Theory of Biodiversity, Extinction and Habitat Change on Islands and Mainlands

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

Abstract

Biodiversity is declining worldwide at a frightening rate; never before have the issues of conservation been more prominent in society. Humans are changing the natural world, with only a basic understanding of the long-term consequences. I aim to develop and use new ways of understanding how clearing or modifying natural habitats will impact the processes that normally generate and maintain biodiversity. I will focus on two systems: remote groups of islands and tropical rainforests. The rainforest work will be carried out in partnership with project SAFE: 'Stability of Altered Forest Ecosystems'. SAFE has negotiated that, when a large region of rainforest is cleared for an oil palm plantation during 2011, carefully chosen patches of forest will be left untouched within the plantation. This makes SAFE one of the world's largest ecological experiments; it will collect extensive data both before and after 2011. 'Prediction is very difficult, especially about the future.' (Niels Bohr, Physicist.) To predict future biodiversity loss in partly cleared natural habitat, a simple mathematical formula is most commonly used which gives the number of species in the region as a function of area. However, we are also interested in how common or rare the remaining species are and how the spatial arrangement of the rainforest and oil palm plays a role. Furthermore, many rainforest species can live in oil palm so this is not the same as total habitat destruction. To account for these additional factors, I will develop a simulation approach capable of modelling a large area of forest by sampling individuals from the computer-generated forest in much the same way as they would be sampled from a real forest. I will make general predictions about how biodiversity will respond to the habitat modification over time and will compare these to data collected by SAFE. For modelling biodiversity on islands I will face other challenges: the accepted theory for islands close to the mainland is that a natural balance exists between the immigration of species from the mainland and the loss of species through local extinction. This classic theory does not cover more distant islands, where endemic species are expected to evolve. On more distant islands, a more complex balance exists between immigration, extinction and the evolution of new species. Islands are often in groups, so immigration must be considered between every possible pair of islands. I will begin by developing further models for islands and their biodiversity, a particularly interesting area of research that links to both ecology and evolution. These models will follow the progress of immigrants onto the archipelago as they change their abundance and possibly form different species on each island. Later, I will apply this to study the effects on islands of habitat modification and increased immigration from the mainland. Both rainforests and distant archipelagos contribute in important ways to biodiversity and are threatened by similar factors; especially habitat destruction. Islands support many endemic species that exist nowhere else, whilst rainforests are valuable for the shear number of species they support. Similar technical methods can be used for modelling both systems and comparisons can be made between them. I find this topic exciting because it addresses import issues for society. We must be able to make informed decisions about conservation based on theory that can predict the consequences of our actions. Furthermore my project contains significant, yet not insurmountable technical challenges, which will make the very best use of my existing skills and experience. I believe that computer simulations such as the ones I propose will have an increasingly important role in future research into ecology and conservation; I am thrilled at having the chance to play a role in that future.

Publications

10 25 50
 
Title Ecological Neutral Theory: is it Madness or Misunderstood? 
Description A full video of James Rosindell's seminar presentation on 31st October 2013 at the University of York. This is an introduction to ecological neutral theory and its applications. The presentation also includes new research not yet published elsewhere and a demonstration of the OneZoom tree of life explorer 
Type Of Art Film/Video/Animation 
Year Produced 2014 
Impact This video has been watch 150 times. 
URL https://www.youtube.com/watch?v=RlSTT1vux2Y
 
Title The neutral theory of biodiversity and macroevolution 
Description The unification of ecology and evolution represents a great challenge for understanding the natural world. One promising direction that has received a great deal of recent attention is the neutral theory of biodiversity. Neutral theory provides a suite of mechanistic models that encompass speciation over evolutionary timescales as well as ecological processes such as dispersal limitation. These models make a wide variety of predictions; however in practice most studies have been restricted to species abundance distributions and other purely ecological patterns. We will investigate the evolutionary predictions of neutral theory that have either gone unexplored, or appear to contradict neutral theory. These include the lifetimes of species, the shapes of phylogenies and the distributions of endemic species on different islands. We show that whilst the best-known neutral model does not produce empirically realistic predictions of these evolutionary patterns, more advanced neutral models often can. Perhaps the most useful insights emerging from neutral models will be an understanding of when they fail to match empirical observations of ecology and evolution, and the details of which additional factors need to be incorporated to resolve the problems. We conclude that the neutral theory of biodiversity does indeed take a significant step towards integrating ecology into macroevolutionary research. 
Type Of Art Film/Video/Animation 
Year Produced 2011 
Impact This video has been watched over 300 times. 
URL http://vimeo.com/21981986
 
Title Tree of life branches out online 
Description Press release video to accompany the paper by Rosindell and Harmon in PLoS Biology 2012 
Type Of Art Film/Video/Animation 
Year Produced 2012 
Impact This video has been watched over 59,000 times 
URL https://www.youtube.com/watch?v=LZ3n3mV4uVc
 
Description This project has produced a total of 19 peer reviewed scientific publications, including many in leading journals such as Ecology Letters and PLoS Biology. Key findings have focused of the effects of extinction in modified habitats. 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.) 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

3.) 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.

4.) Nunes, L.A., Turvey, S.T. and Rosindell, J. The price of conserving avian phylogenetic diversity: a global prioritization approach. Philosophical Transactions of the Royal Society of London B 370 (1662) (2015). Develops new methods of conservation prioritisation that incorporate costs, extinction risk, and phylogeny. It shows four orders of magnitude difference in the cost effectiveness between different actions. This was an unanticipated outcome of the grant.

5.) Rosindell, J. and Harmon, L. J. OneZoom: A fractal explorer for the tree of life PLoS Biology 10(10) e1001406 (2012) (59 citations). Introduced a new method of big data visualisation based on fractal geometry, and thus cracked the previously unsolved problem of how to visualise large phylogenetic trees. This was an unanticipated outcome of the grant and also produced impact outside the academic community.
Exploitation Route I expect the models, software and concepts produced during this grant may be utilised broadly within the academic community and outside of it.
Sectors Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Environment,Other

URL http://www.onezoom.org
 
Description I published OneZoom, software for visualising phylogenies, in PLoS Biology and on line. OneZoom provides a novel way to explore evolutionary trees with an intuitive zooming interface and appealing imagery. The software has led to a popular public outreach website, use by teachers and conservation projects, features at science festivals, and exhibitions at many public venues. Open source versions of the software have found a wide variety of uses whilst other versions have been licensed commercially. Screenshots from OneZoom feature regularly in the media and are lined up to appear prominently in popular science books. OneZoom is now being applied in new areas with commercial potential including genealogy and government spending visualisation. OneZoom shows environmental science research having many and varied impacts including in unexpected areas apparently unconnected with it. OneZoom is now a registered charity in the UK and the total number of users of the website recently exceeded one million.
Sector Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Other
Impact Types Cultural,Societal,Economic

 
Description Individual Research Fellowship
Amount £488,022 (GBP)
Funding ID NE/L011611/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2015 
End 12/2019
 
Description NERC impact acceleration awards
Amount £26,543 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2014 
End 10/2015
 
Description NERC impact acceleration awards
Amount £38,929 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2013 
End 10/2014
 
Description Collaboration with Luke Harmon 
Organisation University of Idaho
Country United States 
Sector Academic/University 
PI Contribution Further work on neutral theory and it's predictions in phylogenetics.
Collaborator Contribution Co-authorship and advice on a number of scientific publications.
Impact A number of scientific publications.
Start Year 2009
 
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 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 Nikolai Friberg 
Organisation Norwegian Institute for Water Research (NIVA)
Country Norway 
Sector Public 
PI Contribution Paper publishing, workshop organisation, inclusion in grant applications
Collaborator Contribution Field support and planning, data sharing, data analysis, paper publishing, exploration of new field sites
Impact Papers in Global Change Biology (x2), Freshwater Biology (x2), Advances in Ecological Research (x2), and Aquatic Botany, Field site exploration in summer 2013 has formed the basis of a large grant submission to NERC.
Start Year 2008
 
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
 
Description Wyatt Cross 
Organisation Montana State University
Country United States 
Sector Academic/University 
PI Contribution Field support, workshop organisation, paper publication, inclusion in follow-up, grant applications
Collaborator Contribution Field support, data sharing, paper publication
Impact Published papers in Global Change Biology and Advances in Ecological Research
Start Year 2010
 
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 OneZoom registered trademark 
Description The trademark OneZoom has now been registered in the USA and in the UK. It is my intention to grow this into a well known brand for public outreach and education on the subjects of evolution, biodiversity and conservation. Some of the activities around the trademark have been commercial, but the primary goal has always been to acquire funding to further develop the original vision of OneZoom into a project with an even greater impact. 
IP Reference  
Protection Trade Mark
Year Protection Granted 2014
Licensed Yes
Impact Trademark was licensed alongside the associated software - OneZoom Tree of Life Explorer Interactive Kisok Software.
 
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 Dynamic islands simulator 
Description Accompanying the paper "A unified model of species immigration, extinction and abundance on islands" This software is freely available for general use as an appendix to the paper. 
Type Of Technology Software 
Year Produced 2012 
Open Source License? Yes  
Impact The software has been used by other researchers working in this field to assist with their own outputs. 
 
Title OneZoom Tree of Life Explorer 
Description written in html5 and javascript the code for the website www.onezoom.org is open source and freely available 
Type Of Technology Webtool/Application 
Year Produced 2012 
Impact The website has received 600,000 page views from over 200,000 unique users in 196 countries. The related software has been shown in at least 5 public outreach presentations and my scientific conferences. The related software has been used widely in schools and universities for educational purposes. The project has appeared in at least 77 instances of media coverage. The software has been used in at least 12 other software projects including being embedded in various websites. The associated video is the second most watched press release video ever produced by Imperial College London Versions of the software are being used commercially and in varied visualisation applications with a great deal more planned. See http://www.onezoom.org/impact.htm for more details or refer to two impact statements submitted to NERC. Further details can also be seen in an early career impact award application also submitted to NERC in 2014. 
URL http://www.onezoom.org
 
Title OneZoom Tree of Life explorer Android App 
Description An Android app version of the tree of life explorer website www.onezoom.org 
Type Of Technology Software 
Year Produced 2014 
Impact Has only just been published, but so far has been used by 99 devices. 10% of users have graded the software giving it a star rating of 4.7/5 I have not yet advertised the software, but will do after the latest update soon. The software is not open source but is free to download and use. 
URL https://play.google.com/store/apps/details?id=com.onezoom&hl=en_GB
 
Title Spatially explicit neutral phylogeny simulator 
Description SImulation software for a spatially explicit neutral model Outputs: the spatial distribution of all species within a sample region and the phylogenetic tree of all sampled species in newick format Variables: dispersal kernel, speciation mode, speciation rate, speciation duration (if applicable), boundary conditions, survey area Application: Numerous studies are underway with different collaborators to analyse the output of this software. The software will ultimately be released for general use. 
Type Of Technology Software 
Year Produced 2011 
Impact At this time, only I have used the software for producing further research. 
 
Company Name ZoomPast 
Description Big data visualisation company with a focus on human genealogy 
Year Established 2016 
Impact Please see http://www.zoompast.org
Website http://www.zoompast.org
 
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 http://www.onezoom.org/impact.htm tells about impacts of the work that led to the formation of the charity.
Website http://www.onezoom.org
 
Description Coverage for research on New York Times website 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Microscopic Neighbors, Evolving Together





It seems obvious that how different living things in a community or ecological system bump up against one another would affect how they evolve. That would include everything from the mix of fish in a lake to the bacteria, fungi and insects that coexist in rainwater that pools in the roots at the base of a beech tree...

Readers of the website found out about this research
Year(s) Of Engagement Activity 2012
URL http://www.nytimes.com/2012/05/16/science/microscopic-neighbors-evolving-together.html?_r=0
 
Description Hengill Documentary 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Resulted in a documentary on the ecological importance of geothermal areas

This documentary has been used to discourage geothermal energy expansion in Iceland by highlighting the ecological importance of these areas
Year(s) Of Engagement Activity 2012
 
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 http://www.onezoom.org/impact.htm 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, SchoolScience.co.uk
RichardDawkins.net, teachersfirst.com, 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 mail@onezoom.org receives fairly regular fan-mail. A collection of user comments can be seen here http://www.onezoom.org/impact.htm
Year(s) Of Engagement Activity 2012,2013,2015
URL http://www.onezoom.org/impact.htm
 
Description Planet Earth article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Article has received positive feedback in social media
Year(s) Of Engagement Activity 2014
URL http://planetearth.nerc.ac.uk/features/story.aspx?id=1749
 
Description Public engagement at Science Uncovered event at the Natural History Museum, 28th September 2012 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Public learned scientific information about microbial diversity and evolution in the context of digestive health

Public expressed interest and learned new facts
Year(s) Of Engagement Activity 2012
 
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
URL http://www.onezoom.org/impact.htm
 
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
http://www.onezoom.org/impact.htm

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
URL http://www.onezoom.org/impact.htm
 
Description Science Uncovered - Natural History Museum (September 2013) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Schools
Results and Impact Science Uncovered is a widely-advertised and well-attended public outreach event hosted at the Natural History Museum in London, where scientist engage with the public face-to-face basis to discuss their research and its implications in an informal setting. I represented Imperial College London, accompanied by two PhD students, and discussed my group's work, which included the current grant, under the general theme of ecological responses and alterations to energy flux in food webs due to environmental stressors. At our stall we spoke to several hundred visitors throughout the day.

See description above.
Year(s) Of Engagement Activity 2013
 
Description Website highlighting research on the model system in Iceland 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact https://sites.google.com/site/hengillresearch/

Numerous Skype discussions with potential collaborators, and the preparation of a NERC Large Grant bid
Year(s) Of Engagement Activity 2013
URL https://sites.google.com/site/hengillresearch