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2015
Philosophical Transactions of the Royal Society B
Phylogeny, extinction and conservation
http://rstb.royalsocietypublishing.org/content/phylogeny-extinction-and-conservation
Organised and edited by: Félix Forest, Keith Crandall, Mark Chase and Daniel Faith
Editor contact details: Felix Forest, f.forest@kew.org [Corresponding Editor]; Keith Crandall,
kcrandall@gwu.edu; Mark Chase, m.chase@kew.org; Daniel Faith, danfaith9@yahoo.com.au
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 https://royalsociety.org/events/2014/phylogeny-extinction-conservation/.
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
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0002
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, F.Forest@kew.org
The Sampled Red List Index for Plants, phase II: ground-truthing specimen-based
conservation assessments
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0015
by Brummitt, Neil; Bachman, Steven; Aletrari, Elina; Chadburn, Helen; Griffiths-Lee, Janine; Lutz,
Maiko; Moat, Justin; Rivers, Malin; Syfert, Mindy; Nic Lughadha, 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, n.brummitt@nhm.ac.uk
A practical guide to the application of the IUCN Red List of Ecosystems criteria
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0003
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; OliveiraMiranda, 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 ‘bestpractice’ methods for ecosystem assessments and outline approaches to ensure operational rigour of
assessments. Contact: Dr Jon Paul Rodríguez, Instituto Venezolano de Investigaciones Cientificas,
jonpaul@ivic.gob.ve
Why and how might genetic and phylogenetic diversity be reflected in the identification of key
biodiversity areas?
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0019
[OPEN ACCESS]
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,
t.brooks@iucn.org
Losing history: how extinctions prune features from the tree-of-life
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0006
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, j.davies@mcgill.ca
Effects of logging and recruitment on community phylogenetic structure in 32 permanent
forest plots of Kampong Thom, Cambodia
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0008
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, htohyscb@kyushu-u.org
The future of evolutionary diversity in reef corals
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0010
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, huangdanwei@nus.edu.sg
Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0060
[OPEN ACCESS]
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; LópezMejía, 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, nadia.richman@ioz.ac.uk
The synthetic phylogeny of freshwater crayfish: insights for conservation
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0009
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,
kcrandall@gwu.edu
Conserving the functional and phylogenetic trees of life of European tetrapods
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0005
[OPEN ACCESS]
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 Wilfried Thuiller, Université Grenoble Alpes,
wilfried.thuiller@ujf-grenoble.fr
Incorporating evolutionary history into conservation planning in biodiversity hotspots
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0014
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, sven.buerki@gmail.com
Toward a general framework for predicting threat status of data-deficient species from
phylogenetic, spatial and environmental information
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0016
by Jetz, 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, walter.jetz@yale.edu
Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt
lineages
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0007
[OPEN ACECSS]
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,
laurajs@unimelb.edu.au
Ensuring the success of IPBES: between interface, market place and parliament
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0012
by Vohland, 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 Katrin Vohland, Museum für Naturkunde Berlin, Katrin.Vohland@mfnberlin.de
Global evolutionary isolation measures can capture key local conservation species in Nearctic
and Neotropical bird communities
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0013
[OPEN ACCESS]
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, d.redding@ucl.ac.uk
The price of conserving avian phylogenetic diversity: a global prioritization approach
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0004
[OPEN ACCESS]
by Nunes, 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, j.rosindell@imperial.ac.uk
Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and
worst-case losses
URL after publication: http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2014.0011
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, dan.faith@austmus.gov.au
NOTES FOR EDITORS
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.
The Royal Society is a self-governing Fellowship of many of the world’s most distinguished scientists
drawn from all areas of science, engineering, and medicine. The Society’s fundamental purpose,
reflected in its founding Charters of the 1660s, is to recognise, promote, and support excellence in
science and to encourage the development and use of science for the benefit of humanity.
The Society’s strategic priorities are:
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Promoting science and its benefits
Recognising excellence in science
Supporting outstanding science
Providing scientific advice for policy
Fostering international and global cooperation
Education and public engagement
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