Forecasting biodiversity losses in Wallacea from ecological and evolutionary patterns and processes.

Lead Research Organisation: University of Aberdeen
Department Name: Inst of Biological and Environmental Sci

Abstract

The Wallacea region, lying between the Borneo to the west and Papau New Guinea to the east, is one of the world's biodiversity hotspots, hosting incredibly high levels of biodiversity, much of which is unique to the region. This exceptional level of biodiversity and endemism reflects evolutionary diversification and radiation over millions of years in one of the world's most geologically complex and active regions. The region's exceptional biodiversity, however, is threatened by climate change, direct exploitation and habitat destruction and fragmentation from land use change. Continued habitat loss and fragmentation is expected to precipitate population declines, increase extinction rates, and could also lead to 'reverse speciation' where disturbance pushes recently diverged species together, leading to increased hybridisation, genetic homogenisation, and species' collapse. Already, approximately 1,300 Indonesian species have been listed as at risk of extinction, but the vast majority of the region's biodiversity has not been assessed and we lack basic information on the distribution and diversification of many groups, let alone understanding of what processes drove their diversification, how they will respond to future environmental change, and how to minimize species' extinctions and losses of genetic diversity while balancing future sustainable development needs.

In response to the need for conservation and management strategies to minimize the loss of Wallacea's unique biodiversity under future environmental change and future development scenarios, we will develop ForeWall, a genetically explicit individual-based model of the origin and future of the region's biodiversity. ForeWall will integrate state-of-the-art eco-evolutionary modelling with new and existing ecological and evolutionary data for terrestrial and aquatic taxa including mammals, reptiles, amphibians, freshwater fish, snails, damselflies and soil microbes, to deliver fresh understanding of the processes responsible for the generation, diversification, and persistence of Wallacea's endemic biodiversity. After testing and calibrating ForeWall against empirical data, we will forecast biodiversity dynamics across a suite of taxa under multiple environmental change and economic development scenarios. We will develop a set of alternative plausible biodiversity management/mitigation options to assess the effectiveness of these for preserving ecological and evolutionary patterns and processes across the region, allowing for policy-makers to minimise biodiversity losses during sustainable development. Our project will thus not only provide novel understanding of how geological and evolutionary processes have interacted to generate this biodiversity hotspot, but also provide policy- and decision-makers with tools and evidence to help preserve it.

Planned Impact

Developing management options that can mitigate against the potential loss of Wallacea's incredibly high levels of biodiversity and endemism is vital - not only for preserving the highly unique evolutionary lineages there, but also for protecting the many ecosystem services that biodiversity provides within the region. This project focuses on the co-development of models of the historical, contemporary, and future drivers of Wallacea's unique taxa. The project can result in a number of important impacts and we will put in place mechanisms such that these impacts can be delivered during and after this particular project has ended.

Development need for a new modelling approach: Many organisations and individuals working across a broad range of sectors can benefit from an increased understanding of how best to protect biodiversity in Wallacea. Sectors that can benefit include tourism, especially the rapidly growing ecotourism sector, agriculture and agroforestry (for example, pollination and pest control services are much better delivered by a rich and healthy natural biota), and organisations tasked with conservation management (e.g. National Parks, conservation NGO's and provincial governments). They will all benefit by being able to co-develop and apply the novel spatial planning tool ForeWall that will be produced during this project.

Our soil microbial research has further potential benefits to several industries, including biotechnology companies, interested in the physiology and ecology of microorganisms. For example, this project will contribute significantly to understanding of the spatial distribution of archaeal and bacterial nitrifiers, including recently discovered Comammox organisms, for which metabolism understanding is still at its infancy. Greater understanding of their distribution and associated trials of cultivation may lead on a longer-term basis to the discovery of novel genes and gene products, with potential economic impact for pharmaceutical and biotechnological industries.

Furthermore, our project is designed to facilitate development of the scientific capabilities of Indonesian ecologists and evolutionary biologists in a way that can provide lasting benefits to the academic community itself as well as to a range of stakeholders that can benefit from stronger local expertise in spatial ecology and evolutionary biology, in particular in the application of models to inform policies aimed at balancing the competing needs of different sectors for land use. Specifically, we will provide two training courses to Indonesian participants (both available for up to 20 participants). One will be focused on connectivity and spatial population modelling and will draw on successful previous courses that we have run in Europe, North and South America and in China. The second will focus on the application of phylogenetic analyses.

Impacts outside of Wallacea: While this project focuses on Wallacea, the functionality in ForeWall can have utility in many other regions. Comparing spatial prioritisation of areas for protected status when they are gained using a model such as ForeWall with those delivered using existing methods will be of substantial interest in any region where there has been substantial diversification. As such a wide community of organisations with interests in protecting biodiversity are likely to benefit from the availability of the ForeWall software. As well as a paper presenting ForeWall, we will run workshops introducing the software at major international conferences to potentially include, ESEB, IALE and SCB. IALE and SCB are both particularly good venues for publicising the availability of the software to a mixed audience of both academics and conservation organisations or spatial planners.
 
Description We have developed a new and sophisticated model for predicting the sex ratio of a clutch of eggs that accounts for a broad range of factors. The model has been validated against empirical data and has been used to explain the changes observed in adult sex ratio on Cape Verde.
Exploitation Route It can be used by NGOs to better manage their turtle hatcheries to ensure more balanced sex ratios.
Sectors Education

Environment

 
Title Fauxcurrence 
Description This is an R package for simulating null models of multi-species biogeographic distributions to be used in hypothesis testing for a range of questions. 
Type Of Material Improvements to research infrastructure 
Year Produced 2021 
Provided To Others? Yes  
Impact Groups now starting to make use of it. A Julia version has been developed and published by another group that enhances processing speed - the algorithm is identical to that we developed. 
URL https://rdrr.io/github/ogosborne/fauxcurrence/f/doc/Using-Fauxcurrence.Rmd
 
Title LEMAD 
Description see paper at https://onlinelibrary.wiley.com/doi/full/10.1111/jbi.14489 This is a first method for reconstructing biogeographic histories of clades while accounting for extinct lineages. It is an R package. 
Type Of Material Improvements to research infrastructure 
Year Produced 2022 
Provided To Others? Yes  
Impact These will be coming downstream - collaborations have already started with groups very excited to apply the new method. 
URL https://github.com/leonelhalsina/lemad
 
Title Sulawesi Caridina whole genome sequencing 
Description Whole genome sequencing for 240 individuals of Caridina species from Sulawesi. 
Type Of Material Improvements to research infrastructure 
Year Produced 2022 
Provided To Others? No  
Impact None 
 
Title Sulawesi Cyrtandra whole genome sequencing 
Description Whole genome sequencing for 30 individuals from Sulawesi Cyrtandra species 
Type Of Material Improvements to research infrastructure 
Year Produced 2022 
Provided To Others? No  
Impact none 
 
Description Caridina collaboration - TvR 
Organisation Natural History Museum, Berlin
Country Germany 
Sector Private 
PI Contribution Planned project and generated genomic data for Sulawesi shrimp species
Collaborator Contribution Thomas von Rintelen provided samples for DNA extraction and Sequencing
Impact genomic data for 240 Caridina specimens
Start Year 2021
 
Description Cyrtandra collaboration - HA 
Organisation Royal Botanic Garden Edinburgh (RBGE)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution DNA extraction and sequencing of 30 species of Cyrtandra from Sulawesi
Collaborator Contribution Hanna Atkins provided tissue samples DNA extraction and sequencing of 30 species of Cyrtandra from Sulawesi
Impact Whole genome sequencing for 30 species of cyrtandra from Sulawesi
Start Year 2019
 
Description FOREWALL - Bogor 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Initial workshop for the project to bring together researchers and stakeholders from Indonesia with UK researchers to plan the project, codevelop outputs and exchange knowledge.
Year(s) Of Engagement Activity 2018
 
Description Phylogenetics - Bogor 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 45 Indonesian students, researchers and third sector workers trained in the theory and application of phylogenetic to address ecological and evolutionary questions, and to apply these techniques to conservation.
Year(s) Of Engagement Activity 2023
 
Description Phylogenetics - Manado 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 30 Indonesian students, researchers and third sector workers trained in the theory and application of phylogenetic to address ecological and evolutionary questions, and to apply these techniques to conservation.
Year(s) Of Engagement Activity 2023
 
Description Rangeshifter - BOGOR 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 25 Indonesian students, researchers and third sector workers trained in the theory and application of individual based models to address ecological and evolutionary questions, and to apply these techniques to conservation and land management planning
Year(s) Of Engagement Activity 2018
 
Description Wallacea Consortium - Wrap up 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Consoritum meeting of all Wallacea programme projects for interaction and knowledge exchange between UK and Indonesian researchers, Third sector and policy makers.
Year(s) Of Engagement Activity 2022
 
Description Wallacea consortium - kick off 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Consoritum meeting of all Wallacea programme projects for interaction and knowledge exchange between UK and Indonesian researchers, Third sector and policy makers.
Year(s) Of Engagement Activity 2018