Publications
60 results found
Smith TP, Clegg T, Ransome E, et al., 2024, High-throughput characterization of bacterial responses to complex mixtures of chemical pollutants., Nat Microbiol
Our understanding of how microbes respond to micropollutants, such as pesticides, is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience multiple pollutants simultaneously. Here we perform a matrix of multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors (antibiotics, herbicides, fungicides and pesticides). We found that bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Increasingly complex chemical mixtures were both more likely to negatively impact bacterial growth in monoculture and more likely to reveal net interactive effects. A mixed co-culture of strains proved more resilient to increasingly complex mixtures and revealed fewer interactions in the growth response. These results show predictability in microbial population responses to chemical stressors and could increase the utility of next-generation eco-toxicological assays.
Gumbs R, Scott O, Bates R, et al., 2024, Global conservation status of the jawed vertebrate Tree of Life, Nature Communications, Vol: 15, ISSN: 2041-1723
Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups—such as testudines, crocodylians, amphibians and chondrichthyans—as conservation priorities from a phylogenetic perspective.
Rosindell J, Manson K, Gumbs R, et al., 2023, Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage., Syst Biol
Phylogenetic 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.
Dimitrov D, Xu X, Su X, et al., 2023, Diversification of flowering plants in space and time., Nat Commun, Vol: 14
The rapid diversification and high species richness of flowering plants is regarded as 'Darwin's second abominable mystery'. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous-Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.
Dunne EM, Thompson SED, Butler RJ, et al., 2023, Mechanistic neutral models show that sampling biases drive the apparent explosion of early tetrapod diversity, Nature Ecology and Evolution, Vol: 7, Pages: 1480-1489, ISSN: 2397-334X
Estimates of deep-time biodiversity typically rely on statistical methods to mitigate the impacts of sampling biases in the fossil record. However, these methods are limited by the spatial and temporal scale of the underlying data. Here we use a spatially explicit mechanistic model, based on neutral theory, to test hypotheses of early tetrapod diversity change during the late Carboniferous and early Permian, critical intervals for the diversification of vertebrate life on land. Our simulations suggest that apparent increases in early tetrapod diversity were not driven by local endemism following the ‘Carboniferous rainforest collapse’. Instead, changes in face-value diversity can be explained by variation in sampling intensity through time. Our results further demonstrate the importance of accounting for sampling biases in analyses of the fossil record and highlight the vast potential of mechanistic models, including neutral models, for testing hypotheses in palaeobiology.
Rosindell J, 2023, Indicators to monitor the status of the Tree of Life, Conservation Biology, ISSN: 0888-8892
Fattorini R, Egan PA, Rosindell J, et al., 2023, Grayanotoxin I variation across tissues and species of Rhododendron suggests pollinator-herbivore defence trade-offs, Phytochemistry: the international journal of plant chemistry, plant biochemistry and molecular biology, Vol: 212, Pages: 1-7, ISSN: 0031-9422
Grayanotoxin I (GTX I) is a major toxin in leaves of Rhododendron species, where it provides a defence against insect and vertebrate herbivores. Surprisingly, it is also present in R. ponticum nectar, and this can hold important implications for plant-pollinator mutualisms. However, knowledge of GTX I distributions across the genus Rhododendron and in different plant materials is currently limited, despite the important ecological function of this toxin. Here we characterise GTX I expression in the leaves, petals, and nectar of seven Rhododendron species. Our results indicated interspecific variation in GTX I concentration across all species. GTX I concentrations were consistently higher in leaves compared to petals and nectar. Our findings provide preliminary evidence for phenotypic correlation between GTX I concentrations in defensive tissues (leaves and petals) and floral rewards (nectar), suggesting that Rhododendron species may commonly experience functional trade-offs between herbivore defence and pollinator attraction.
Gumbs R, Gray C, Böhm M, et al., 2023, The EDGE2 protocol: advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action, PLoS Biology, Vol: 21, Pages: 1-22, ISSN: 1544-9173
The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an “EDGE2” protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world’s mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity.
Fernandes LD, Hintzen RE, Thompson SED, et al., 2022, Species Richness and Speciation Rates for all Terrestrial Animals Emerge from a Synthesis of Ecological Theories
<jats:title>A<jats:sc>bstract</jats:sc></jats:title><jats:p>The total number of species on earth and the rate at which new species are created are fundamental questions for ecology, evolution and conservation. These questions have typically been approached separately, despite their obvious interconnection. In this manuscript we approach both questions in conjunction, for all terrestrial animals, which enables a more holistic integration and generates novel emergent predictions. To do this, we combine two previously unconnected bodies of theory: general ecosystem modelling and individual based ecological neutral theory. General ecosystem models provide us with estimated numbers of individual organisms, separated by functional group and body size. Neutral theory, applied within a guild of functionally similar individuals, connects species richness, speciation rate and number of individual organisms. In combination, for terrestrial endotherms where species numbers are known, they provide us with estimates for speciation rates as a function of body size and diet class. Extrapolating the same rates to guilds of ectotherms enables us to estimate the species richness of those groups, including species yet to be described. We find that speciation rates per species per million years decrease with increasing body size. Rates are also higher for carnivores compared to omnivores or herbivores of the same body size. Our estimate for the total number of terrestrial species of animals is in the range 1.03 − 2.92 million species, a value consistent with estimates from previous studies, despite having used a fundamentally new approach. Perhaps what is most remarkable about these results is that they have been obtained using only limited data from larger endotherms and their speciation rates, with the rest of the predictive process being based on mechanistic theory. This work illustrates the potential of a new approach to classic eco-evolutionary q
Rosindell J, Manson K, Gumbs R, et al., 2022, Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage
<jats:title>A<jats:sc>bstract</jats:sc></jats:title><jats:p>Phylogenetic 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.</jats:p><jats:sec><jats:title>Candidate cover image</jats:title><jats:fig
Barker J, Davies J, Goralczyk M, et al., 2022, The distribution, ecology and predicted habitat use of the Critically Endangered angelshark (Squatina squatina) in coastal waters of Wales and the central Irish Sea, Journal of Fish Biology, Vol: 101, Pages: 640-658, ISSN: 0022-1112
The angelshark (Squatina squatina) has the northernmost range of any angel shark species, but there is limited information on its distribution, habitat use and ecology at higher latitudes. To address this, Angel Shark Project: Wales gathered 2231 S. squatina records and 142 anecdotal resources from fishers, coastal communities and archives. These spanned the coastal waters of Wales and the central Irish Sea and were dated from 1812 to 2020, with 97.62% of records within 11.1 km (6 nm) of the coast. Commercial, recreational and charter boat fishers provided the majority of S. squatina records (97.18%), with significantly more sightings from three decades (1970s, 1980s and 1990s) and in the months of September, June, August and July (in descending order). The coastal area between Bardsey Island and Strumble Head had the most S. squatina records (n = 1279), with notable concentrations also found in Carmarthen Bay, Conwy Bay and the Outer Severn Estuary. Species distribution models (SDM) identified four environmental variables that had significant influence on S. squatina distribution, depth, chlorophyll-a concentration, sea surface temperature (SST) and salinity, and these varied between the quarters (Q) of the year. SDM model outputs predicted a larger congruous area of suitable habitat in Q3 (3176 km2) compared to Q2 (2051 km2), with suitability along the three glacial moraines (Sarn Badrig, Sarn-y-Bwch and Sarn Cynfelyn) strongly presented. Comparison of modelled environmental variables at the location of S. squatina records for each Q identified reductions in depth and salinity, and increases in chlorophyll-a and SST when comparing Q2 or Q3 with Q1 or Q4. This shift may suggest S. squatina are making seasonal movements to shallow coastal waters in Q2 and Q3. This is supported by 23 anecdotal resources and may be driven by reproductive behaviour, as there were 85 records of S. squatina individuals ≤60 cm in the dataset, inferred as recently b
Wong Y, Rosindell J, 2022, Dynamic visualisation of million-tip trees: the OneZoom project, Methods in Ecology and Evolution, Vol: 13, Pages: 303-313, ISSN: 2041-210X
1. The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.2. Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.3. The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.4. The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species. 5. The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.6. After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.
Woodward G, Morris O, Barquin J, et al., 2021, Using food webs and metabolic theory to monitor, model, and manage Atlantic salmon - a keystone species under threat, Frontiers in Ecology and Evolution, Vol: 9, ISSN: 2296-701X
Populations of Atlantic salmon are crashing across most of its natural range: understanding the underlying causes and predicting these collapses in time to intervene effectively are urgent ecological and socioeconomic priorities. Current management techniques rely on phenomenological analyses of demographic population time-series and thus lack a mechanistic understanding of how and why populations may be declining. New multidisciplinary approaches are thus needed to capitalize on the long-term, large-scale population data that are currently scattered across various repositories in multiple countries, as well as marshaling additional data to understand the constraints on the life cycle and how salmon operate within the wider food web. Here, we explore how we might combine data and theory to develop the mechanistic models that we need to predict and manage responses to future change. Although we focus on Atlantic salmon—given the huge data resources that already exist for this species—the general principles developed here could be applied and extended to many other species and ecosystems.
Overcast I, Ruffley M, Rosindell J, et al., 2021, A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities, Molecular Ecology Resources, Vol: 21, Pages: 2782-2800, ISSN: 1471-8278
Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community-scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multidimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine MESS with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales.
Tao R, Sack L, Rosindell J, 2021, Biogeographic drivers of evolutionary radiations, Frontiers in Ecology and Evolution, Vol: 9, Pages: 1-14, ISSN: 2296-701X
Some lineages radiate spectacularly when colonising a region, but others do not. Large radiations are often attributed to species’adaptation into niches, but sometimes instead to other drivers, such as biogeography. Here we aim to disentangle the factorsdetermining radiation size, by modelling simplified scenarios without the complexity of explicit niches. We build a spatiallystructured neutral model free from niches and incorporating a form of protracted speciation that accounts for gene flow betweenpopulations. We characterise the behaviour of the model for a range of different networks of connectivity between patches. Wefind that a wide range of radiation sizes are possible depending on the combination of geographic isolation and species' dispersalability. For example, when considering isolated archipelagos, low rates of dispersal from the mainland result in decreasedcompetition and thus increased radiation size. Dispersal between habitat patches also has an important effect. At extremely lowdispersal rates, each habitat patch has its own endemic species, intermediate dispersal rates foster larger radiations. Asdispersal rates increase further, a critical point is reached at which identical lineages can vary greatly in radiation size due torare and stochastic dispersal events. At the critical point, some lineages remain a single species for a long time, whilst otherswith identical characteristics produce the largest radiations of all. The mechanism for this is a ‘radiation cascade’ in whichspeciation leads to reduced numbers of individuals per species, and thus reduced gene flow between conspecifics in isolatedpatches, leading to yet more speciation. Once a radiation cascade begins, it continues rapidly until it is arrested by a newequilibrium between speciation and extinction. We speculate that such cascades may occur more generally and are not onlypresent in neutral models. This may help to explain rapid radiation, and the extreme radiation si
Leroi AM, Lambert B, Rosindell J, et al., 2021, Neutral Theory is a tool that should be wielded with care, NATURE HUMAN BEHAVIOUR, Vol: 5, Pages: 809-809, ISSN: 2397-3374
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Luiselli J, Overcast I, Rominger A, et al., 2021, Detecting the ecological footprint of selection
<jats:title>Abstract</jats:title><jats:p>The structure of communities is influenced by many ecological and evolutionary processes, but the way this manifests in classic biodiversity patterns often remains unclear. Here, we aim to distinguish the ecological footprint of selection – through competition or environmental filtering – from that of neutral processes that are invariant to species identity. We build on existing Massive Eco-evolutionary Synthesis Simulations (MESS), which uses information from three biodiversity axes – species abundances, genetic diversity, and trait variation – to distinguish between mechanistic processes. In order to correctly detect and characterise competition, we add a new and more realistic form of competition that explicitly compares the traits of each pair of individuals. Our results are qualitatively different to those of previous work in which competition is based on the distance of each individual’s trait to the community mean. We find that our new form of competition is easier to identify in empirical data compared to the alternatives. This is especially true when trait data are available and used in the inference procedure. Our findings hint that signatures in empirical data previously attributed to neutrality may in fact be the result of pairwise-acting selective forces. We conclude that gathering more different types of data, together with more advanced mechanistic models and inference as done here, could be the key to unravelling the mechanisms of community assembly.</jats:p>
Rizos G, Lawson J, Han Z, et al., 2021, Multi-Attentive Detection of the Spider Monkey Whinny in the (Actual) Wild, Interspeech Conference, Publisher: ISCA-INT SPEECH COMMUNICATION ASSOC, Pages: 471-475, ISSN: 2308-457X
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Thompson SED, Chisholm RA, Rosindell J, 2020, pycoalescence and rcoalescence : packages for simulating spatially explicit neutral models of biodiversity, Methods in Ecology and Evolution, Vol: 11, Pages: 1237-1246, ISSN: 2041-210X
Neutral theory proposes that some macroscopic biodiversity patterns can be explained in terms of drift, speciation and immigration, without invoking niches. There are many different varieties of neutral model, all assuming that the fitness of an individual is unrelated to its species identity. Variants that are spatially explicit provide a means for making quantitative predictions about spatial biodiversity patterns.We present software packages that make spatially explicit neutral simulations straightforward and efficient. The packages allow the user to customize both dispersal and landscape structure in a wide variety of ways. We provide a Python package pycoalescence and a functionally equivalent R package rcoalescence. In both packages, the core routines are written in C++ and make use of coalescence methods to optimize performance.We explain the technical details of the packages and give examples for their application, with a particular focus on two scenarios of ecological and evolutionary interest: a landscape with habitat fragmentation, and an archipelago of islands.Spatially explicit neutral models represent an important tool in ecology for understanding the processes of biodiversity generation and predicting outcomes at large scales. The effort required to implement these complex spatially explicit simulations efficiently has thus far been a barrier to entry. Our packages increase the accessibility of these models and encourage further investigation of the primary mechanisms underpinning biodiversity.
Leroi AM, Ben L, Rosindell J, et al., 2020, Neutral syndrome, Nature Human Behaviour, Vol: 4, Pages: 780-790, ISSN: 2397-3374
Neutral models of evolution assume the absence of natural selection. Formerly confined to ecology and evolutionary biology, neutral models are spreading. In recent years they’ve been applied to explaining the diversity of baby names, scientific citations, cryptocurrencies, pot decorations, literary lexica, tumour variants and much more besides. Here, we survey important neutral models and highlight their similarities. We investigate the most widely used tests of neutrality, show that they are weak and suggest more powerful methods. We conclude by discussing the role of neutral models in the explanation of diversity. We suggest that the ability of neutral models to fit low-information distributions should not be taken as evidence for the absence of selection. Nevertheless, many studies, in increasingly diverse fields, make just such claims. We call this tendency ‘neutral syndrome’.
Thompson SED, Chisholm RA, Rosindell J, 2020, Example code for pycoalescence from: pycoalescence and rcoalescence: packages for simulating spatially explicit neutral models of biodiversity
Release of pycoalescence examples to accompany publication.Using Zenodo for code archival.
McGill BJ, Chase JM, Hortal J, et al., 2020, Unifying macroecology and macroevolution to answer fundamental questions about biodiversity (vol 28, pg 1925, 2019), Global Ecology and Biogeography, Vol: 29, Pages: 1095-1095, ISSN: 1466-822X
Correction to Unifying macroecology and macroevolution to answer fundamental questions about biodiversityhttps://onlinelibrary.wiley.com/doi/10.1111/geb.13020
Hintzen RE, Papadopoulou M, Mounce R, et al., 2020, Relationship between conservation biology and ecology shown through machine reading of 32,000 articles, Conservation Biology, Vol: 34, Pages: 721-732, ISSN: 0888-8892
Conservation biology was founded on the idea that efforts to save nature depend on a scientific understanding of how it works. It sought to apply ecological principles to conservation problems. We investigated whether the relationship between these fields has changed over time through machine reading the full texts of 32,000 research articles published in 16 ecology and conservation biology journals. We examined changes in research topics in both fields and how the fields have evolved from 2000 to 2014. As conservation biology matured, its focus shifted from ecology to social and political aspects of conservation. The 2 fields diverged and now occupy distinct niches in modern science. We hypothesize this pattern resulted from increasing recognition that social, economic, and political factors are critical for successful conservation and possibly from rising skepticism about the relevance of contemporary ecological theory to practical conservation. Article Impact statement: Quantitative literature evaluation reveals that the research topics of ecology and conservation biology are drawing apart. This article is protected by copyright. All rights reserved.
Gumbs R, Gray C, Böhm M, et al., 2020, Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts, Nature Communications, Vol: 11, ISSN: 2041-1723
Phylogenetic diversity measures are increasingly used in conservation planning to represent aspects of biodiversity beyond that captured by species richness. Here we develop two new metrics that combine phylogenetic diversity and the extent of human pressure across the spatial distribution of species — one metric valuing regions and another prioritising species. 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 regions under high human pressure coincide with the most irreplaceable areas of reptilian diversity, and more than expected by chance. The highest priority reptile species score far above the top mammal and bird species, and reptiles include a disproportionate number of species with insufficient extinction risk data. Data Deficient species are, in terms of our species-level metric, comparable to Critically Endangered species and therefore may require urgent conservation attention.
Murphy B, Forest F, Barraclough T, et al., 2020, A phylogenomic analysis of Nepenthes (Nepenthaceae)., Molecular Phylogenetics and Evolution, Vol: 144, ISSN: 1055-7903
Nepenthaceae is one of the largest carnivorous plant families and features ecological and morphological adaptations indicating an impressive adaptive radiation. However, investigation of evolutionary and taxonomic questions is hindered by poor phylogenetic understanding, with previous molecular studies based on limited loci and taxa. We use high-throughput sequencing with a target-capture methodology based on a 353-loci, probe set to recover sequences for 197 samples, representing 151 described or putative Nepenthes species. Phylogenetic analyses were performed using supermatrix and maximum quartet species tree approaches. Our analyses confirm five Western outlier taxa, followed by N. danseri, as successively sister to the remainder of the group. We also find mostly consistent recovery of two major Southeast Asian clades. The first contains common or widespread lowland species plus a Wallacean-New Guinean clade. Within the second clade, sects. Insignes and Tentaculatae are well supported, while geographically defined clades representing Sumatra, Indochina, Peninsular Malaysia, Palawan, Mindanao and Borneo are also consistently recovered. However, we find considerable conflicting signal at the site and locus level, and often unstable backbone relationships. A handful of Bornean taxa are inconsistently placed and require further investigation. We make further suggestions for a modified infra-generic classification of genus Nepenthes.
Holt RD, Gravel D, Stier A, et al., 2020, On the Interface of Food Webs and Spatial Ecology: The Trophic Dimension of Species-Area Relationships, SPECIES-AREA RELATIONSHIP, Editors: Matthews, Triantis, Whittaker, Publisher: CAMBRIDGE UNIV PRESS, Pages: 289-318, ISBN: 978-1-108-70187-7
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Rosindell J, Chisholm RA, 2020, The Species-Area Relationships of Ecological Neutral Theory, SPECIES-AREA RELATIONSHIP, Editors: Matthews, Triantis, Whittaker, Publisher: CAMBRIDGE UNIV PRESS, Pages: 259-288, ISBN: 978-1-108-70187-7
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Thompson S, Chisholm RA, Rosindell J, 2019, Characterizing extinction debt following habitat fragmentation using neutral theory, Ecology Letters, Vol: 22, Pages: 2087-2096, ISSN: 1461-023X
Habitat loss leads to species extinctions, both immediately and over the long-term as “extinction debt” is repaid. The same quantity of habitat can be lost in different spatial patterns with varying habitat fragmentation. How this translates to species loss remains an open problem requiring an understanding of the interplay between community dynamics and habitat structure across temporal and spatial scales. Here we develop formulas that characterize extinction debt in a spatial neutral model after habitat loss and fragmentation. Central to our formulas are two new metrics, which depend on properties of the taxa and landscape: “effective area”, measuring the remaining number of individuals; and “effective connectivity”, measuring individuals’ ability to disperse through fragmented habitat. This formalizes the conventional wisdom that habitat area and habitat connectivity are the two critical requirements for long term preservation of biodiversity. Our approach suggests that mechanistic fragmentation metrics help resolve debates about fragmentation and species loss.
McGill BJ, Chase JM, Hortal J, et al., 2019, Unifying macroecology and macroevolution to answer fundamental questions about biodiversity, Global Ecology and Biogeography, Vol: 28, Pages: 1925-1936, ISSN: 1466-822X
The study of biodiversity started as a single unified field that spanned both ecology and evolution and both macro and micro phenomena. But over the 20th century, major trends drove ecology and evolution apart and pushed an emphasis towards the micro perspective in both disciplines. Macroecology and macroevolution re‐emerged as self‐consciously distinct fields in the 1970s and 1980s, but they remain largely separated from each other. Here, we argue that despite the challenges, it is worth working to combine macroecology and macroevolution. We present 25 fundamental questions about biodiversity that are answerable only with a mixture of the views and tools of both macroecology and macroevolution.
Bongalov B, Burslem DFRP, Jucker T, et al., 2019, Reconciling the contribution of environmental and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy, Ecology Letters, Vol: 22, Pages: 1608-1619, ISSN: 1461-023X
Both niche and stochastic dispersal processes structure the extraordinary diversity of tropical plants, but determining their relative contributions has proven challenging. We address this question by using airborne imaging spectroscopy to estimate canopy β-diversity for an extensive region of a Bornean rainforest and challenge these data with models incorporating niches and dispersal. We show that remotely-sensed and field-derived estimates of pairwise dissimilarity in community composition are closely matched, proving the applicability of imaging spectroscopy to provide β-diversity data for entire landscapes of over 1000 ha containing contrasting forest types. Our model reproduces the empirical data well and shows that the ecological processes maintaining tropical forest diversity are scale dependent. Patterns of β-diversity are shaped by stochastic dispersal processes acting locally whilst environmental processes act over a wider range of scales.
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