Biology subjects

Gumbs, R.

Publications and source records attributed to Gumbs, R..

14 recordsLinked to original sources

bioRxiv2026

A framework for measuring national trends in the extinction risk of evolutionarily distinct species using the EDGE Index

The biodiversity crisis is threatening evolutionarily distinct species, those that constitute long periods of unique evolutionary history or that are from highly imperilled lineages. The EDGE (Evolutionarily Distinct and Globally Endangered) index was designed to track the changing extinction risks of these species and is listed as an indicator in the Kunming-Montreal Global Biodiversity Framework. Here, we provide a set of guidelines for calculating the EDGE index at the national level and for addressing data uncertainty. We distinguish two approaches for calculating a country-level EDGE index, either generated directly by using national data or from disaggregated global data. Using two national Red Lists, we show the contrasting state of high evolutionarily distinct nesting birds across French territories, and the elevated threat status of high evolutionarily distinct endemic species for South African vertebrates. Using global extinction risk data, we then reveal the deteriorating state of birds, mammals, and amphibians over time, and we highlight the countries with the highest proportions of threatened evolutionarily distinct species. Application of these guidelines should aid countries in monitoring their evolutionarily irreplaceable species, which in turn can help target local conservation actions, while contributing to global efforts to preserve the tree of life.

evolutionary biology↗

bioRxiv2026

Assembling a fully-dated complete tree of life

Time-scaled phylogenetic trees summarising evolutionary relationships are fundamental to many analyses in biology, from diversification rate estimation to conservation prioritisation. The most comprehensive available summary of these relationships, the Open Tree of Life, synthesises information from over two thousand studies into a supertree covering the full range of global biodiversity, but its use in downstream analyses is limited by the lack of divergence times. Previous work has mapped dates from Open Trees database of trees to certain nodes in the supertree, but for the majority of nodes no date is available. While algorithms exist to interpolate missing dates in a tree, we found that their time and memory requirements scaled quadratically with the number of nodes, which made it computationally infeasible to run them on the entire tree. In this work, we describe novel date interpolation algorithms that scale linearly with the number of nodes. These enabled us to produce a distribution of fully-dated trees containing 2.3 million extant described species, greatly expanding the scope of feasible phylogenetic analyses. We illustrate the utility of these trees by computing the most robust estimate yet of the phylogenetic diversity of the complete tree of life, incorporating both topological and temporal uncertainty.

evolutionary biology↗

bioRxiv2025

Phylogenetically-informed crayfish conservation in the face of climate change

Crayfish are an ancient clade of freshwater decapods that play vital and diverse ecological roles in the freshwater systems that they inhabit. One third of assessed crayfish species are threatened with extinction and 87% are highly sensitive to climate change. However, the extent to which the evolutionary history of crayfish is threatened, especially by climate change, remains unclear. To address this, we produced a phylogenetically-informed species prioritisation for the conservation of crayfish and explored the consequences of projected climate change scenarios on crayfish phylogenetic diversity. We used the EDGE2 metric to highlight 70 priority species for conservation. Their combined threatened evolutionary history accounts for 40.7% of the expected phylogenetic diversity loss for all 673 crayfish. Of these priority species, 45.7% are vulnerable to climate change, with the majority (32 species) located in Australia. Under a high warming scenario, individual species that are more evolutionarily distinct are projected to be disproportionately affected. The extinction of climate change vulnerable species could cause the loss of up to 26.3% more phylogenetic diversity than the random expectation, equivalent to 409 million years of evolutionary history. Our results highlight the need to consider climate change effects on phylogenetic diversity to fully understand its impact on biodiversity. If actions were taken to avoid a worst-case warming scenario in favour of an intermediate scenario, we could safeguard 251 million years of unique crayfish evolutionary history.

ecology↗

bioRxiv2025

300 billion years of angiosperm evolution at risk of extinction

Extinction results in not only loss of species, but also loss of the unique evolutionary history that they represent and the irreplaceable features they exhibit. There is broad consensus regarding the necessity to optimise the preservation of the tree of life by including evolutionary information in conservation prioritisation, a notion also endorsed by major policy frameworks1-4. However, evolutionarily-informed prioritisations are lacking for most plants, resulting in a taxonomic imbalance in the evolutionary information incorporated in global biodiversity analyses, which has undermined conservation for decades. Here, we use comprehensive species-level phylogenetic trees, and extinction risk estimates, to generate the first global assessment of angiosperm evolutionary history at risk, and to identify phylogenetically-informed conservation priorities for the worlds flowering plants. We estimate that more than one fifth of angiosperm evolutionary history is at risk of extinction in the short term. Using the Evolutionarily Distinct and Globally Endangered5,6 approach, we identify 9,945 threatened plant species that disproportionately account for total evolutionary history at risk. Species and area prioritisations incorporating evolutionary history are urgently needed to correct imbalances between plants and animals, monitor the effectiveness of conservation efforts, and optimise conservation resource allocation in the face of increasing human pressures on Earths biodiversity.

evolutionary biology↗

bioRxiv2024

Diseases and invasive species have synergistic effects with other anthropogenic threats on the functional and phylogenetic diversity in Testudines and Crocodilia

Understanding how multiple threats interact is crucial for the prioritization of conservation measures. Here, we investigate how interactions between six common threats (climate change, habitat disturbance, global trade, overconsumption, pollution, and emerging diseases/invasive species) affect the functional and phylogenetic diversity of 230 species of Testudines and 21 of Crocodilia. We classify two-way threat interactions into additive, synergistic, and antagonistic according to their effects on functional and phylogenetic diversity. Most threat interactions are antagonistic, the effect of threats jointly is lower than the sum of the effects of threats separately. However, we find that the interaction between emerging diseases or invasive species with other threats has synergistic and additive effects, meaning that the combined effects are greater or equal to the effects of threats separately. Our work can help target conservation strategies and detect key places to address multiple threats when they appear together.

ecology↗

bioRxiv2024

Prioritising Functionally Distinct and Globally Endangered (FuDGE) sharks for conservation action

Robust species-level methods for quantifying ecological differences have yet to be incorporated into conservation strategies. Here, we present a conservation prioritisation approach that integrates species trait data and extinction risk to quantify the contribution of individual species to overall functional diversity. The Functionally Irreplaceable with Risk of Extinction (FIRE) metric directs conservation action to species whose extinction is expected to result in significant losses of functional diversity. We applied our framework to sets of species at the global scale. First we assessed the worlds birds, highlighting congruent and divergent priorities identified by trait-based and phylogenetic approaches. Second, we applied FIRE to the worlds sharks, exploring the impact of imputed traits on prioritisation robustness. For birds and sharks, we show that prioritising by functional irreplaceability is an effective strategy to conserve exploited species. The FIRE metric provides a robust tool to facilitate the incorporation of functional diversity into conservation policy and practice, revealing species that may be overlooked by existing approaches.

ecology↗

bioRxiv2024

Quantifying the IUCN Red List: Using historical assessments to calculate future extinction risk

The IUCN Red List of Threatened Species assigns species to discrete categories based on a common set of criteria to capture relative extinction risk. Some quantitative analyses require a continuous probability of extinction not provided by discrete categories. Furthermore, the criteria may not translate to extinction risk in a universal way across species, because some species attributes are not incorporated into the criteria. Here we calculate extinction risk using Markov Models parameterised with historical IUCN Red List assessment data, and we provide quantitative extinction risk for use in downstream analyses. We find that taxonomy, body size, and habitat specialism interact with extinction risk in ways not fully captured by the existing categories. For example, an Endangered habitat specialist appears equally at risk compared to a Critically Endangered habitat generalist. We hope our findings will support more accurate quantitative biodiversity analyses of species extinctions and declines using Red List data.

ecology↗

bioRxiv2023

Advancing EDGE Zones: spatial priorities for the conservation of tetrapod evolutionary history

The biodiversity crisis is set to prune the Tree of Life in a way that threatens billions of years of evolutionary history. To secure this evolutionary heritage along with the benefits it provides to humanity, there is a need to understand where in space the greatest losses are predicted to occur. We therefore present threatened evolutionary history mapped for all tetrapod groups, globally and within Biodiversity Hotspots, and identify priority regions of Evolutionarily Distinct and Globally Endangered (EDGE) species at both a grid cell and national level. We find that threatened evolutionary history peaks in Cameroon, whilst EDGE species richness peaks in Madagascar. We refined and advanced the 2013 EDGE Zone concept for spatially prioritising phylogenetic diversity using a novel complementarity procedure with uncertainty incorporated for 33,628 tetrapod species. This involved using extinction risk, phylogenetic, and spatial data to iteratively select areas with the highest accumulated threatened evolutionary history driven by unique species compositions. We identify 25 priority EDGE Zones, which are insufficiently protected and disproportionately exposed to high levels of human pressure. Together, the 25 EDGE Zones occupy 0.723% of the worlds surface but harbour one-third of the worlds threatened evolutionary history, half of which is endemic to these grid cells. They also contain part of the distribution of 918 EDGE tetrapod species, representing near one-third of all EDGE species, with 480 being endemic. Our tetrapod EDGE Zones highlight areas of immediate concern for researchers, practitioners, policymakers, and communicators looking to safeguard the Tree of Life.

zoology↗

bioRxiv2022

Information Accumulation and Loss as a Foundation for Sound Phylogenetic Biodiversity Metrics

AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity, and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce EvoHeritage, a generalisation of PD that is founded on the joint processes of accumulation and attrition of features. We argue that whilst PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition. Candidate cover image O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/499419v5_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@1a4b8cforg.highwire.dtl.DTLVardef@16145dborg.highwire.dtl.DTLVardef@1316b1eorg.highwire.dtl.DTLVardef@16fb06b_HPS_FORMAT_FIGEXP M_FIG C_FIG Artistic cover image prepared for this manuscript. The central tree depicts the gain and loss of Evolutionary Heritage (EvoHeritage) along each edge with its many coloured sections. EvoHeritage is proposed as an expansion of the concept of phylogenetic diversity. Around the outside of the tree are species that feature in our two practical applications of the EvoHeritage calculus: mammals identified as living fossils and plants included in our study of community productivity. The cover image was generated by James Rosin-dell following discussions with co-authors. The Caenolestes outline (representing shrew opossums) and Dromiciops outline (monito del monte) used as components of this image are credited to Sarah Werning and provided under a CC BY 3.0 license; both images were recoloured in brown and placed over a shaded circle. All other images used as components are from the public domain. We thank Mina Mincheva for useful feedback on earlier drafts of the cover image.

evolutionary biology↗

bioRxiv2022

EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action

The global biodiversity crisis threatens the natural world and its capacity to provide benefits to humans into the future. The conservation of evolutionary history, captured by the measure phylogenetic diversity (PD), is linked to the maintenance of these benefits and future options. The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to identify species for conservation action that embody large amounts of threatened evolutionary history. In 2017, we convened a workshop to update the EDGE metric to incorporate advances in the field of phylogenetically-informed conservation. Building on that workshop, we devised the metric EDGE2, which we present here. EDGE2 uses a modular, tiered approach to provide priority rankings--and associated measures of uncertainty in both phylogenetic and extinction risk data--for all species in a clade. EDGE2 takes into account the extinction risk of closely-related species to better reflect the contribution a species is expected to make to overall PD in the future. We applied EDGE2 to the worlds mammals to identify an updated list of priority EDGE species and compare the results with the original EDGE approach. Despite similarity in the priority lists produced between EDGE and EDGE2, EDGE2 places greater priority on species with fewer close relatives on the Tree of Life. As we approach a crossroads for global biodiversity policy, EDGE2 exemplifies how academic and applied conservation biologists can collaborate to guide effective priority-setting to conserve the most irreplaceable components of biodiversity upon which humanity depends.

zoology↗

bioRxiv2021

The Post-2020 Global Biodiversity Framework must safeguard the Tree of Life

Following our failure to fully achieve any of the 20 Aichi biodiversity targets, the future of biodiversity rests in the balance. The Convention on Biological Diversitys Post-2020 Global Biodiversity Framework (GBF) presents us with the opportunity to preserve Natures Contributions to People (NCPs) for current and future generations through conserving biodiversity and averting extinction across the Tree of Life. Here we call attention to our need to conserve the Tree of Life to maintain its benefits into the future as a key mechanism for achieving intergenerational equity. We highlight two indicators available for adoption in the post-2020 GBF to monitor our progress towards safeguarding the Tree of Life. The Phylogenetic Diversity indicator, adopted by IPBES, can be used to monitor biodiversitys capacity to maintain NCPs for future generations. The EDGE (Evolutionarily Distinct and Globally Endangered) Index monitors how well we are performing at averting the greatest losses across the Tree of Life by conserving the most distinctive species. By committing to safeguarding the Tree of Life post-2020, we can reduce biodiversity loss to preserve natures contributions to humanity now and into the future.

ecology↗

bioRxiv2020

Poor protection of amphibian evolutionary history reveals opportunities for global protected areas

As habitat loss is a major driver of amphibian population declines, protected areas (PAs) can play a crucial role in amphibian conservation. Documenting how well the global PA network captures the evolutionary history of amphibians can inform conservation prioritisation and action. We conducted a phylogenetic gap analysis to assess the extent to which amphibian phylogenetic diversity (PD) is unprotected by the PA network and compared this to other terrestrial vertebrate groups. 78% of amphibian species and 64% of global amphibian PD remains unprotected, which is higher than corresponding figures for squamates, mammals and birds. Amongst amphibians, salamanders were the least well protected, with 78% of PD unprotected, compared with 64% for caecilians and 63% for frogs. We identify areas that offer the greatest opportunity to capture unprotected amphibian evolutionary history. We could capture an additional 29.4% of amphibian PD, representing 40 billion years of evolutionary history, by protecting an additional 1.9% of global amphibian distributions (1.74% of global land area) and increasing the restrictions in 0.6% of amphibian distributions to match the management objectives of PAs in IUCN categories I or II. Importantly, we found that the spatial distribution of unprotected PD was correlated across all groups, indicating that expanding the PA network to conserve amphibian PD can secure imperilled vertebrate diversity more generally.

evolutionary biology↗

bioRxiv2019

Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts

Phylogenetic Diversity (PD) is increasingly recognised as an important measure that can provide information on evolutionary and functional aspects of biodiversity for conservation planning that are not readily captured by species diversity. Here we develop and analyse two new metrics that combine the effects of PD and human encroachment on species range size -- one metric valuing regions and another enabling species prioritisation. We evaluate these metrics for reptiles, which have been largely neglected in previous studies, and contrast these results with equivalent calculations for all terrestrial vertebrate groups. We find that high human impacted areas unfortunately coincide with the most valuable areas of reptilian diversity, more than expected by chance. We also find that, under our species-level metric, the highest priority reptile species score far above the top mammal and bird species, and they include a disproportionate number of species with insufficient information on potential threats. Such Data Deficient species are, in terms of our metric, comparable to Critically Endangered species and may require urgent conservation attention.

ecology↗

bioRxiv2017

Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities

The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. The EDGE metric, which prioritises species based on their Evolutionary Distinctiveness (ED) and Global Endangerment (GE), relies on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic analyses of large clades are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to impute ED for species missing from a phylogeny whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogeny, the new method provided the closest estimates of their \"true\" score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous imputation methods. Previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogeny. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.

zoology↗