Philosophical Transactions of the Royal Society B

Philosophical Transactions of the Royal Society B


Philosophical Transactions of the Royal Society B

Phylogeny, extinction and conservation

Organised and edited by:Félix Forest, Keith Crandall, Mark Chase and Daniel Faith

Editor contact details:Felix Forest, [Corresponding Editor]; Keith Crandall, ; Mark Chase, ; Daniel Faith,

The integration of phylogenetic information with metrics of extinction risk such as the IUCN Red List provides powerful tools for the conservation of phylogenetic diversity. This issue offers a detailed overview of the state of play in the field, presents advances and comparative analyses of methodologies and provides case studies that apply these methods to support conservation efforts.

This theme issue of Philosophical Transactions of the Royal Society B* is based on a discussion meeting which was held at The Royal Society in March 2014. More information and speaker lists can be found at

Research includes: A practical guide to application of the IUCN Red List- which ecosystems are under great threat and require urgent conservation action? And how 1 in 5 plant species are threatened with extinction under the Red List criteria.

Please note that both the media summaries and the journal issue itself represent the views of the authors and not the position of the Royal Society.

Please note that these papers are not available on our press site; full papers available on request.

*Please note and reference the full title if possible in print

Introduction: Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency

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by Forest, Félix; Crandall, Keith; Chase, Mark; Faith, Daniel

Ever since the revolutionary ideas put forward by Darwin, evolution has played a fundamental role in our understanding of life. Until recently, however, it had only a relatively modest involvement in helping to address conservation issues. The main goal of the present Themed Issue is to discuss the merits of integrating evolutionary and extinction risk data in conservation planning, identify the main gaps in our knowledge, and present some of the available methods as well as introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science. Contact: Dr Félix Forest, Royal Botanic Gardens,

The Sampled Red List Index for Plants, phase II: ground-truthing specimen-based conservation assessments

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by Brummitt, Neil; Bachman, Steven; Aletrari, Elina; Chadburn, Helen; Griffiths-Lee, Janine; Lutz, Maiko; Moat, Justin; Rivers, Malin; Syfert, Mindy; NicLughadha, Eimear

In 2010 the first report of the IUCN Sampled Red List Index (SRLI) for Plants was published which showed for the first time that one in five plant species is threatened with extinction under Red List criteria. Now, as we reach the half-way point to meeting the Aichi Targets by 2020, we set out our plans for the next phase of the SRLI for Plants to monitor the conservation status of the world's plants. Contact: Dr Neil Brummitt, Natural History Museum,

A practical guide to the application of the IUCN Red List of Ecosystems criteria

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by Rodríguez, Jon Paul; Keith, David; Rodríguez-Clark, Kathryn; Murray, Nicholas; Nicholson, Emily; Regan, Tracey; Miller, Rebecca; Barrow, Edmund; Bland, Lucie; Boe, Kaia; Brooks, Thomas; Oliveira-Miranda, María; Spalding, Mark; Wit, Piet

The IUCN Red List of Ecosystems is a tool to help assist planners and conservationists to identify which ecosystems are under greater threat and may require more urgent conservation action. We review the intended application of the Red List of Ecosystems assessment process, summarize ‘best-practice’ methods for ecosystem assessments and outline approaches to ensure operational rigour of assessments. Contact: Dr Jon Paul Rodríguez, InstitutoVenezolano de InvestigacionesCientificas,

Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

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by Brooks, Thomas; Cuttelod, Annabelle; Faith, Daniel; Garcia-Moreno, Jaime; Langhammer, Penny; Pérez-Espona, Silvia

Numerous approaches have been developed for identifying of important sites for different components of biodiversity. This diversity has yielded many benefits, but also risks confusion. IUCN is therefore attempting to consolidate these approaches into a single standard for identifying key biodiversity areas which “contribute significantly to the global persistence of biodiversity”. This definition requires consideration of biodiversity at genetic and phylogenetic levels, as well as of species and ecosystems. We make three recommendations for how biodiversity below the species level might be incorporated into the key biodiversity areas standard, and one regarding use of such information in subsequent prioritization efforts. Contact: Prof. Thomas Brooks, IUCN,

Losing history: how extinctions prune features from the tree-of-life

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by Davies, Jonathan

Understanding the process of evolution is essential for prioritizing biodiversity conservation. Rapid expansion of the human population has placed increasing pressure on natural systems, and we may soon enter a sixth mass extinction. Extinction results in the loss of plants and animals that provide many valuable services to humanity, such as clean air and water, crop pollination and nutrient cycling. Some species contribute to providing these services more than others because they have unique features important in the functioning of ecosystems, but identifying which species contribute the most requires a better understanding of how such features have evolved. Contact: Dr Jonathan Davies, McGill University,

Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia

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by Toyama, Hironori; Kajisa, Tsuyoshi; Tagane, Shuichiro; Mase, Keiko; Chhang, Phourin; Samreth, Vanna; Ma, Vuthy; Sokh, Heng; Ichihashi, Ryuji; Onoda, Yusuke; Mizoue, Nobuya; Yahara, Tetsukazu

Tropical rain forest harbours the world highest diversity of plant species that evolved through long evolutionary history. Unfortunately, tropical rain forest is being rapidly lost and thus we are losing long history of plant evolution. Here, we demonstrated how long evolutionary history was needed for diversification of 325 plant species found in 32 forest plots of lowland Cambodia by reconstructing their phylogenetic relationship using DNA sequences. Based on this relationship, we showed that logging of tropical lowland forest is reducing phylogenetic diversity both within and between forest plots. Our findings illustrate urgent needs to reduce illegal logging of tropical forest. Contact: Dr Hironori Toyama, Kyushu University,

The future of evolutionary diversity in reef corals

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by Huang, Danwei; Roy, Kaustuv

One-third of the world's reef-building corals are facing heightened extinction risk, but the effects of species loss on evolutionary diversity remain poorly known. We use phylogenetic and geographic data for all living reef corals to predict regional diversity changes resulting from anthropogenic extinctions. Projected loss of evolutionary diversity is relatively low in the most species-rich areas, while many regions with fewer species such as the Caribbean and eastern Pacific are likely to lose greater proportions of evolutionary diversity. Our findings underscore the importance of integrating evolutionary history into conservation planning to safeguard the future of reef corals. Contact: Dr Danwei Huang, National University of Singapore,

Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)

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by Richman, Nadia; Bohm, Monika; Adams, Susan; Alvarez, Fernando; Bergey, Elizabeth; Bunn, John; Burnham, Quinton; Cordeiro, Jay; Coughran, Jason; Crandall, Keith; Dawkins, Kathryn; DiStefano, Robert; Doran, Niall; Edsman, Lennart; Eversole, Arnold; Füreder, Leopold; Furse, James; Gherardi, Francesca; Hamr, Premek; Holdich, David; Horwitz, Pierre; Johnston, Kerrylyn; Jones, Clive; Jones, Julia; Jones, Robert; Jones, Thomas; Kawai, Tadashi; Lawler, Susan; López-Mejía, Marilú; Miller, Rebecca; Pedraza-Lara, Carlos; Reynolds, Julian; Richardson, Alastair; Schultz, Mark; Schuster, Guenter; Sibley, Peter; Souty-Grosset, Catherine; Taylor, Christopher; Thoma, Roger; Walls, Jerry; Walsh, Todd; Collen, Ben

Nearly a third of the world’s crayfish species are threatened with extinction, making them one of the most threatened groups of species to appear on the IUCN Red List of Threatened Species. Results from this study show that crayfish are being threatened by climate change, urban development, pollution, water management, agriculture, invasive species and disease. However, at present only a small fraction of species fall within the boundaries of protected areas. There is a rapid and growing threat from invasive species and climate change which if left unchecked could significantly increase current extinction rates. Contact: Ms Nadia Richman, Institute of Zoology,

The synthetic phylogeny of freshwater crayfish: insights for conservation

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by Owen, Christopher; Bracken-Grissom, Heather; Stern, David; Crandall, Keith

We capitalize on a novel synthesis approach to bring together phylogeny and taxonomy for an overall picture of the diversity of the freshwater crayfish. Using this synthetic phylogeny, we map conservation status and estimate phylogenetic diversity and evolutionary distinctiveness to rank crayfish species for conservation efforts. Those species with the highest priority for conservation efforts are concentrated in Australia, but include predominantly cave species from the United States. Our study demonstrates the power and insights from a synthesis of taxonomy and phylogeny for conservation efforts. Contact: Dr Keith Crandall, George Washington University,

Conserving the functional and phylogenetic trees of life of European tetrapods

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by Thuiller, Wilfried; Maiorano, Luigi; Mazel, Florent; Guilhaumon, François; Ficetola, Francesco; Lavergne, Sébastien; Renaud, Julien; Roquet, Cristina; Mouillot, David

The extent to which the European protected areas cover not only the diversity of vertebrates, but also their evolutionary history and functional diversity, has never been evaluated. In this study, we found that the current system adequately covers the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history. Contact: Dr WilfriedThuiller, Université Grenoble Alpes,

Incorporating evolutionary history into conservation planning in biodiversity hotspots

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by Buerki, Sven; Callmander, Martin; Bachman, Steven; Moat, Justin; Labat, Jean-Noël; Forest, Félix

The fact that extinction is not random and that evolutionary history is lost at a higher rate than species, provide evidence for the benefit of incorporating evolutionary history in conservation. This evidence is even more compelling in biodiversity hotspots, such as Madagascar where less than 10% of the original vegetation remains. In this study, we use the pea family (Leguminosae), an ecologically and economically important group of plants, and a combination of evolutionary and spatial data to assess how biodiversity is distributed in Madagascar. By identifying for the first time for this island a network of zones and dispersal corridors that enable species survival during environmental changes, as well as showcasing the importance of living and extinct animal species dispersing fruits and seeds, we provide crucial information to protect and restore ecosystem services. Contact: Dr Sven Buerki, Royal Botanic Gardens,

Toward a general framework for predicting threat status of data-deficient species from phylogenetic, spatial and environmental information

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byJetz, Walter; Freckleton, Robert

In this study we present an integrative analysis framework to answer these questions for a whole class of vertebrates, mammals, worldwide. Specifically, using remotely-sensed landcover data, species distribution information, body size and phylogenetic information we identify 331 new, hitherto data-deficient mammal species as likely threatened. We find that data-deficient species are much more threatened than assessed species, with potentially 69% of them ‘at-risk’ compared to 29% among nondata-deficient species. Specific taxa (rodents, bats, shrews) and regions (Columbia, Sulawesi, Philippines) hold substantially more threatened species than has been appreciated. More generally, our findings demonstrate the future potential for phylogenies and remotely sensed data, together with information on species distributions, to help identify additional species and regions of conservation concern. Contact: Dr Walter Jetz, Yale University,

Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages

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by Pollock, Laura; Rosauer, Dan; Thornhill, Andrew; Kujala, Heini; Crisp, Michael; Miller, Joseph; McCarthy, Michael

The importance of the tree of life in conservation has been known for decades, but evolutionary history very rarely makes it into real-life conservation. This research enables widespread use of phylogenetic diversity in conservation by providing a method that links a phylogeny and spatial distributions with software that sets conservation priorities. This technique allows us to show how phylogenetic diversity of forest trees in Victoria, Australia, is relevant to current conservation policy. Small land areas translate to large gains in phylogenetic diversity if the protected areas are expanded or potentially large losses under current policy. Contact: Dr Laura Pollock, University of Melbourne,

Ensuring the success of IPBES: between interface, market place and parliament

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byVohland, Katrin; Nadim, Tahani

We analysed success factors of IPBES with regard to different processes, measured along the criteria decided within IPBES itself (credibility, relevance, legitimacy). We concluded that without the backing of large publics the policy-supporting function of IPBES will be limited. Capacity-building but also the empowerment of communities to actively participate in research projects dealing with biodiversity are key processes. Contact: Dr KatrinVohland, Museum fürNaturkunde Berlin,

Global evolutionary isolation measures can capture key local conservation species in Nearctic and Neotropical bird communities

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by Redding, David; Mooers, Arne; Şekercioğlu, Çağan; Collen, Ben

Understanding how to prioritise among the most deserving imperilled species has been a focus of biodiversity science for several decades. Selecting species with long evolutionary history and high likelihood of its loss has been successfully implemented at a global level, but conservation is typically carried out at a different scale, on communities of species. Whether global measures map to a local scale has received little scrutiny. We examine this for a large sample of Neotropical and Nearctic bird communities. We find that prioritizing the most Evolutionarily Distinctive species globally safeguards more than twice the total phylogenetic diversity of local communities, but this does not translate into more local trait diversity, which could also be important for long-term persistence of species. Contact: Dr David Redding, University College London,

The price of conserving avian phylogenetic diversity: a global prioritization approach

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byNunes, Laura; Turvey, Samuel; Rosindell, James

Conservationists are facing the “Noah’s Ark Problem” – conservation has limited funding, making it necessary to prioritise species considered most “important” to protect. We present a new prioritisation approach called ADEPD, which calculates the increase in phylogenetic diversity (a measure of biodiversity incorporating evolutionary history) resulting when conservation efforts reduce species’ threat status. Using bird ADEPD scores and costs associated with conservation projects, we provide a novel cost-benefit analysis for prioritising conservation through return-on-investment. Current spending patterns will only preserve one-quarter of the phylogenetic diversity that optimal spending could with the same budget, highlighting dangers with uninformed spending of limited resources. Contact: Dr James Rosindell, Imperial College London,

Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses

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by Faith, Daniel

The phylogenetic diversity measure, “PD” measures the relative feature diversity of different subsets of taxa from a phylogeny. At this level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the EDGE methods. Contact: Dr Daniel Faith, The Australian Museum,


Please note that both the media summaries and the journal issue itself represent the views of the authors and not the position of the Royal Society.

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