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Phylogeny, extinction risks and conservation

Event

Starts:

March
102014

09:00

Ends:

March
112014

17:00

Location

The Royal Society, London, 6-9 Carlton House Terrace, London, SW1Y 5AG

Overview

Adélie penguins (Pygoscelis adeliae), Antarctica, courtesy of Dr Ben Collen

Scientific discussion meeting organised by Dr Felix Forest, Professor Mark Chase FRS, Professor Keith Crandall and Dr Daniel Faith.

Event details

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. The meeting offered a detailed overview of the state of play in the field, presented advances and comparative analyses of methodologies and provided case studies that apply these methods to support conservation efforts.

Biographies of the organisers and speakers and audio recordings of the presentations are available below.

Enquiries: Contact the events team

Schedule of talks

Session 1: Setting the scene

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IUCN Red List of Ecosystems

Dr Jon Paul Rodriguez, Centro de Ecología, Instituto Venezolano de Investigaciones Científicas, Venezuela

Abstract

There are two fundamental conceptual differences between risk assessment for species and risk assessment for ecosystems: the endpoint of the decline and the definition of the assessment unit. When the last individual of a species dies, the species is unequivocally extinct. The ecosystem analog of species extinction is collapse, but thresholds of collapse are not absolute, and at least in theory collapse may be reversible: as long as all individual components of an ecosystem persist somewhere in the world, it could potentially be reassembled. Assessment units for species red lists rely on the platform provided by taxonomy, but no equivalent hierarchical, nested, widely agreed system for classification of ecosystems exists. Therefore, the burden of defining units for ecosystem risk assessment rests on the assessors and thematic groups of specialists, and requires the provision of relatively detailed information on their characteristic native biota (the primary target of ecosystem risk assessment), distinctive biotic and abiotic features, and precise spatial boundaries. The assessment of risk of collapse begins with definition of an ecosystem process model and quantification of a series of measures of extent (past and present), substrate condition, and state of biotic interactions. By systematically contrasting these measures against a set of criteria, assessors are able to assign categories that reflect increasing levels of risk of collapse.

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

Dr Jonathan Davies, McGill University, Canada

Abstract

Current estimates suggest that we are losing species at rates unprecedented since the mass extinction events recorded in the fossil record. In vertebrates, species traits, such as body size, fecundity, and geographic range are important predictors of vulnerability, and often show a strong phylogenetic signal. Therefore, if a particular species is threatened with extinction it is likely that its close evolutionary relatives are also vulnerable because they share similar traits conferring sensitivity to extinction drivers. In mammals and birds, this non-random pattern of extinction has been argued to elevate the rates of loss of evolutionary history from the vertebrate tree-of-life. In contrast, patterns of species loss in plants are inconsistent with a simple trait-based model of extinction; rather, there is evidence that the most vulnerable species are found in species rich and more rapidly diversifying clades. If this is the case for plants more generally, extinctions might result in little loss of plant evolutionary history. However, loss of evolutionary history, measured in millions of years, might not reflect losses of functional diversity, which is critical for maintaining ecosystem processes. Under a punctuated model of evolution, in which trait differences accrue in bursts at speciation, the number of branches lost is more important than their summed lengths, and the impact of extinctions might be much greater for both plants and vertebrates.

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The IUCN Sampled Red List Index for Plants

Dr Neil Brummitt, Natural History Museum

Abstract

The IUCN Sampled Red List Index (SRLI) is a policy response by biodiversity scientists to the need to measure the status and trends of the world’s diminishing biological diversity. Assessments of plant species for the SRLI project rely predominantly on herbarium specimen data from natural history collections, in the overwhelming absence of accurate population data or reliable distribution maps for the vast majority of plant species. This creates an issue for re-assessing these species in order to measure genuine changes in conservation status and thus re-calculate the SRLI. However, the same specimen data identifies precise localities where threatened species have previously been collected and can be used to target ground-truthing expeditions to collect population data for SRLI plant species. Here we outline a strategy for prioritising ground-truthing efforts in order to apply a wider range of IUCN Red List Criteria to plant assessments for a more robust estimation of the SRLI, and further examine the extent to which the SRLI also captures change in genetic diversity for plant species.

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Why and how might phylogeny and evolutionary processes be reflected in the identification of key biodiversity areas?

Professor Thomas Brooks, International Union for Conservation of Nature, Switzerland

Abstract

In 2004, the ~200 government and government agency members and ~1,000 NGO members of the International Union for Conservation of Nature requested that the union consolidate standards for identification of significant sites for biodiversity. After extensive consultation, this process of consolidation is now nearing completion, for launch at the November 2014 World Parks Congress. The draft umbrella standard builds heavily on existing approaches (e.g., Important Bird Areas, Important Plant Areas, Alliance for Zero Extinction) and their criteria (e.g., for threatened and restricted-range species, biome-restricted assemblages, and congregations), although it proposes revision of the structure and level of thresholds for global significance of sites identified under these criteria. The draft also proposes several additional criteria, for threatened and restricted-range ecosystems, exceptional ecological integrity, and outstanding ecological and evolutionary process. For the latter of these, despite recognition of the potential importance of consideration of phylogeny and evolutionary processes in the identification of significant sites for biodiversity, it has not yet been possible to propose thresholds which could allow such a criterion to become operational. Here, we review both the rationale for why such a criterion is desirable, and the challenges for putting it into practice. We conclude by suggesting priority research towards resolving these challenges, while recognizing properties of the other draft criteria, which may de facto address phylogeny and evolutionary processes in the interim.

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Session 2: Methodologies

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Extinction risk analyses in Southeast Asian Angiosperms

Professor Tetsukazu Yahara, Kyushu University, Japan

Abstract

Tropical Asia and tropical America are known as global centers of species richness of vascular plants and also as areas where forest loss is most rapid. We are conducting a series of field surveys on plant diversity in tropical Asia to determine how rapidly plant species are being lost and where are the centers of plant species richness and threats. From 2011-13, we conducted field surveys in Cambodia (7 locations), Thailand (4), Vietnam (1), Malaysia (1) and Indonesia (6) using forest plots (1 ha<) or standardized transects (100m x 5m). We started our survey from Cambodia because lowland tropical forest still remains but is rapidly being lost while the flora is least known. In Cambodia, Forest Administration established permanent plots in six locations and we collected all species of plot trees. To identify sterile specimens and also to determine Phylogenetic Diversity (PD), we determined DNA sequences of rbcL and matK for all the species. In addition, we examined the flora of Bokor National Park where many endemic species has been known by using a standardized transect method. A total of 325 tree species were recorded with reliable identification for forest plots and more than 700 tree species were recorded in Bokor National Park. Also, we determined how species richness and PD have been declined since 1998 using census data of 1998, 2000, 2004 and 2010. These data are now used for distribution modeling and extinction risk analysis. In transect surveys, we recorded all the vascular plant species within 100m x 5m including trees, shrubs, herbs, and epiphytes. In some locations including Doi Inthanon (Thailand), Bokor (Cambodia), Hon Ba (Vietnam) and Gede/Pangrango (Indonesia), we conducted surveys along altitudinal gradients. Species richness declines with altitude above 1200m. Below 1200m, species richness declines in the lower elevation where climate is dry, or does not decline where climate is wet. The highest species richness was recorded in Borneo and W Sumatra, suggesting a neglected hot spot in the latter. Using those data and also the location records of herbarium specimens, we are conducting extinction risk analysis using range-size vs human impact plots. Human impact is determined as a proportion of deforested area per grid. We assume that species with a narrower range in more deforested area is more threatened. A preliminary analysis for some legume genera showed that species assessed as critically endangered by our method are not listed in IUCN Red List. Our dataset and method are considered to provide more reliable basis for plant Red List in tropical Asia.

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Predicting future vulnerabilities of the reef coral phylogeny

Dr Danwei Huang, University of Iowa & National University of Singapore, USA and Singapore

Abstract

One-third of the world's reef-building corals are facing heightened extinction risk from climate change and local impacts. Previous studies have shown that threats against corals are not distributed randomly on the coral tree of life, and that anthropogenic extinction has the potential to disproportionately reduce phylogenetic diversity on a global scale. How species losses affect evolutionary diversity on a regional scale remains poorly known. In this study, I use phylogenetic metrics in conjunction with geographic distributions of all 842 reef coral species to predict regional diversity changes resulting from anthropogenic extinctions. I will present tree-based approaches to prioritise areas for conservation and also highlight the most vulnerable regions. Interestingly, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle in the Central Indo-Pacific realm, while many regions with fewer species are likely to lose greater proportions of evolutionary diversity due to future extinctions. These findings underscore the importance of integrating phylogenetic measures into conservation planning.

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The synthetic phylogeny of the decapod crustaceans: insights to conservation and extinction

Professor Keith Crandall

Abstract

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analysis.  The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a (THE?) synthetic Tree of Life.  We demonstrate this approach and the insights that come from such a synthetic tree using decapod crustaceans.  After a 5 year effort to estimate phylogenetic relationships, build and revise taxonomies, and integrate phylogenetic work by researchers from around the world, we use these newly developed synthesis tools to estimate a comprehensive phylogeny for the decapod crustaceans, document areas in need of future phylogenetic work, and explore diversity patterns through time and space for the major decapod lineages.  We explicitly map IUCN Red List categories across decapod crustaceans to examine conservation assessment efforts and phylogenetic distribution of species of concern.

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Timetrees and extinction risk in tetrapods

Professor Blair Hedges, Pennsylvania State University, USA

Abstract

Many types of analyses of biodiversity require information on evolutionary history. The two primary components of evolutionary history are the relationships of organisms (phylogeny) and their times of divergence. Together they form a timetree: a phylogenetic tree scaled to time. Methods for constructing timetrees continue to evolve as data sets become larger. The most common approach for constructing a timetree, using a sequence alignment or superalignment, is not practical because of data matrix sparseness. For example, genes appropriate for closely related species are unalignable at higher levels, and those appropriate for higher levels are too conserved for resolving relationships of species. Disproportionate attention to some species, such as model organisms and groups of general interest (e.g., mammals and birds), also results in an uneven distribution of knowledge. Instead, our approach has been to synthesize a timetree of life drawn from global knowledge contained in thousands of published timetrees. The results have illuminated novel patterns and processes in evolution, which we believe will assist biodiversity researchers in understanding and mapping extinction risk and other variables of importance for conservation.

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Session 3: Real life case studies

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Conserving the functional and phylogenetic tree of life in Europe

Dr Wilfried Thuiller, National Center for Scientific Research, France

Abstract

Protected areas are the pivotal tools of biodiversity conservation on Earth. Europe has one of the most extensive protected area networks since the implementation of the Natura 2000 conservation network, in combination with traditional parks and reserves. However, it was never tested whether this network is efficient to protect taxonomic diversity and other facets of biodiversity such as evolutionary history and functional diversity. Using high-resolution distribution and phylogenetic data of all european tetrapods, we assessed whether the existing European protection network is efficient enough to protect not only all the species, but also species with high evolutionary or functional distinctiveness. Additionally, we tested its efficacy in protecting the entire phylogenetic and functional tree of life in Europe, by mapping an estimate of protection achievement on every branch of these two trees. We found that the existing network fails to adequately protect the evolutionary history of birds, mammals and reptiles, while it is relatively successful for amphibians. The most functionally distinct species were better protected than expected under random species’ target achievements. This suggests a better protection of the tetrapod functional tree of life, which could help insuring long-term ecosystem functioning. By using an innovative gap analysis that builds on species distinctiveness and by mapping species’ target achievements onto phylogenetic and functional tree of life, our study pioneers multi-faceted assessments of existing protected area networks.

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Incorporating evolutionary processes into conservation programmes: Madagascar as a case study

Dr Sven Buerki, Royal Botanic Gardens, Kew, UK

Abstract

Conservation programmes in biodiversity hotspots such as Madagascar are generally supported by a framework of species distribution and their associated threats. This framework serves as basis for the identification of areas within a given region that comprise high species richness and/or endemism and that experience environmental pressures. These areas will then be proposed as part of a network of protected areas. Future human population growth and food requirements, together with the effect of climate change, have great impact on biodiversity (e.g. <10% of the primary vegetation remains in Madagascar) and there is an urgency to provide new conservation solutions that fully incorporate evolutionary processes into decision-making. The approach described here has the advantage of going one-step further from the simple description of patterns and providing valuable insights into the evolutionary mechanisms that shaped biodiversity communities through time (e.g. what is the importance of sympatric speciation and dispersals in the establishment of communities?; how can this information be incorporated into the definition of protected areas to allow species to thrive?). In this context, a conservation network would be designed to protect current biodiversity patterns as well as their evolutionary potential, thus ensuring a sustainable future for biodiversity. This study uses the plant family Leguminosae, the third most species rich family in Madagascar (ca. 660 species), as a case study. Leguminosae provide several advantages in the context of this study: i) they are shown to be a good proxy for plant biodiversity worldwide (especially in dry ecosystems); ii) good taxonomical knowledge; iii) one of the most comprehensive distribution datasets of the Madagascan flora (>30,000 collections), iv) large amount of available DNA sequence data. A framework combining species distribution modelling, biogeographical and phylogenetic diversity analyses is proposed to examine the evolutionary history of Leguminosae in Madagascar and discuss these results in light of the current network of protected areas.

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Integrating species distributions, threats, and evolutionary distinctness for global conservation monitoring and prioritization

Professor Walter Jetz, Yale University, USA

Abstract

Integrating phylogenetic information into the conservation prioritization of species and areas may offer an efficient way to steward and maintain phylogenetic diversity and ecosystem function in a rapidly changing world. In my presentation I will explore, for birds, how species-level measures, derived from a complete global phylogeny, are able to identify species and regions of particular value for safeguarding evolutionary information. Prioritizing imperiled species by their evolutionary distinctness and its geographic rarity is a surprisingly effective and spatially economical way to maintain the total evolutionary information. I will discuss how these types of metrics could be integrated with spatiotemporal biodiversity data and monitoring to identify conservation gaps and future priority areas for conserving the tree of life.

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Using phylogenetic diversity to prioritise areas for conservation and evaluate conservation decisions in Australia

Dr Laura Pollock, University of Melbourne, Australia

Abstract

Conservation often focuses on only a few threatened species. A more robust approach is to select species for conservation that represent a wide selection of biological diversity. Phylogenetic diversity is a measure of biological diversity that considers evolutionary relationships. Here, I demonstrate an approach that uses modelled species distributions and phylogenetic diversity to prioritise areas for conservation based on forest species (100 species) in Victoria, Australia. Most (60%) of the woody vegetation in the state has been cleared. On average, just over half (55%) of the spatial distribution of each branch of the phylogeny remains and only 23% are protected in reserves. Following from two recent policy changes, the vast majority of the phylogenetic diversity is found on areas that have recently been open to clearing, and only approximately 10% of the spatial distribution of each branch is located in a conservation reserve protected from development. The remaining protected areas are a suboptimal spatial configuration with some species missing entirely, but the addition of a few small areas into the protected category would greatly improve the diversity outlook. Importantly, the same number of species is retained when prioritizing for branches or species. In other words, we do not lose any species with the phylogenetic approach, but we gain a wider representation of evolutionary history.

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Session 4: Implementation

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Ensuring the success of IPBES

Dr Katrin Vohland, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Research, Germany

Abstract

After years of protracted negotiations the Intergovernmental science-policy Platform on Biodiversity and Ecosystem Services, IPBES, was finally established in 2012. One year on and we have already witnessed two plenary sessions which had mainly been concerned with defining procedures for nominating  persons responsible for specific functions and with determining the work programme for the next years. There are great expectations voiced in relation to IPBES’ fair and sustainable organisational development. In order to be successful, IPBES should be reliable, relevant, and fitted with appropriate powers. Its reliability hinges in considerable part on the transparency of the processes within IPBES and their governance. In addition, science must be free and independent while following high quality standards.  Relevance can be increased by integrating different and different networks and knowledge systems right from the beginning when deciding about assessment topics. Currently, IPBES can be characterised somewhat paradoxically as embodying both, an open and integrative processes and a convenient trading floor for hidden agendas formulated in other political sectors. In any case, without the backing of large publics the policy-supporting function of IPBES might be limited. Capacity-building but also the empowerment of communities to actively participate in research projects dealing with biodiversity are key for furthering a practical and emancipatory understanding of the relationship between political and economic decisions, the state and functioning of biodiversity and ecosystems, and human well-being.

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Integrating extinction probabilities and the PD phylogenetic diversity measure

Dr Daniel Faith, Australian Museum, Australia

Abstract

The phylogenetic diversity measure, PD, illustrates a general strategy for exploring biodiversity at multiple levels of variation. A pattern/process model, defined at one level of variation (among sites, species, etc), allows calculations at some lower level of variation (among species, features, etc). This strategy helps to overcome our inability to directly count all lower-level elements or units. PD uses a phylogenetic/evolutionary process model to link the degree of representation of phylogeny, by a set of species, populations, crop varieties, or other taxa, to their degree of representation of lower-level feature diversity. This feature diversity interpretation under-pins the original rationale for conserving PD – it provides a storehouse of possible benefits for both the taxa and for humans, and it provides evolutionary potential in the face of environmental change. One practical advantage of this inferential approach is illustrated by the PD calculus. A wide range of indices are calculated using the phylogenetic pattern, but are interpretable as if they count-up features. This helps to clarify properties of alternative phylogeny- based measures. All measures based on “evolutionary distinctiveness”, including the popular EDGE program, can awkwardly double-count features, because the methods do not take phylogenetic overlap among taxa into account. The PD framework provides a natural calculus of “expected PD”, integrating information about taxon extinction probabilities. Expected PD calculations provide one way to define phylogenetic “essential biodiversity variables” for the global biodiversity observation program, GEO BON. Applied to localities, expected PD calculations can quantify phylogenetic endemism. They can help prioritise among Key Biodiversity Areas, identifying places that make a significant contribution towards the persistence of threatened PD and/or restricted-range PD. Expected PD is not always a good basis for priority setting. An important modification of expected PD is “phylogenetic risk analysis”, which shifts focus from average expected outcomes to the minimisation of worst case losses. Phylogenetic risk analysis may be helpful in identifying and avoiding phylogenetic tipping points, where deeper branches are at risk of loss.

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Integrating population dynamics and evolutionary history to support conservation

Dr Ben Collen, University College London, UK

Abstract

Understanding change in population level metrics of diversity over time is critical to understanding change in biodiversity. The loss of populations is a prelude to species extinction, and tends to reduce taxonomic, genetic, and functional diversity, so is integrally related to many different elements of biodiversity.  The development of species level metrics integrating evolutionary history and likelihood of loss has abounded over the past two decades.  Whether and how such measures map to a local scale has received less scrutiny so far.  At a local scale, conservation relevant assemblages of species are likely to be made up of relatively few species spread across a large tree.  The consequence is that there are potentially relatively greater amounts of evolutionary history at stake.  We ask to what extent global metrics of evolutionary history are useful for conservation priority setting at the community level.  Specifically, we examine to what extent global metrics capture community level phylogenetic and trait diversity.

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Saving species on the EDGE of Existence: Implementing phylogeny-based conservation from theory to practice

Dr Samuel Turvey, Zoological Society of London, UK

Abstract

The use of evolutionary history in a conservation prioritization setting was first proposed at least two decades ago. Recent years have seen the development of a range of metrics based on measures of phylogenetic diversity combined with threat data that provide quantitative prioritization indices of species requiring urgent conservation attention. We assess the recent history and legacy of the EDGE approach, which combines evolutionary distinctiveness (ED, also known as fair proportion, and which is closely correlated with other phylogeny-based metrics) with IUCN Red List status (“global endangerment” or GE). The EDGE approach has been used to generate global prioritization rankings for mammals and amphibians, and has also inspired more recent approaches such as ADEPD (After Down-listing Expected Phylogenetic Diversity). Evolutionary history still provides only a limited contribution to practical conservation decision-making at a global scale, however, with a continuing focus of conservation resources towards well-studied and “charismatic” species. Although the EDGE approach has prompted new research and attention towards high-ranking species, most of these species still receive little or no conservation effort in terms of increased funding or protection, and resources remain insufficient to prevent species such as the Yangtze River dolphin from becoming globally extinct.

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Phylogeny, extinction risks and conservation The Royal Society, London 6-9 Carlton House Terrace London SW1Y 5AG UK