Imperial College London

DrJamesRosindell

Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Reader in Biodiversity Theory
 
 
 
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Contact

 

+44 (0)20 7594 2242j.rosindell

 
 
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Location

 

W1.5KennedySilwood Park

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Summary

 

Publications

Publication Type
Year
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54 results found

Fattorini R, Egan PA, Rosindell J, Farrell IW, Stevenson PCet al., 2023, Grayanotoxin I variation across tissues and species of Rhododendron suggests pollinator-herbivore defence trade-offs., Phytochemistry, Vol: 212

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.

Journal article

Dunne EM, Thompson SED, Butler RJ, Rosindell J, Close RAet al., 2023, Mechanistic neutral models show that sampling biases drive the apparent explosion of early tetrapod diversity, Nature Ecology and Evolution, 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-valuediversity 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 testinghypotheses in palaeobiology.

Journal article

Gumbs R, Gray C, Böhm M, Burfield I, Couchman O, Faith D, Forest F, Hoffmann M, Isaac N, Jetz W, Mace G, Mooers A, Safi K, Scott O, Steel M, Tucker C, Pearse W, Owen N, Rosindell Jet 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.

Journal article

Fernandes LD, Hintzen RE, Thompson SED, Barychka T, Tittensor D, Harfoot M, Newbold T, Rosindell Jet 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

Journal article

Rosindell J, Manson K, Gumbs R, Pearse WD, Steel Met 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 and other sources of variety 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>

Journal article

Barker J, Davies J, Goralczyk M, Patel S, O'Connor J, Evans J, Sharp R, Gollock M, Wood FR, Rosindell J, Bartlett C, Garner BJ, Jones D, Quigley D, Wray Bet 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

Journal article

Dunne EM, Thompson SED, Butler RJ, Rosindell J, Close RAet al., 2022, Early tetrapod diversification under neutral theory

<jats:title>Abstract</jats:title><jats:p>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 neutral simulations suggest, in contrast to previous studies, that increases in early tetrapod diversity were not driven by local endemism following the ‘Carboniferous Rainforest Collapse’. We show that apparent changes in face-value diversity can instead 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 demonstrate the vast potential of mechanistic models, including neutral models, for testing hypotheses in palaeobiology.</jats:p>

Journal article

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.

Journal article

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

Journal article

Woodward G, Morris O, Barquin J, Belgrano A, Bull C, de Eyto E, Friberg N, Guobergsson G, Layer-Dobra K, Lauridsen RB, Lewis HM, McGinnity P, Pawar S, Rosindell J, O'Gorman EJet 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.

Journal article

Overcast I, Ruffley M, Rosindell J, Harmon L, Borges PA, Emerson BC, Etienne RS, Gillespie R, Krehenwinkel H, Mahler DL, Massol F, Parent CE, Patino J, Peter B, Week B, Wagner C, Hickerson MJ, Rominger Aet 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: 1755-098X

Journal article

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

Journal article

Leroi AM, Lambert B, Rosindell J, Kokkoris GDet al., 2021, Neutral Theory is a tool that should be wielded with care, NATURE HUMAN BEHAVIOUR, Vol: 5, Pages: 809-809, ISSN: 2397-3374

Journal article

Luiselli J, Overcast I, Rominger A, Ruffley M, Morlon H, Rosindell Jet 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 form of competition to MESS that explicitly compares the traits of each pair of individuals, allowing us to distinguish between inter- and intra-specific competition. Our results are qualitatively different to those of previous work that only compares each individual’s trait to the community mean. We find that neutral forces receive much less support from real systems when trait data is available and incorporated into the inference algorithm. We conclude that gathering more different types of data could be the key to unravelling the mechanisms of community assembly.</jats:p>

Journal article

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.

Journal article

Leroi AM, Ben L, Rosindell J, Zhang X, Kokkoris GDet 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’.

Journal article

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.

Software

McGill BJ, Chase JM, Hortal J, Overcast I, Rominger AJ, Rosindell J, Borges PAV, Emerson BC, Etienne R, Hickerson MJ, Mahler DL, Massol F, McGaughran A, Neves P, Parent C, Patino J, Ruffley M, Wagner CE, Gillespie Ret 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

Journal article

Hintzen RE, Papadopoulou M, Mounce R, Banks-Leite C, Holt RD, Mills M, Knight A, Leroi AM, Rosindell Jet 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.

Journal article

Gumbs R, Gray C, Böhm M, Hoffmann M, Grenyer R, Jetz W, Meiri S, Roll U, Owen N, Rosindell Jet 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.

Journal article

Murphy B, Forest F, Barraclough T, Rosindell J, Bellot S, Cowan R, Golos M, Jebb M, Cheek Met 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.

Journal article

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.

Journal article

McGill BJ, Chase JM, Hortal J, Overcast I, Rominger AJ, Rosindell J, Borges PAV, Emerson BC, Etienne R, Hickerson MJ, Mahler DL, Massol F, McGaughran A, Neves P, Parent C, Patiño J, Ruffley M, Wagner CE, Gillespie Ret 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.

Journal article

Bongalov B, Burslem DFRP, Jucker T, Thompson SED, Rosindell J, Swinfield T, Nilus R, Clewley D, Philips OL, Coomes DAet 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.

Journal article

Vila JCC, Jones ML, Patel M, Bell T, Rosindell Jet al., 2019, Uncovering the rules of microbial community invasions, Nature Ecology and Evolution, Vol: 3, Pages: 1162-1171, ISSN: 2397-334X

Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognised as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate numerous empirical patterns and lead to a description of five general rules of invasion: 1) larger communities evolve better invaders and better defenders; 2) where invader and resident fitness difference is large invasion success is essentially deterministic; 3) propagule pressure contributes to invasion success if and only if invaders and residents are competitively similar; 4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; 5) more diverse communities better resist invasion.

Journal article

Alzate A, Janzen T, Bonte D, Rosindell J, Etienne RSet al., 2019, A simple spatially explicit neutral model explains the range size distribution of reef fishes, Global Ecology and Biogeography, Vol: 28, Pages: 875-890, ISSN: 1466-822X

Journal article

Alzate A, Janzen T, Bonte D, Rosindell J, Etienne Ret al., 2019, A simple spatially explicit neutral model explains range size distribution of reef fishes, Global Ecology and Biogeography, Vol: 28, Pages: 875-890, ISSN: 1466-822X

Aim: The great variation in range sizes among species has fascinated ecologists for decades. In reef-associated fish species, which live in fragmented habitats and adopt a wide range of dispersal strategies, we may expect species with greater dispersal ability to spread over larger ranges. However, empirical evidence for such a positive relationship between dispersal and range size in reef fishes remains scarce. Here, we unveil the more nuanced role of dispersal on the range size distribution of reef associated fishes using empirical data and a novel spatially explicit model. Location: Tropical Eastern Pacific Major taxa studied: Reef-associated fishes Methods: We estimated range size distributions for six different guilds of all reef-associated fishes with different dispersal abilities. We used a one-dimensional spatially explicit neutral model, which simulates the distribution of species along a linear coastline to explored the effect of dispersal, speciation and sampling on the distribution of range sizes. Our model adopts a more realistic gradual speciation process (protracted speciation) and incorporates important long distance dispersal events with a fat-tail dispersal kernel. We simulated our model using a highly efficient coalescence approach, which guarantees the metacommunity, is sampled at dynamic equilibrium. We fitted the model to the empirical data using an approximate Bayesian computation approach, with a sequential Monte Carlo algorithm. Results: Stochastic birth, death, speciation and dispersal events alone can accurately explain empirical range size distributions for six different guilds of tropical, reef-associated fishes. Variation in range size distributions among guilds are explained purely by differences in dispersal ability with the best dispersers covering larger ranges. Main conclusions: A simple combination of neutral processes with guild-specific dispersal ability provides a general explanation for both within- and across-guild range size

Journal article

Banks-Leite C, Fletcher R, Didham R, Barlow J, Ewers RM, Rosindell JL, Holt RD, Gonzalez A, Pardini R, Damschen E, Melo FPL, Ries L, Prevedello JA, Tscharntke WF, Laurance WF, Lovejoy T, Haddad NMet al., 2018, Is habitat fragmentation good for biodiversity?, Biological Conservation, Vol: 226, Pages: 9-15, ISSN: 0006-3207

Habitat loss is a primary threat to biodiversity across the planet, yet contentious debate has ensued on the importance of habitat fragmentation ‘per se’ (i.e., altered spatial configuration of habitat for a given amount of habitat loss). Based on a review of landscape-scale investigations, Fahrig (2017; Ecological responses to habitat fragmentation per se. Annual Review of Ecology, Evolution, and Systematics 48:1-23) reports that biodiversity responses to habitat fragmentation ‘per se’ are more often positive rather than negative and concludes that the widespread belief in negative fragmentation effects is a ‘zombie idea’. We show that Fahrig's conclusions are drawn from a narrow and potentially biased subset of available evidence, which ignore much of the observational, experimental and theoretical evidence for negative effects of altered habitat configuration. We therefore argue that Fahrig's conclusions should be interpreted cautiously as they could be misconstrued by policy makers and managers, and we provide six arguments why they should not be applied in conservation decision-making. Reconciling the scientific disagreement, and informing conservation more effectively, will require research that goes beyond statistical and correlative approaches. This includes a more prudent use of data and conceptual models that appropriately partition direct vs indirect influences of habitat loss and altered spatial configuration, and more clearly discriminate the mechanisms underpinning any changes. Incorporating these issues will deliver greater mechanistic understanding and more predictive power to address the conservation issues arising from habitat loss and fragmentation.

Journal article

Chisholm RA, Lim F, Yeoh YS, Seah WW, Condit R, Rosindell Jet al., 2018, Species–area relationships and biodiversity loss in fragmented landscapes, Ecology Letters, Vol: 21, Pages: 804-813, ISSN: 1461-023X

To estimate species loss from habitat destruction, ecologists typically use species–area relationships, but this approach neglects the spatial pattern of habitat fragmentation. Here we provide new, easily applied, analytical methods that place upper and lower bounds on immediate species loss at any spatial scale and for any spatial pattern of habitat loss. Our formulas are expressed in terms of what we name the “Preston function”, which describes tri-phasic species¬–area relationships for contiguous regions. We apply our method to case studies of deforestation and tropical tree species loss at three different scales: a 50 ha forest plot in Panama, the tropical city-state of Singapore, and the Brazilian Amazon. Our results show that immediate species loss is somewhat insensitive to fragmentation pattern at small scales but highly sensitive at larger scales: predicted species loss in the Amazon varies by a factor of 16 across different spatial structures of habitat loss.

Journal article

Jordan S, Barraclough T, Rosindell JL, 2016, Quantifying the effects of the break up of Pangaea on global terrestrial diversification with neutral theory, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 371, ISSN: 1471-2970

The historic richness of most taxonomic groups increases substantially over geological time. Explanations for this fall broadly into two categories: bias in the fossil record and elevated net rates of diversification in recent periods. For example, the break up of Pangaea and isolation between continents might have increased net diversification rates. In this study, we investigate the effect on terrestrial diversification rates of the increased isolation between land masses brought about by continental drift. We use ecological neutral theory as a means to study geologically complex scenarios tractably. Our models show the effects of simulated geological events that affect all species equally, without the added complexity of further ecological processes. We find that continental drift leads to an increase in diversity only where isolation between continents leads to additional speciation through vicariance, and where higher taxa with very low global diversity are considered. We conclude that continental drift by itself is not sufficient to account for the increase in terrestrial species richness observed in the fossil record.

Journal article

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