, National Tsing Hua University, Taiwan and Dr Sandra Diaz, Profesora Titular Ecología de Comunidades y Ecosistemas, Universidad Nacional de Cordoba, Argentina |
| Organisation | University of Vermont |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Ongoing collaboration towards developing new, effective methods of quantifying biodiversity change |
| Collaborator Contribution | This is work in progress towards new of methodologies of quantifying biodiversity change, with the partners bringing complementary statistical and ecological skills to the project. To be clear the 540000TWD mentioned above is the funding for the associated MOST grant to Anne Chao |
| Impact | This is work in progress that has inevitably been delayed by the pandemic. New methods have been developed and are in review. These outputs will be reported in subsequent years |
| Start Year | 2020 |