Biodiversity Theory for Understanding the Effects of Habitat Fragmentation at Multiple Scales

Lead Research Organisation: Imperial College London
Department Name: Life Sciences


Biodiversity, the huge variety of life on earth, is declining with species going extinct at a frightening rate. Consequently, there is a pressing need to better understand biodiversity and how it reacts to the way humans are changing the natural world. The main focus of this project is on fragmentation: the separation of different areas of habitat. When human activities cause fragmentation, for example by separating chunks of rainforest between farms or other altered landscapes, this can have devastating effects on biodiversity. Paradoxically, however, geographic processes, such as the formation of islands and mountain ranges, leave isolated fragments of habitat, but are thought to increase biodiversity by fostering the creation of new species. Reconnecting such naturally isolated landscapes can also be damaging for biodiversity by introducing alien species that compete with the native species. This project will develop a unified set of tools to study both human induced and geographic forms of fragmentation and reconnection.

I will use "neutral models" as a foundation for simulations of biodiversity. Neutral models typically assume a basic set of rules about how organisms interact, but I will develop ways to make them more realistic. For example, by allowing for different types of species to exist in different habitats and allowing some species to evolve slight competitive advantages. Methods I have developed enable these models to be simulated efficiently, even on complex landscapes with many fragments of different shapes and sizes.

I am especially interested in patterns of biodiversity and evolutionary history on islands and I plan to use my models to study evolution on island systems and its response to geological changes. I will then progress to predict the effects of human impacts on islands such as those of global transport networks that cause the artificial movement of species to isolated places. This work is important because being able to understand biodiversity and how it responds to change is the first step towards minimising our impacts on the environment we rely on.

The effects of recent fragmentation events are not all necessarily seen immediately. Environmental changes such as fragmentation leave us with an "extinction debt", a debt of species extinctions that needs to be paid at some point in the future. One aim of the models constructed in this project is to improve methods of predicting extinction debt. I will test these models with data showing the effects of fragmenting a tropical forest by the creation of oil palm plantations.

In addition to my central research work, I will continue to improve my public outreach project at, a novel and popular website where members of the public can explore the tree of life, and see how different species are related through evolution. Ten months after release it has already been frequently used for teaching, as a tool by scientists, and in displays at public venues. OneZoom can place unlimited amounts of information onto one virtual page that is explored intuitively by zooming. I hope to expand and enhance OneZoom to enable more people to discover the beauty of biodiversity and the elegance of evolution.

I find the work in this proposal exciting because it addresses import issues for society. My work will focus on understanding biodiversity and how it responds to change; this is the first step towards making informed decisions about conservation to minimise our impacts on the natural world. Furthermore, my project contains significant technical challenges, which will make the best use of my existing skills in biology, maths and computing. I believe that computer simulations such as the ones I propose in this project will have an increasingly important role in future research into ecology and conservation; I am excited to have the chance to play a role in that future.

Planned Impact

The impact and benefits to society of this research will be realised by reaching out to a range of beneficiaries.

1.) Scientists
The more theoretical advances of my work will benefit other researchers including project partners. The work of these other scientists will in turn be of benefit to a range of "second order beneficiaries". I will make new simulation software available to the wider scientific community and introduce novel and potentially far-reaching concepts such as the nearly neutral theory for ecology.

2) Policy Makers
There are often a number of alternative land use development scenarios available to policy makers and any knowledge provided by scientists on issues such as fragmentation is of value enabling informed decisions to be made. The SAFE project team has excellent links to policy makers in Malaysian Borneo who will benefit from the output of project SAFE to which my work will contribute. More generally, my work on the effects of human-induced habitat fragmentation and reconnection will be of benefit to policy makers, but would need to be properly interpreted and compared against alternative models by conservation biologists. These conservation biologists would be the most suitable people to communicate their findings to policy makers.

3) Members of the public
It is important that the public is educated on subjects such as evolution, fragmentation and conservation science. Tropical rainforests and islands represent ecosystems that easy capture the public imagination. The public will benefit from direct communication via press releases, public presentations of the scientific advancements of this project and visits to science fairs. This will both enhance their knowledge of recent scientific advances and provide entertainment.

My project will further develop the OneZoom website to significantly enhance the user experience and make a greater amount of content accessible to a broader audience. This will enable more people to wonder at the diversity of life on earth and understand the fundamental process of evolution that created it and the human activity that is now threatens it.

4.) Educators
Many educators at schools and universities across the world have written saying how useful they find OneZoom for teaching evolution. I also frequently receive requests for extra functionality and improvements that would significantly enhance its impact as a learning tool. As part of this proposal I will incorporate the most promising of such improvements and increase awareness of the work and its capabilities in collaboration with the National Science Learning Centre.

5.) Musuems and Zoos
OneZoom is a perfect interactive learning tool ripe for deployment in museums, zoos, botanical gardens and other venues. I will make the software customisable to include directions to animals and plants on display and thus provides an evolution centred index for the diversity on display in public education venues. I will collaborate with the Zoological Society of London, which will use my software to communicate phylogenetic based conservation prioritisation to the public and possible supporters of their conservation programs.

6.) Industry
The SAFE project has links with industry and will advise on best practice minimising environmental impacts. This is a further example of a "second order beneficiary". In addition, OneZoom has potential as a visualisation engine for other forms of big data such as industrial process plant monitoring.


10 25 50
Title Extinction debt in 60 seconds 
Description The concept of extinction debt explained with a bottle of water and a screwdriver. 
Type Of Art Film/Video/Animation 
Year Produced 2017 
Impact None yet 
Title GCEE Research Focus - Dr. James Rosindell 
Description A video summary of my research 
Type Of Art Film/Video/Animation 
Year Produced 2016 
Impact Enhanced profile of research work 
Description This project has produced a total of 15 peer reviewed scientific publications, including many in leading journals such as Ecology Letters and Nature Ecology and Evolution. Further work is still being completed and so more is likely to be reported here in the future. I will describe the key findings by highlighting the most important results of key publications arising from the grant.

1.) Thompson, S.E., Chisholm, R.A. and Rosindell, J., Characterising extinction debt following habitat fragmentation using neutral theory. Ecology letters. 22: 2087-2096 (2019). Advances our mechanistic understanding of species loss in spatially complex environments. Specifically, it introduces an analytical solution to the long-term species richness expected in spatially fragmented habitats under the assumptions of a particular class of models known as neutral models. It introduces a new 'effective connectivity' metric, which measures landscape connectivity from the perspective of the group of species under consideration, an important conceptual advance that provided a pathway to the analytical solution. This is conceptually important in the field where there is a lot of debate about the effects of habitat loss and habitat fragmentation. The finding that habitat loss and habitat connectivity is consistent with long standing conservation practice. This work also shows that the more often used species-area relationships will underestimate species losses in the long term.

2.) Hintzen, R.E., Papadopoulou, M., Mounce, R., BanksLeite, C., Holt, R.D., Mills, M., Knight, A., Leroi, A.M.* and Rosindell, J.* Relationship between conservation biology and ecology shown through machine reading of 32,000 articles. Conservation Biology. (2019) DOI: 10.1111/cobi.13435 (*equal contributions). Provides automated analyses of full texts from journals in ecology and conservation at a scale much larger than previously attempted, and reveals a possible rift between the two. This was an unanticipated finding of the grant.

3.) Vila, J.C., Jones, M.L., Patel, M., Bell, T. and Rosindell, J. Uncovering the rules of microbial community invasions. Nature Ecology and Evolution, 3(8) 1162-1171. (2019) The five rules, though individually consistent with numerous experimental and theoretical studies, had not previously been formalised or derived from a single model. We derived them from 'experiments' using the model introduced in my 2015 Ecology Letters paper below.

4.) Chisholm, R.A., Lim, F., Yeoh, Y.S., Seah, W.W., Condit, R. and Rosindell, J. Species-area relationships and biodiversity loss in fragmented landscapes Ecology Letters. 21(6) 804-813. (2018). Provides new analytical methods that place upper and lower bounds on the short-term species loss following any spatial pattern of habitat loss and introduces a novel special function: the 'Preston Function'. This work laid the foundations for Thomspon et al. 2019

5.) Rosindell, J., Harmon, L.J. and Etienne, R.S. Unifying ecology and macroevolution with individual-based theory. Ecology Letters. 18(5): 472-482 (2015). Develops a new, parsimonious, individual-based theory making predictions both about macroevolution and traditional ecology. This gives solutions to both philosophical and practical problems with mainstream ecological 'neutral theory' and supports a much larger movement to combine ecology and evolutionary biology with new theories.
Exploitation Route The main uses are conceptual in our understanding of habitat fragmentation, of the link between ecology and evolution, and of invasive species. The results reported in the impact summary are likely to be very widely used.
Sectors Digital/Communication/Information Technologies (including Software),Education,Environment

Description The OneZoom tree of life explorer has continued to be developed during this grant: it has appeared in museums as permanent features, it has been used by over 1000,000 unique users on the website, it has inspired public outreach presentations and books appearing on the cover of a book, it has yielded a spin off charity registered in the UK. During 2017 we attended numerous science outreach events with the project including a high profile launch of our latest version held at the Linnean Society of London. One further particularly significant impact was the contribution of OneZoom to the One Tree, One Planet project which is a collaborative effort between scientists and a renowned digital artist. One Tree, One Planet has been shown at five venues so far as well as being released as an android app, it encourages individual actions to reduce impacts on biodiversity and has the OneZoom tree explorer engine at its core.
First Year Of Impact 2015
Sector Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Environment,Culture, Heritage, Museums and Collections,Other
Impact Types Cultural,Societal,Economic

Description A Novel Framework for Predicting Emerging Chemical Stressor Impacts in Complex Ecosystems
Amount £1,311,118 (GBP)
Funding ID NE/S000348/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 09/2018 
End 02/2022
Description Research Project Grant
Amount £261,181 (GBP)
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 09/2021
Description Collaboration with Nisha Owen and EDGE of Existence programme 
Organisation Zoological Society of London
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Joint supervision of a PhD student and working together on a workshop titled "Cutting EDGE: science for conservation" which is expected to lead to real world conservation impact and a publication.
Collaborator Contribution Joint supervision of a PhD student and working together on a workshop titled "Cutting EDGE: science for conservation" which is expected to lead to real world conservation impact and a publicatio
Impact None yet, but expected soon.
Start Year 2015
Description Collaboration with Rampal Etienne 
Organisation University of Groningen
Country Netherlands 
Sector Academic/University 
PI Contribution Ideas, software, time
Collaborator Contribution Ideas, time, expertise - in general we have both contributed similarly to the collaboration, but come from different perspectives.
Impact 10 publications - see publications list
Start Year 2006
Description Collaboration with Ryan Chisholm 
Organisation National University of Singapore
Country Singapore 
Sector Academic/University 
PI Contribution Expertise in computer simulations of neutral community models
Collaborator Contribution Expertise in mathematics and applications of neutral community models
Impact We have drafted a paper about habitat fragmentation that will soon be submitted. We co-supervise a joint PhD student who started in October 2015. We have plans for further publications that could be co-authored together.
Start Year 2015
Description Collaboration with Stephen Hubbell 
Organisation University of California, Los Angeles (UCLA)
Country United States 
Sector Academic/University 
PI Contribution Ideas, software, working on joint projects and papers
Collaborator Contribution Expertise in the specific area of study that is of interest.
Impact Three publication have so far come from this collaboration, two in TREE and one in Ecology Letters.
Start Year 2010
Description Collaboration with Thomas Bell 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Supervision of joint students, sharing of ideas, leading on a grant application to support further research.
Collaborator Contribution Supervision of joint students, sharing of ideas
Impact Several students graduated, one grant submitted and one paper in preparation.
Start Year 2012
Description Volker Grimm 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Centre for Environmental Research - UFZ
Country Germany 
Sector Academic/University 
PI Contribution Analysis, writing and support for the submission of a publication
Collaborator Contribution Analysis, writing and support for the submission of a publication
Impact A paper has recently been submitted from this collaboration.
Start Year 2013
Title OneZoom Tree of Life Explorer Interactive Kiosk Software Licensing 
Description This is a fork of the open source OneZoom software, but with enhanced features. The purpose is to provide an interactive multi-touch educational experience themed around the tree of life. Evolution, Common ancestry, Biodiversity and conservation are key themes to the customisable display. 
IP Reference  
Protection Copyrighted (e.g. software)
Year Protection Granted 2013
Licensed Yes
Impact The software as so far been licensed to the British Library for use in their Beautiful Science exhibition. The impact of this was that over 60,000 visitors had the opportunity to learn from the OneZoom display and even benefit from it as a cultural or artistic work as well as a scientific one. Three other venues make use of more primitive versions of the software released under an open source license. The Biodiversity Institute at the University of Wyoming have two permanent OneZoom kiosks and the Natural History Museum in Sydney has a further instance of OneZoom. As of 2016 the software has been made freely available open source and commercial licensing has ceased. Ongoing development has been taken over by a not for profit organisation.
Title ZoomPast genealogy visualisation software 
Description Big data visualisation tools for human genealogy. 
IP Reference  
Protection Copyrighted (e.g. software)
Year Protection Granted 2016
Licensed Yes
Impact Formal set up of a spinout company.
Title ZoomPast genealogy explorer 
Description A genealogy explorer website with built in social network based on the technology and ideas developed for OneZoom 
Type Of Technology Software 
Year Produced 2015 
Impact > 2000 users with signed up accounts and advanced talks with the industry regarding licensing of the software 
Company Name ZoomPast 
Description Big data visualisation company with a focus on human genealogy 
Year Established 2016 
Impact Please see
Company Name OneZoom 
Description The object of the CIO is To advance the education of the public in the subjects of evolution, biodiversity and conservation of the variety of life on earth. In pursuit of this objective, the CIO's planned activities will focus on building and maintaining a scientifically accurate, educational, and visually appealing record of the tree of life that is easily accessible to the public. The CIO has three trustees and expects to fundraise via crowdfunding in order to hire a developer, pay for basic running costs and support three summer placements. 
Year Established 2015 
Impact This is a not for profit organisation (a registered CIO in the UK) the website tells about impacts of the work that led to the formation of the charity.
Description Ascot horticultural society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 30 people attended a presentation about carnivorous plants including a mixture of science exploration and horticulture.
Year(s) Of Engagement Activity 2016
Description Invited speaker at the Ancestor's Tale event in Epping Forest, UK 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A public outreach presentation about evolution. Attendees gave very positive feedback and reported having learned a lot about evolution. Strong interest was indicated regarding an engagement to give similar talks to much larger audiences.
Year(s) Of Engagement Activity 2015
Description Invited speaker at the Ancestor's Tale event in Epping Forest, UK 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A large number of participants attended a walk and a set of presentations focused on evolution.
Year(s) Of Engagement Activity 2016
Description OneZoom Tree of Life Explorer Press release activities 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact The website has been visited by over 200,000 unique visitors since it's release. A number of phases of press releases have led to at least 77 instances of media coverage (see for a full list ). The list includes the following: Science magazine, ITV news, Science Daily, Popular Science, BBC Wildlife Magazine (January 2013), British Journal of General Practitioners, NRC-Handelsblad,,, National Education Association, Veterinary Sciences Tomorrow, European Commission Resarch and Innovation, F1000, Metro News - Canada, PLoS Biologue, CFAX1070 live interview, BBC Radio4 Saturday Review, The Telegraph, The Guardian, Wired, The Lancet, Policy Options (Canada). In addition to this a number of long term and permanent exhibitions have prominently featured OneZoom bringing the total reach of those who have interactively used the software up to 250,000

The software has been used extensively in schools, public exhibitions and special events. This has reached the stage where receives fairly regular fan-mail. A collection of user comments can be seen here
Year(s) Of Engagement Activity 2012,2013,2015
Description Public outreach long term and permanent exhibitions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Four public exhibitions prominently featuring my software, work and outreach tools.

Sydney natural history museum 2015 (permanent feature)
University of Wyoming 2015 (permanent feature)
Beautiful Science at the British Library 20th February 2014 - 26th May 2014.
Science and Aesthetics at MUT 19th April - 1st September 2013
Simon Fraser University 18th March 2013, permanent feature
The River Project, New York August 2014, permanent feature

The main impacts are heightened public understanding and awareness of evolution, biodiversity and conservation issues.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
Description Science Fair demonstration and public interaction 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Attendances at 8 science festivals as an exhibitor
Hundreds of attendees enjoyed interactively learning about evolution, biodiversity and conservation.
Quotes from attendees are available here

Useful feedback for improving my outreach activities.
The impact is direct on the attendees, helping with understanding of and engagement in science.
Year(s) Of Engagement Activity 2013,2014,2015